A key issue in neuronal circuit regulation is how synapse formation is initiated. Synapse formation could start when one or more synaptic scaffold proteins that can initiate synapse formation reach certain threshold concentrations in the dendritic shaft, which might lead to their oligomerization or even liquid-liquid phase separation (LLPS). By combining in vitro reconstitution of purified proteins with live-cell single-molecule and confocal imaging, we demonstrated that SynGAP alone forms assemblies of nanoscale clusters containing several to several tens of molecules at 10-nM order concentrations and micron-scale LLPS hydrogel-like condensates at submicromolar concentrations. The trimers of SynGAP’s intrinsically disordered region (IDR) induced by its coiled-coil domain are responsible for SynGAP condensation. CaMKII-mediated phosphorylation moderately suppresses SynGAP condensation, and also increases condensate liquidity. While PSD95 fails to form assemblies under these conditions, it is recruited to SynGAP condensates by specifically binding to the PDZ-binding motif of SynGAP. SynGAP[PSD95] condensates selectively immobilize postsynaptic transmembrane proteins, Neuroligin1 and AMPAR-TARP2 complexes, in a manner dependent on their oligomerization state, indicating cooperative recruitment dynamics among SynGAP, PSD95, and transmembrane components, which might mimic initial PSD assembly. These findings suggest that SynGAP may act as a primary nucleator of postsynaptic density assembly, challenging the PSD95-centered models.
", "doi": "10.1101/2025.04.22.649955", "publisher": "bioRxiv", "publication_date": "2025-04-23" }, { "id": "authors:mtx0r-93w55", "collection": "authors", "collection_id": "mtx0r-93w55", "cite_using_url": "https://authors.library.caltech.edu/records/mtx0r-93w55", "type": "article", "title": "A spatial model of autophosphorylation of CaMKII predicts that the lifetime of phospho-CaMKII after induction of synaptic plasticity is greatly prolonged by CaM-trapping", "author": [ { "family_name": "Bartol", "given_name": "Thomas M." }, { "family_name": "Ordyan", "given_name": "Mariam" }, { "family_name": "Sejnowski", "given_name": "Terrence J." }, { "family_name": "Rangamani", "given_name": "Padmini" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Long-term potentiation (LTP) is a biochemical process that underlies learning in excitatory glutamatergic synapses in the Central Nervous System (CNS). A critical early driver of LTP is autophosphorylation of the abundant postsynaptic enzyme, Ca²+/calmodulin-dependent protein kinase II (CaMKII). Autophosphorylation is initiated by Ca²+ flowing through NMDA receptors activated by strong synaptic activity. Its lifetime is ultimately determined by the balance of the rates of autophosphorylation and of dephosphorylation by protein phosphatase 1 (PP1). Here we have modeled the autophosphorylation and dephosphorylation of CaMKII during synaptic activity in a spine synapse using MCell4, an open source computer program for creating particle-based stochastic, and spatially realistic models of cellular microchemistry. The model integrates four earlier detailed models of separate aspects of regulation of spine Ca²+ and CaMKII activity, each of which incorporate experimentally measured biochemical parameters and have been validated against experimental data. We validate the composite model by showing that it accurately predicts previous experimental measurements of effects of NMDA receptor activation, including high sensitivity of induction of LTP to phosphatase activity in vivo, and persistence of autophosphorylation for a period of minutes after the end of synaptic stimulation. We then use the model to probe aspects of the mechanism of regulation of autophosphorylation of CaMKII that are difficult to measure in vivo. We examine the effects of \"CaM-trapping,\" a process in which the affinity for Ca²+/CaM increases several hundred-fold after autophosphorylation. We find that CaM-trapping does not increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Instead, CaM-trapping may dramatically prolong the lifetime of autophosphorylated CaMKII through steric hindrance of dephosphorylation by protein phosphatase 1. The results provide motivation for experimental measurement of the extent of suppression of dephosphorylation of CaMKII by bound Ca²+/CaM. The composite MCell4 model of biochemical effects of complex stimuli in synaptic spines is a powerful new tool for realistic, detailed dissection of mechanisms of synaptic plasticity.
", "doi": "10.3389/fnsyn.2025.1547948", "issn": "1663-3563", "publisher": "Frontiers Media SA", "publication": "Frontiers in Synaptic Neuroscience", "publication_date": "2025-04-04", "volume": "17", "pages": "1547948" }, { "id": "authors:6e0sn-ana02", "collection": "authors", "collection_id": "6e0sn-ana02", "cite_using_url": "https://authors.library.caltech.edu/records/6e0sn-ana02", "type": "monograph", "title": "A spatial model of autophosphorylation of Ca\u00b2\u207a/calmodulin-dependent protein kinase II in a glutamatergic spine reveals dynamics of kinase activation in the first several seconds after a complex synaptic stimulus", "author": [ { "family_name": "Bartol", "given_name": "Thomas M.", "orcid": "0009-0002-2598-0052", "clpid": "Bartol-Thomas-M" }, { "family_name": "Ordyan", "given_name": "Mariam", "orcid": "0000-0003-0064-2997", "clpid": "Ordyan-Mariam" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "clpid": "Sejnowski-Terrence-J" }, { "family_name": "Rangamani", "given_name": "Padmini", "clpid": "Rangamani-Padmini" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Activation of N-methyl-D-aspartate-type glutamate receptors (NMDARs) at synapses in the CNS triggers changes in synaptic strength that underlie memory formation in response to strong synaptic stimuli. The primary target of Ca2+ flowing through NMDARs is Ca2+/calmodulin-dependent protein kinase II (CaMKII) which forms dodecameric holoenzymes that are highly concentrated at the postsynaptic site. Activation of CaMKII is necessary to trigger long-term potentiation of synaptic strength (LTP), and is prolonged by autophosphorylation of subunits within the holoenzyme. Here we use MCell4, an agent-based, stochastic, modeling platform to model CaMKII holoenzymes placed within a realistic spine geometry. We show how two mechanisms of regulation of CaMKII, ‘Ca2+-calmodulin-trapping (CaM-trapping)’ and dephosphorylation by protein phosphatase-1 (PP1) shape the autophosphorylation response during a repeated high-frequency stimulus. Our simulation results suggest that autophosphorylation of CaMKII does not constitute a bistable switch. Instead, prolonged but temporary, autophosphorylation of CaMKII may contribute to a biochemical-network-based ‘kinetic proof-reading” mechanism that controls induction of synaptic plasticity.
", "doi": "10.1101/2024.02.02.578696", "publisher": "BioRxiv", "publication_date": "2024-07-18" }, { "id": "authors:00ahr-z3882", "collection": "authors", "collection_id": "00ahr-z3882", "cite_using_url": "https://authors.library.caltech.edu/records/00ahr-z3882", "type": "article", "title": "MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface", "author": [ { "family_name": "Husar", "given_name": "Adam" }, { "family_name": "Ordyan", "given_name": "Mariam", "orcid": "0000-0003-0064-2997", "clpid": "Ordyan-Mariam" }, { "family_name": "Garcia", "given_name": "Guadalupe C.", "clpid": "Garcia-Guadalupe-C" }, { "family_name": "Yancey", "given_name": "Joel G.", "clpid": "Yancey-Joel-G" }, { "family_name": "Saglam", "given_name": "Ali S.", "clpid": "Saglam-Ali-S" }, { "family_name": "Faeder", "given_name": "James R.", "clpid": "Faeder-James-R" }, { "family_name": "Bartol", "given_name": "Thomas M.", "orcid": "0009-0002-2598-0052", "clpid": "Bartol-Thomas-M" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "clpid": "Sejnowski-Terrence-J" } ], "abstract": "Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum approximations based on concentrations break down and a particle-based approach is more accurate and more efficient. We describe and validate a new version of the open-source MCell simulation program (MCell4), which supports generalized 3D Monte Carlo modeling of diffusion and chemical reaction of discrete molecules and macromolecular complexes in solution, on surfaces representing membranes, and combinations thereof. The main improvements in MCell4 compared to the previous versions, MCell3 and MCell3-R, include a Python interface and native BioNetGen reaction language (BNGL) support. MCell4’s Python interface opens up completely new possibilities for interfacing with external simulators to allow creation of sophisticated event-driven multiscale/multiphysics simulations. The native BNGL support, implemented through a new open-source library libBNG (also introduced in this paper), provides the capability to run a given BNGL model spatially resolved in MCell4 and, with appropriate simplifying assumptions, also in the BioNetGen simulation environment, greatly accelerating and simplifying model validation and comparison.
", "doi": "10.1371/journal.pcbi.1011800", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2024-04-24" }, { "id": "authors:1t84e-c6328", "collection": "authors", "collection_id": "1t84e-c6328", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210927-225706238", "type": "article", "title": "Amplification of neurotoxic HTTex1 assemblies in human neurons", "author": [ { "family_name": "Chongtham", "given_name": "Anjalika", "orcid": "0000-0001-8437-3899", "clpid": "Chongtham-Anjalika" }, { "family_name": "Isas", "given_name": "J. Mario", "clpid": "Isas-J-Mario" }, { "family_name": "Pandey", "given_name": "Nitin K.", "orcid": "0000-0001-6124-4090", "clpid": "Pandey-Nitin-K" }, { "family_name": "Rawat", "given_name": "Anoop", "orcid": "0000-0002-5838-0275", "clpid": "Rawat-Anoop" }, { "family_name": "Yoo", "given_name": "Jung Hyun", "orcid": "0000-0002-5159-8167", "clpid": "Yoo-Jung-Hyun" }, { "family_name": "Mastro", "given_name": "Tara", "orcid": "0000-0003-1302-9753", "clpid": "Mastro-Tara-L" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Langen", "given_name": "Ralf", "orcid": "0000-0003-2816-6531", "clpid": "Langen-Ralf" }, { "family_name": "Khoshnan", "given_name": "Ali", "orcid": "0000-0002-0070-9808", "clpid": "Khoshnan-Ali" } ], "abstract": "Huntington's disease (HD) is a genetically inherited neurodegenerative disorder caused by expansion of a polyglutamine (polyQ) repeat in the exon-1 of huntingtin protein (HTT). The expanded polyQ enhances the amyloidogenic propensity of HTT exon 1 (HTTex1), which forms a heterogeneous mixture of assemblies with a broad neurotoxicity spectrum. While predominantly intracellular, monomeric and aggregated mutant HTT species are also present in the cerebrospinal fluids of HD patients, however, their biological properties are not well understood. To explore the role of extracellular mutant HTT in aggregation and toxicity, we investigated the uptake and amplification of recombinant HTTex1 assemblies in cell culture models. We find that small HTTex1 fibrils preferentially enter human neurons and trigger the amplification of neurotoxic assemblies; astrocytes or epithelial cells are not permissive. The amplification of HTTex1 in neurons depletes endogenous HTT protein with non-pathogenic polyQ repeat, activates apoptotic caspase-3 pathway and induces nuclear fragmentation. Using a panel of novel monoclonal antibodies and genetic mutation, we identified epitopes within the N-terminal 17 amino acids and proline-rich domain of HTTex1 to be critical in neural uptake and amplification. Synaptosome preparations from the brain homogenates of HD mice also contain mutant HTT species, which enter neurons and behave similar to small recombinant HTTex1 fibrils. These studies suggest that amyloidogenic extracellular mutant HTTex1 assemblies may preferentially enter neurons, propagate and promote neurodegeneration.", "doi": "10.1016/j.nbd.2021.105517", "pmcid": "PMC8943833", "issn": "0969-9961", "publisher": "Elsevier", "publication": "Neurobiology of Disease", "publication_date": "2021-11", "volume": "159", "pages": "Art. No. 105517" }, { "id": "authors:wgjvx-w0g19", "collection": "authors", "collection_id": "wgjvx-w0g19", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210419-173243907", "type": "monograph", "title": "Sonicated fibrils of huntingtin exon-1 preferentially seed neurons and produce toxic assemblies", "author": [ { "family_name": "Chongtham", "given_name": "Anjalika", "orcid": "0000-0001-8437-3899", "clpid": "Chongtham-Anjalika" }, { "family_name": "Isas", "given_name": "J. Mario", "clpid": "Isas-J-Mario" }, { "family_name": "Pandey", "given_name": "Nitin K.", "orcid": "0000-0001-6124-4090", "clpid": "Pandey-Nitin-K" }, { "family_name": "Rawat", "given_name": "Anoop", "orcid": "0000-0002-5838-0275", "clpid": "Rawat-Anoop" }, { "family_name": "Yoo", "given_name": "Jung Hyun", "orcid": "0000-0002-5159-8167", "clpid": "Yoo-Jung-Hyun" }, { "family_name": "Mastro", "given_name": "Tara", "clpid": "Mastro-Tara-L" }, { "family_name": "Kennedy", "given_name": "Mary", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Langen", "given_name": "Ralf", "orcid": "0000-0003-2816-6531", "clpid": "Langen-Ralf" }, { "family_name": "Khoshnan", "given_name": "Ali", "orcid": "0000-0002-0070-9808", "clpid": "Khoshnan-Ali" } ], "abstract": "HD is a genetically inherited neurodegenerative disorder caused by expansion of a polyglutamine (polyQ) repeats in the exon-1 of huntingtin protein (HTT). The expanded polyQ enhances the amyloidogenic propensity of HTT exon 1 (HTTex1), which forms a heterogeneous mixture of assemblies with some being neurotoxic. While predominantly intracellular, monomeric and aggregated mutant HTT species are also present in the cerebrospinal fluids of HD patients, however, their biological properties are not well understood. To explore the role of extracellular mutant HTT in aggregation and toxicity, we investigated the possible uptake and amplification of recombinant HTTex1 assemblies in cell culture models. We found seedingcompetent species in the sonicated HTTex1 fibrils, which preferentially entered human neurons and triggered the amplification of neurotoxic assemblies; astrocytes or epithelial cells were not permissive to the HTTex1 seeding. The aggregation of HTTex1 seeds in neurons depleted endogenous HTT protein with non-pathogenic polyQ repeat, activated apoptotic caspase-3 pathway and induced nuclear fragmentation. Using a panel of novel monoclonal antibodies and genetic mutation, we identified epitopes within the N-terminal 17 amino acids and proline-rich domain of HTTex1 mediating neural seeding. Synaptosome preparations from the brains of HD mice also contained similar neurotoxic seeding-competent mutant HTT species. Our findings suggest that amyloidogenic extracellular mutant HTT assemblies may selectively enter neurons, propagate and produce neurotoxic assemblies.", "doi": "10.1101/2021.04.16.440200", "publication_date": "2021-04-19" }, { "id": "authors:fp709-2h285", "collection": "authors", "collection_id": "fp709-2h285", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191113-153420698", "type": "article", "title": "Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator", "author": [ { "family_name": "Ordyan", "given_name": "Mariam", "orcid": "0000-0003-0064-2997", "clpid": "Ordyan-M" }, { "family_name": "Bartol", "given_name": "Tom", "clpid": "Bartol-T-M" }, { "family_name": "Kennedy", "given_name": "Mary", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Rangamani", "given_name": "Padmini", "orcid": "0000-0001-5953-4347", "clpid": "Rangamani-P" }, { "family_name": "Sejnowski", "given_name": "Terrence", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" } ], "abstract": "Calmodulin-dependent kinase II (CaMKII) has long been known to play an important role in learning and memory as well as long term potentiation (LTP). More recently it has been suggested that it might be involved in the time averaging of synaptic signals, which can then lead to the high precision of information stored at a single synapse. However, the role of the scaffolding molecule, neurogranin (Ng), in governing the dynamics of CaMKII is not yet fully understood. In this work, we adopt a rule-based modeling approach through the Monte Carlo method to study the effect of Ca\u00b2\u207a signals on the dynamics of CaMKII phosphorylation in the postsynaptic density (PSD). Calcium surges are observed in synaptic spines during an EPSP and back-propagating action potential due to the opening of NMDA receptors and voltage dependent calcium channels. Using agent-based models, we computationally investigate the dynamics of phosphorylation of CaMKII monomers and dodecameric holoenzymes. The scaffolding molecule, Ng, when present in significant concentration, limits the availability of free calmodulin (CaM), the protein which activates CaMKII in the presence of calcium. We show that Ng plays an important modulatory role in CaMKII phosphorylation following a surge of high calcium concentration. We find a non-intuitive dependence of this effect on CaM concentration that results from the different affinities of CaM for CaMKII depending on the number of calcium ions bound to the former. It has been shown previously that in the absence of phosphatase, CaMKII monomers integrate over Ca\u00b2\u207a signals of certain frequencies through autophosphorylation (Pepke et al, Plos Comp. Bio., 2010). We also study the effect of multiple calcium spikes on CaMKII holoenzyme autophosphorylation, and show that in the presence of phosphatase, CaMKII behaves as a leaky integrator of calcium signals, a result that has been recently observed in vivo. Our models predict that the parameters of this leaky integrator are finely tuned through the interactions of Ng, CaM, CaMKII, and PP1, providing a mechanism to precisely control the sensitivity of synapses to calcium signals.", "doi": "10.1371/journal.pcbi.1008015", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2020-07-17", "series_number": "7", "volume": "16", "issue": "7", "pages": "Art. No. e1008015" }, { "id": "authors:847mz-h6902", "collection": "authors", "collection_id": "847mz-h6902", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200122-112342378", "type": "article", "title": "A sex difference in the response of the rodent postsynaptic density to synGAP haploinsufficiency", "author": [ { "family_name": "Mastro", "given_name": "Tara L.", "clpid": "Mastro-T-L" }, { "family_name": "Preza", "given_name": "Anthony", "clpid": "Preza-A" }, { "family_name": "Basu", "given_name": "Shinjini", "clpid": "Basu-Shinjini" }, { "family_name": "Chattarji", "given_name": "Sumantra", "orcid": "0000-0001-9962-3635", "clpid": "Chattarji-S" }, { "family_name": "Till", "given_name": "Sally M.", "clpid": "Till-S-M" }, { "family_name": "Kind", "given_name": "Peter C.", "orcid": "0000-0002-4256-9639", "clpid": "Kind-P-C" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a postsynaptic density (PSD) protein that binds to PDZ domains of the scaffold protein PSD-95. We previously reported that heterozygous deletion of Syngap1 in mice is correlated with increased steady-state levels of other key PSD proteins that bind PSD-95, although the level of PSD-95 remains constant (Walkup et al., 2016). For example, the ratio to PSD-95 of Transmembrane AMPA-Receptor-associated Proteins (TARPs), which mediate binding of AMPA-type glutamate receptors to PSD-95, was increased in young Syngap1+/- mice. Here we show that only females and not males show a highly significant correlation between an increase in TARP and a decrease in synGAP in the PSDs of Syngap1+/- rodents. The data reveal a sex difference in the adaptation of the PSD scaffold to synGAP haploinsufficiency.", "doi": "10.7554/elife.52656", "pmcid": "PMC6994236", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2020-01-15", "volume": "9", "pages": "Art. No. e52656" }, { "id": "authors:ex8h9-npf21", "collection": "authors", "collection_id": "ex8h9-npf21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190312-144831821", "type": "article", "title": "A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation", "author": [ { "family_name": "Pharris", "given_name": "Matthew C.", "clpid": "Pharris-M-C" }, { "family_name": "Patel", "given_name": "Neal M.", "orcid": "0000-0002-2998-8409", "clpid": "Patel-N-M" }, { "family_name": "VanDyk", "given_name": "Tyler G.", "orcid": "0000-0001-9603-3971", "clpid": "VanDyk-T-G" }, { "family_name": "Bartol", "given_name": "Thomas M.", "clpid": "Bartol-T-M" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Stefan", "given_name": "Melanie I.", "clpid": "Stefan-M-I" }, { "family_name": "Kinzer-Ursem", "given_name": "Tamara L.", "clpid": "Kinzer-Ursem-T-L" } ], "abstract": "Ca\u00b2\u207a/calmodulin-dependent protein kinase II (CaMKII) accounts for up to 2 percent of all brain protein and is essential to memory function. CaMKII activity is known to regulate dynamic shifts in the size and signaling strength of neuronal connections, a process known as synaptic plasticity. Increasingly, computational models are used to explore synaptic plasticity and the mechanisms regulating CaMKII activity. Conventional modeling approaches may exclude biophysical detail due to the impractical number of state combinations that arise when explicitly monitoring the conformational changes, ligand binding, and phosphorylation events that occur on each of the CaMKII holoenzyme's subunits. To manage the combinatorial explosion without necessitating bias or loss in biological accuracy, we use a specialized syntax in the software MCell to create a rule-based model of a twelve-subunit CaMKII holoenzyme. Here we validate the rule-based model against previous experimental measures of CaMKII activity and investigate molecular mechanisms of CaMKII regulation. Specifically, we explore how Ca\u00b2\u207a/CaM-binding may both stabilize CaMKII subunit activation and regulate maintenance of CaMKII autophosphorylation. Noting that Ca\u00b2\u207a/CaM and protein phosphatases bind CaMKII at nearby or overlapping sites, we compare model scenarios in which Ca\u00b2\u207a/CaM and protein phosphatase do or do not structurally exclude each other's binding to CaMKII. Our results suggest a functional mechanism for the so-called \"CaM trapping\" phenomenon, wherein Ca\u00b2\u207a/CaM may structurally exclude phosphatase binding and thereby prolong CaMKII autophosphorylation. We conclude that structural protection of autophosphorylated CaMKII by Ca\u00b2\u207a/CaM may be an important mechanism for regulation of synaptic plasticity.", "doi": "10.1371/journal.pcbi.1006941", "pmcid": "PMC6957207", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2019-12-23", "series_number": "12", "volume": "15", "issue": "12", "pages": "Art. No. e1006941" }, { "id": "authors:f31jk-vnw59", "collection": "authors", "collection_id": "f31jk-vnw59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191014-134400805", "type": "monograph", "title": "A sex difference in the composition of the rodent postsynaptic density", "author": [ { "family_name": "Mastro", "given_name": "Tara L.", "clpid": "Mastro-T-L" }, { "family_name": "Preza", "given_name": "Anthony", "clpid": "Preza-A" }, { "family_name": "Basu", "given_name": "Shinjini", "clpid": "Basu-Shinjini" }, { "family_name": "Chattarji", "given_name": "Shona", "orcid": "0000-0001-9962-3635", "clpid": "Chattarji-S" }, { "family_name": "Till", "given_name": "Sally M.", "clpid": "Till-S-M" }, { "family_name": "Kind", "given_name": "Peter", "orcid": "0000-0002-4256-9639", "clpid": "Kind-P" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a postsynaptic density (PSD) protein that binds to PDZ domains of the scaffold protein PSD-95. We previously reported that heterozygous deletion of synGAP in mice is correlated with increased steady-state levels of other key PSD proteins that bind PSD-95, although the level of PSD-95 remains constant (Walkup et al., 2016). For example, the ratio to PSD-95 of Transmembrane AMPA-Receptor-associated Proteins (TARPs), which mediate binding of AMPA-type glutamate receptors to PSD-95, was increased in young synGAP+/- mice. Here we show that a highly significant increase in TARP in the PSDs of young synGAP+/- rodents is present only in females and not in males. The data reveal a sex difference in the adaptation of the PSD scaffold to synGAP heterozygosity.", "doi": "10.1101/802538", "publication_date": "2019-10-12" }, { "id": "authors:5jf21-gfe44", "collection": "authors", "collection_id": "5jf21-gfe44", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190102-135256095", "type": "article", "title": "In memoriam: John Lisman \u2013 commentaries on CaMKII as a memory molecule", "author": [ { "family_name": "Bear", "given_name": "Mark F.", "clpid": "Bear-Mark-F" }, { "family_name": "Cooke", "given_name": "Sam F.", "clpid": "Cooke-Sam-F" }, { "family_name": "Giese", "given_name": "Karl Peter", "clpid": "Giese-Karl-Peter" }, { "family_name": "Kaang", "given_name": "Bong-Kiun", "clpid": "Kaang-Bong-Kiun" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Kim", "given_name": "Ji-il", "clpid": "Kim-Ji-il" }, { "family_name": "Morris", "given_name": "Richard G. M.", "clpid": "Morris-Richard-G-M" }, { "family_name": "Park", "given_name": "Pojeong", "clpid": "Park-Pojeong" } ], "abstract": "Shortly before he died in October 2017, John Lisman submitted an invited review to Molecular Brain on 'Criteria for identifying the molecular basis of the engram (CaMKII, PKM\u03b6)'. John had no opportunity to read the referees' comments, and as a mark of the regard in which he was held by the neuroscience community the Editors decided to publish his review as submitted. This obituary takes the form of a series of commentaries on Lisman's review. At the same time we are publishing as a separate article a longer response by Todd Sacktor and Andr\u00e9 Fenton entitled 'What does LTP tell us about the roles of CaMKII and PKM\u03b6 in memory?' which presents the case for a rival memory molecule, PKM\u03b6.", "doi": "10.1186/s13041-018-0419-y", "pmcid": "PMC6309094", "issn": "1756-6606", "publisher": "Springer Nature", "publication": "Molecular Brain", "publication_date": "2018-12", "volume": "11", "pages": "Art. No. 76" }, { "id": "authors:5tn97-x6h78", "collection": "authors", "collection_id": "5tn97-x6h78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180724-092809061", "type": "article", "title": "Phosphorylation of synaptic GTPase-activating protein (synGAP) by polo-like kinase (Plk2) alters the ratio of its GAP activity toward HRas, Rap1 and Rap2 GTPases", "author": [ { "family_name": "Walkup", "given_name": "Ward G., IV", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-Ward-G-IV" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-Michael-J" }, { "family_name": "Graham", "given_name": "Robert L.", "clpid": "Graham-Robert-L-J" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-Sonja" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a Ras and Rap GTPase-activating protein (GAP) found in high concentration in the postsynaptic density (PSD) fraction from mammalian forebrain where it binds to PDZ domains of PSD-95. Phosphorylation of pure recombinant synGAP by Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII) shifts the balance of synGAP's GAP activity toward inactivation of Rap1; whereas phosphorylation by cyclin-dependent kinase 5 (CDK5) has the opposite effect, shifting the balance toward inactivation of HRas. These shifts in balance contribute to regulation of the numbers of surface AMPA receptors, which rise during synaptic potentiation (CaMKII) and fall during synaptic scaling (CDK5). Polo-like kinase 2 (Plk2/SNK), like CDK5, contributes to synaptic scaling. These two kinases act in concert to reduce the number of surface AMPA receptors following elevated neuronal activity by tagging spine-associated RapGAP protein (SPAR) for degradation, thus raising the level of activated Rap. Here we show that Plk2 also phosphorylates and regulates synGAP. Phosphorylation of synGAP by Plk2 stimulates its GAP activity toward HRas by 65%, and toward Rap1 by 16%. Simultaneous phosphorylation of synGAP by Plk2 and CDK5 at distinct sites produces an additive increase in GAP activity toward HRas (\u223c230%) and a smaller, non-additive increase in activity toward Rap1 (\u223c15%). Dual phosphorylation also produces an increase in GAP activity toward Rap2 (\u223c40\u201350%), an effect not produced by either kinase alone. As we previously observed for CDK5, addition of Ca^(2+)/CaM causes a substrate-directed doubling of the rate and stoichiometry of phosphorylation of synGAP by Plk2, targeting residues also phosphorylated by CaMKII. In summary, phosphorylation by Plk2, like CDK5, shifts the ratio of GAP activity of synGAP to produce a greater decrease in active Ras than in active Rap, which would produce a shift toward a decrease in the number of surface AMPA receptors in neuronal dendrites.", "doi": "10.1016/j.bbrc.2018.07.087", "pmcid": "PMC7894274", "issn": "0006-291X", "publisher": "Elsevier", "publication": "Biochemical and Biophysical Research Communications", "publication_date": "2018-09-10", "series_number": "3", "volume": "503", "issue": "3", "pages": "1599-1604" }, { "id": "authors:vxw2z-2cw13", "collection": "authors", "collection_id": "vxw2z-2cw13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180619-094616549", "type": "article", "title": "The Protein Biochemistry of the Postsynaptic Density in Glutamatergic Synapses Mediates Learning in Neural Networks", "author": [ { "family_name": "Kennedy", "given_name": "Mary", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The strength of each excitatory synapse in the central nervous system is regulated by its prior activity in a process called synaptic plasticity. The initiation of synaptic plasticity occurs when calcium ions enter the postsynaptic compartment and encounter a subcellular structure called the postsynaptic density (PSD). The PSD is attached to the postsynaptic membrane just underneath the concentrated plaque of neurotransmitter receptors. It is comprised of a core set of 30\u201360 proteins, approximately 20 of which are scaffold proteins. The rest include protein kinases and phosphatases, some of which respond to calcium ion; small GTPases and their regulators; chaperones; ubiquitins; and proteases. The assembly of the PSD involves competitive binding among a variety of specific protein binding sites to form a dynamic network. A biochemical challenge for the future is to understand how the dynamic regulation of the structure, composition, and activity of the PSD mediates synaptic plasticity and how mutations in PSD proteins lead to mental and neurodegenerative diseases.", "doi": "10.1021/acs.biochem.8b00496", "pmcid": "PMC7879948", "issn": "0006-2960", "publisher": "American Chemical Society", "publication": "Biochemistry", "publication_date": "2018-07-10", "series_number": "27", "volume": "57", "issue": "27", "pages": "4005-4009" }, { "id": "authors:2xwmx-t2568", "collection": "authors", "collection_id": "2xwmx-t2568", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180321-145303826", "type": "article", "title": "Competition in the postsynaptic density for PDZ domains of PSD-95", "author": [ { "family_name": "Mastro", "given_name": "T.", "orcid": "0000-0003-1302-9753", "clpid": "Mastro-Tara-L" }, { "family_name": "Preza", "given_name": "A.", "clpid": "Preza-Anthony" }, { "family_name": "Kind", "given_name": "P.", "orcid": "0000-0002-4256-9639", "clpid": "Kind-Peter-C" }, { "family_name": "Kennedy", "given_name": "M. B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Molecular mechanisms of synaptic plasticity are of great interest because derangement of synaptic plasticity contributes to neural diseases such as autism, schizophrenia, cognitive impairment, neuropathic pain, epilepsy, and stroke. This work addresses the molecular mechanisms underlying NMDA\u2010type glutamate receptor\u2010triggered plasticity at excitatory synapses. A critical step in this process is a change in the rate of trapping of AMPA\u2010type receptors (AMPARs) in the postsynaptic density (PSD), which increases the number of AMPARs and strengthens the electrical signal at the synapse. Our work aims to determine whether trapping of AMPARs in the PSD is mediated by rearrangement of the PSD scaffold caused by changes in the affinity of different PSD proteins for the PDZ domains of the major synaptic scaffold protein, PSD\u201095. Our earlier publication (1) supports this notion by showing that: 1.\nPhosphorylation of the abundant PSD protein synGAP by CaMKII reduces its affinity for the PDZ domains of PSD\u201095; and 2. The composition of the PSD is altered in synGAP deficient mice such that AMPAR-binding proteins with PDZ ligands, including TARPs and LRRTM2, are increased in concentration relative to PSD\u201095. We have now replicated these finding in synGAP\u2010deficient rats. These findings suggest that the extent of binding of particular synaptic proteins to the PDZ domains of PSD\u201095 is regulated by\nactivity\u2010dependent phosphorylation of synGAP. We are testing this hypothesis in cultured rat neurons.\nWe have isolated PSDs from neuronal cultures before and after induction of synGAP phosphorylation by\npharmacological activation of NMDARs. The ratios of AMPAR\u2010associated proteins to PSD\u201095 in the PSDs\nare determined by quantitative immunoblotting. We have found that the ratio of TARPs to PSD\u201095 is\nconsistently increased in PSDs after chemical activation of synaptic NMDARs. We are using cultures from\nsynGAP\u2010deficient rats to determine if synGAP deficiency alters the composition of the PSD in rat cultures. We plan to transfect with a variety of synGAP mutant proteins in order to determine which domains or phosphorylation sites on synGAP are important for regulating PSD composition.", "doi": "10.1091/mbc.E17-10-0618", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "2017-12-15", "series_number": "26", "volume": "28", "issue": "26", "pages": "Art. No. P3216" }, { "id": "authors:w0q62-j9c60", "collection": "authors", "collection_id": "w0q62-j9c60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170410-130729438", "type": "article", "title": "Densin-180 controls the trafficking and signaling of L-type voltage-gated Ca_v 1.2 Ca^(2+) channels at excitatory synapses", "author": [ { "family_name": "Wang", "given_name": "Shiyi", "orcid": "0000-0003-3433-3025", "clpid": "Wang-Shiyi" }, { "family_name": "Stanika", "given_name": "Ruslan I.", "clpid": "Stanika-Ruslan-I" }, { "family_name": "Wang", "given_name": "Xiaohan", "orcid": "0000-0001-7895-2333", "clpid": "Wang-Xiaohan" }, { "family_name": "Hagen", "given_name": "Jussara", "clpid": "Hagen-Jussara" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Obermair", "given_name": "Gerald J.", "clpid": "Obermair-Gerald-J" }, { "family_name": "Colbran", "given_name": "Roger J.", "orcid": "0000-0001-7401-8244", "clpid": "Colbran-Roger-J" }, { "family_name": "Lee", "given_name": "Amy", "orcid": "0000-0001-8021-0443", "clpid": "Lee-Amy" } ], "abstract": "Voltage-gated Ca_v1.2 and Ca_v1.3 (L-type) Ca^(2+) channels regulate neuronal excitability, synaptic plasticity, and learning and memory. Densin-180 (densin) is an excitatory synaptic protein that promotes Ca^(2+)-dependent facilitation of voltage-gated Ca_v1.3 Ca^(2+) channels in transfected cells. Mice lacking densin (densin KO) exhibit defects in synaptic plasticity, spatial memory, and increased anxiety-related behaviors --phenotypes that more closely match those in mice lacking Ca_v1.2 than Ca_v1.3. Thus, we investigated the functional impact of densin on Ca_v1.2. We report that densin is an essential regulator of Ca_v1.2 in neurons, but has distinct modulatory effects compared to its regulation of Ca_v1.3. Densin binds to the N-terminal domain of Ca_v1.2 but not Ca_v1.3, and increases Ca_v1.2 currents in transfected cells and in neurons. In transfected cells, densin accelerates the forward trafficking of Ca_v1.2 channels without affecting their endocytosis. Consistent with a role for densin in increasing the number of postsynaptic Ca_v1.2 channels, overexpression of densin increases the clustering of Ca_v1.2 in dendrites of hippocampal neurons in culture. Compared to wild-type mice, the cell-surface levels of Ca_v1.2 in the brain as well as Ca_v1.2 current density and signaling to the nucleus are reduced in neurons from densin KO mice. We conclude that densin is an essential regulator of neuronal Ca_v1 channels and ensures efficient Ca_v1.2 Ca^(2+) signaling at excitatory synapses.", "doi": "10.1523/JNEUROSCI.2583-16.2017", "pmcid": "PMC5426563", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2017-05-03", "series_number": "18", "volume": "37", "issue": "18", "pages": "4679-4691" }, { "id": "authors:sxm5a-9ry08", "collection": "authors", "collection_id": "sxm5a-9ry08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170202-102002485", "type": "article", "title": "Biochemistry and neuroscience: the twain need to meet", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Neuroscience has come to mean the study of electrophysiology of neurons and synapses, micro and macro-scale neuroanatomy, and the functional organization of brain areas. The molecular axis of the field, as reflected in textbooks, often includes only descriptions of the structure and function of individual channels and receptor proteins, and the extracellular signals that guide development and repair. Studies of cytosolic 'molecular machines', large assemblies of proteins that orchestrate regulation of neuronal functions, have been neglected. However, a complete understanding of brain function that will enable new strategies for treatment of the most intractable neural disorders will require that in vitro biochemical studies of molecular machines be reintegrated into the field of neuroscience.", "doi": "10.1016/j.conb.2017.01.004", "pmcid": "PMC5447485", "issn": "0959-4388", "publisher": "Elsevier", "publication": "Current Opinion in Neurobiology", "publication_date": "2017-04", "volume": "43", "pages": "79-86" }, { "id": "authors:j92xr-azk08", "collection": "authors", "collection_id": "j92xr-azk08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161207-091914338", "type": "article", "title": "Liquid Phase Transition in the Postsynaptic Density?", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Mastro", "given_name": "Tara L.", "orcid": "0000-0003-1302-9753", "clpid": "Mastro-Tara-L" } ], "abstract": "An assembly of scaffold proteins termed the postsynaptic density (PSD) is attached to the postsynaptic membrane of excitatory glutamatergic synapses [1]. The scaffold serves to immobilize glutamate receptors in the membrane directly across from the position where glutamate is released from the presynaptic terminal. It also houses and organizes biochemical machinery whose job is to respond to particular patterns of electrical activity by increasing the strength of the synapse [2]. Synaptic strengthening helps to form new circuits that represent our experience [3]. These circuits are our memories. Biochemical machinery in the PSD strengthens the synapse by increasing the size of the PSD scaffold, the number of anchored receptors, and the size of the presynaptic active zone. A larger scaffold, more release sites, and more receptors means a stronger synapse, and vice versa.", "doi": "10.1016/j.tibs.2016.11.005", "pmcid": "PMC6357955", "issn": "0968-0004", "publisher": "Cell Press", "publication": "Trends in Biochemical Sciences", "publication_date": "2017-01", "series_number": "1", "volume": "42", "issue": "1", "pages": "2-4" }, { "id": "authors:csv3y-qgv30", "collection": "authors", "collection_id": "csv3y-qgv30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160919-144341349", "type": "article", "title": "A model for regulation by SynGAP-\u03b11 of binding of synaptic proteins to PDZ-domain 'Slots' in the postsynaptic density", "author": [ { "family_name": "Walkup", "given_name": "Ward G., IV", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-W-G-IV" }, { "family_name": "Mastro", "given_name": "Tara L.", "clpid": "Mastro-T-L" }, { "family_name": "Schenker", "given_name": "Leslie T.", "clpid": "Schenker-L-T" }, { "family_name": "Vielmetter", "given_name": "Jost", "clpid": "Vielmetter-J" }, { "family_name": "Hu", "given_name": "Rebecca", "clpid": "Hu-Rebecca" }, { "family_name": "Iancu", "given_name": "Ariella", "clpid": "Iancu-A" }, { "family_name": "Reghunathan", "given_name": "Meera", "clpid": "Reghunathan-M" }, { "family_name": "Bannon", "given_name": "B. Dylan", "clpid": "Bannon-B-D" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a Ras/Rap GTPase-activating protein (GAP) that is a major constituent of postsynaptic densities (PSDs) from mammalian forebrain. Its \u03b11 isoform binds to all three PDZ (PSD-95, Discs-large, ZO-1) domains of PSD-95, the principal PSD scaffold, and can occupy as many as 15% of these PDZ domains. We present evidence that synGAP-\u03b11 regulates the composition of the PSD by restricting binding to the PDZ domains of PSD-95. We show that phosphorylation by Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII) and Polo-like kinase-2 (PLK2) decreases its affinity for the PDZ domains by several fold, which would free PDZ domains for occupancy by other proteins. Finally, we show that three critical postsynaptic signaling proteins that bind to the PDZ domains of PSD-95 are present in higher concentration in PSDs isolated from mice with a heterozygous deletion of synGAP.", "doi": "10.7554/eLife.16813", "pmcid": "PMC5040590", "issn": "2050-084X", "publisher": "eLife Sciences Publications", "publication": "eLife", "publication_date": "2016-09-13", "volume": "5", "pages": "Art. No. e16813" }, { "id": "authors:4v36z-r4204", "collection": "authors", "collection_id": "4v36z-r4204", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160718-135600220", "type": "monograph", "title": "Binding of synGAP to PDZ Domains of PSD-95 is Regulated by Phosphorylation and Shapes the Composition of the Postsynaptic Density", "author": [ { "family_name": "Walkup", "given_name": "Ward G.", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-W-G-IV" }, { "family_name": "Mastro", "given_name": "Tara", "clpid": "Mastro-T-L" }, { "family_name": "Schenker", "given_name": "Leslie T.", "clpid": "Schenker-L-T" }, { "family_name": "Vielmetter", "given_name": "Jost", "clpid": "Vielmetter-J" }, { "family_name": "Hu", "given_name": "Rebecca", "clpid": "Hu-Rebecca" }, { "family_name": "Iancu", "given_name": "Ariella", "clpid": "Iancu-A" }, { "family_name": "Reghunathan", "given_name": "Meera", "clpid": "Reghunathan-M" }, { "family_name": "Bannon", "given_name": "B. Dylan", "clpid": "Bannon-B-D" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a Ras/Rap GTPase-activating protein (GAP) present in high concentration in postsynaptic densities (PSDs) from mammalian forebrain where it binds to all three PDZ (PSD-95, Discs-large, ZO-1) domains of PSD-95. We show that phosphorylation of synGAP by Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII) decreases its affinity for the PDZ domains as much as 10-fold, measured by surface plasmon resonance. SynGAP is abundant enough in postsynaptic densities (PSDs) to occupy about one third of the PDZ domains of PSD-95. Therefore, we hypothesize that phosphorylation by CaMKII reduces synGAP\u2032s ability to restrict binding of other proteins to the PDZ domains of PSD-95. We support this hypothesis by showing that three critical postsynaptic signaling proteins that bind to the PDZ domains of PSD-95 are present at a higher ratio to PSD-95 in PSDs isolated from synGAP heterozygous mice.", "doi": "10.1101/058016", "publication_date": "2016-06-09" }, { "id": "authors:k2xan-ye883", "collection": "authors", "collection_id": "k2xan-ye883", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140109-094515875", "type": "article", "title": "Synaptic Signaling in Learning and Memory", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Learning and memory require the formation of new neural networks in the brain. A key mechanism underlying this process is synaptic plasticity at excitatory synapses, which connect neurons into networks. Excitatory synaptic transmission happens when glutamate, the excitatory neurotransmitter, activates receptors on the postsynaptic neuron. Synaptic plasticity is a higher-level process in which the strength of excitatory synapses is altered in response to the pattern of activity at the synapse. It is initiated in the postsynaptic compartment, where the precise pattern of influx of calcium through activated glutamate receptors leads either to the addition of new receptors and enlargement of the synapse (long-term potentiation) or the removal of receptors and shrinkage of the synapse (long-term depression). Calcium/calmodulin-regulated enzymes and small GTPases collaborate to control this highly tuned mechanism.", "doi": "10.1101/cshperspect.a016824", "pmcid": "PMC4743082", "issn": "1943-0264", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Cold Spring Harbor Perspectives in Biology", "publication_date": "2016-02", "series_number": "2", "volume": "8", "issue": "2", "pages": "Art. No. a016824" }, { "id": "authors:rhrkr-d4z50", "collection": "authors", "collection_id": "rhrkr-d4z50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151019-092747172", "type": "article", "title": "Computational reconstitution of spine calcium transients from individual proteins", "author": [ { "family_name": "Bartol", "given_name": "Thomas M.", "clpid": "Bartol-T-M" }, { "family_name": "Keller", "given_name": "Daniel X.", "clpid": "Keller-D-X" }, { "family_name": "Kinney", "given_name": "Justin P.", "clpid": "Kinney-J-P" }, { "family_name": "Bajaj", "given_name": "Chandrajit L.", "clpid": "Bajaj-C-L" }, { "family_name": "Harris", "given_name": "Kristen M.", "clpid": "Harris-K-M" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "We have built a stochastic model in the program MCell that simulates Ca^(2+) transients in spines from the principal molecular components believed to control Ca^(2+) entry and exit. Proteins, with their kinetic models, are located within two segments of dendrites containing 88 intact spines, centered in a fully reconstructed 6 \u00d7 6 \u00d7 5 \u03bcm^3 cube of hippocampal neuropil. Protein components include AMPA- and NMDA-type glutamate receptors, L- and R-type voltage-dependent Ca^(2+) channels, Na^+/Ca^(2+) exchangers, plasma membrane Ca^(2+) ATPases, smooth endoplasmic reticulum Ca^(2+) ATPases, immobile Ca2+ buffers, and calbindin. Kinetic models for each protein were taken from published studies of the isolated proteins in vitro. For simulation of electrical stimuli, the time course of voltage changes in the dendritic spine was generated with the desired stimulus in the program NEURON. Voltage-dependent parameters were then continuously re-adjusted during simulations in MCell to reproduce the effects of the stimulus. Nine parameters of the model were optimized within realistic experimental limits by a process that compared results of simulations to published data. We find that simulations in the optimized model reproduce the timing and amplitude of Ca^(2+) transients measured experimentally in intact neurons. Thus, we demonstrate that the characteristics of individual isolated proteins determined in vitro can accurately reproduce the dynamics of experimentally measured Ca^(2+) transients in spines. The model will provide a test bed for exploring the roles of additional proteins that regulate Ca^(2+) influx into spines and for studying the behavior of protein targets in the spine that are regulated by Ca^(2+) influx.", "doi": "10.3389/fnsyn.2015.00017", "issn": "1663-3563", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Synaptic Neuroscience", "publication_date": "2015-10-07", "series_number": "Art. No. 17", "volume": "7", "issue": "Art. No. 17" }, { "id": "authors:jynaj-0e497", "collection": "authors", "collection_id": "jynaj-0e497", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150409-142656249", "type": "article", "title": "Protein Purification Using PDZ Affinity Chromatography", "author": [ { "family_name": "Walkup", "given_name": "Ward G., IV", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-Ward-G-IV" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands.", "doi": "10.1002/0471140864.ps0910s80", "pmcid": "PMC4435810", "issn": "1934-3655", "publisher": "Wiley", "publication": "Current Protocols in Protein Science", "publication_date": "2015-04-01", "volume": "80", "pages": "Unit 9.10" }, { "id": "authors:kwvxj-5bz98", "collection": "authors", "collection_id": "kwvxj-5bz98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150108-105520667", "type": "article", "title": "Phosphorylation of Synaptic GTPase Activating Protein (synGAP) by Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5) alters the ratio of its GAP activity toward Ras and Rap GTPases", "author": [ { "family_name": "Walkup", "given_name": "Ward G., IV", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-W-G-IV" }, { "family_name": "Washburn", "given_name": "Lorraine", "clpid": "Washburn-L" }, { "family_name": "Sweredoski", "given_name": "Michael J.", "orcid": "0000-0003-0878-3831", "clpid": "Sweredoski-M-J" }, { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Graham", "given_name": "Robert L.", "clpid": "Graham-R-L" }, { "family_name": "Hess", "given_name": "Sonja", "orcid": "0000-0002-5904-9816", "clpid": "Hess-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a neuron-specific Ras and Rap GTPase-activating protein (GAP) found in high concentration in the postsynaptic density (PSD) fraction from mammalian forebrain. We have previously shown that, in situ in the PSD fraction or in recombinant form in Sf9 cell membranes, synGAP is phosphorylated by Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII), another prominent component of the PSD. Here we show that recombinant synGAP (r-synGAP), lacking 102 residues at the N-terminus, can be purified in soluble form and is phosphorylated by cyclin-dependent kinase 5 (CDK5) as well as by CaMKII. Phos-phorylation of r-synGAP by CaMKII increases its HRas GAP activity by 25% and its Rap1 GAP activity by 76%. Conversely, phosphorylation by CDK5 increases r-synGAPs HRas GAP activity by 98% and its Rap1 GAP activity by 20%. Thus, phosphorylation by both kinases increases synGAP activity, but CaMKII shifts the relative GAP activity toward inactivation of Rap1; whereas CDK5 shifts the relative activity toward inactivation of HRas. GAP activity toward Rap2 is not altered by phosphorylation by either kinase. CDK5 phosphorylates synGAP primarily at two sites, S773 and S802. Phosphorylation at S773 inhibits r-synGAP activity, whereas phosphorylation at S802 increases it. However, the net effect of concurrent phosphorylation of both sites, S773 and S802, is an increase in GAP activity. SynGAP is phosphorylated at S773 and S802 in the PSD fraction, and its phosphorylation by CDK5 and CaMKII is differentially regulated by activation of NMDA-type glutamate receptors in cultured neurons.", "doi": "10.1074/jbc.M114.614420", "pmcid": "PMC4335230", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2015-02-20", "series_number": "8", "volume": "290", "issue": "8", "pages": "4908-4927" }, { "id": "authors:a50pw-c4176", "collection": "authors", "collection_id": "a50pw-c4176", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141106-111638499", "type": "article", "title": "Multi-state Modeling of Biomolecules", "author": [ { "family_name": "Stefan", "given_name": "Melanie I.", "clpid": "Stefan-M-I" }, { "family_name": "Bartol", "given_name": "Thomas M.", "clpid": "Bartol-T-M" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behavior of biological molecules or complexes that can adopt a large number of possible functional states. Biological signaling systems often rely on complexes of biological macromolecules that can undergo several functionally significant modifications that are mutually compatible. Thus, they can exist in a very large number of functionally different states. Modeling such multi-state systems poses two problems: the problem of how to describe and specify a multi-state system (the \"specification problem\") and the problem of how to use a computer to simulate the progress of the system over time (the \"computation problem\"). To address the specification problem, modelers have in recent years moved away from explicit specification of all possible states and towards rule-based formalisms that allow for implicit model specification, including the \u03ba-calculus [1], BioNetGen [2]\u2013[5], the Allosteric Network Compiler [6], and others [7], [8]. To tackle the computation problem, they have turned to particle-based methods that have in many cases proved more computationally efficient than population-based methods based on ordinary differential equations, partial differential equations, or the Gillespie stochastic simulation algorithm [9], [10]. Given current computing technology, particle-based methods are sometimes the only possible option. Particle-based simulators fall into two further categories: nonspatial simulators, such as StochSim [11], DYNSTOC [12], RuleMonkey [9], [13], and the Network-Free Stochastic Simulator (NFSim) [14], and spatial simulators, including Meredys [15], SRSim [16], [17], and MCell [18]\u2013[20]. Modelers can thus choose from a variety of tools, the best choice depending on the particular problem. Development of faster and more powerful methods is ongoing, promising the ability to simulate ever more complex signaling processes in the future.", "doi": "10.1371/journal.pcbi.1003844", "pmcid": "PMC4201162", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2014-09", "series_number": "9", "volume": "10", "issue": "9", "pages": "Art. No. e1003844" }, { "id": "authors:2psj2-mvp73", "collection": "authors", "collection_id": "2psj2-mvp73", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140320-145341209", "type": "article", "title": "PDZ affinity chromatography: A general method for affinity purification of proteins based on PDZ domains and their ligands", "author": [ { "family_name": "Walkup", "given_name": "Ward G.", "orcid": "0000-0002-0385-6256", "clpid": "Walkup-W-G-IV" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise \u223c90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain ligands, eluting the proteins with free PDZ domain peptide ligands. We show that Proteins of Interest (POIs) lacking endogenous PDZ domain ligands can be engineered as fusion products containing C-terminal PDZ domain ligand peptides or internal, N- or C-terminal PDZ domains and then can be purified by the same method. Using this method, we recovered recombinant GFP fused to a PDZ-domain ligand in active form as verified by fluorescence yield. Similarly, chloramphenicol acetyltransferase (CAT) and \u03b2-Galactosidase (LacZ) fused to a C-terminal PDZ domain ligand or an N-terminal PDZ domain were purified in active form as assessed by enzymatic assay. In general, PDZ domains and ligands derived from PSD-95 were superior to those from nNOS for this method. PDZ Domain Affinity Chromatography promises to be a versatile and effective method for purification of a wide variety of natural and recombinant proteins.", "doi": "10.1016/j.pep.2014.02.015", "pmcid": "PMC4024478", "issn": "1046-5928", "publisher": "Elsevier", "publication": "Protein Expression and Purification", "publication_date": "2014-06", "volume": "98", "pages": "46-62" }, { "id": "authors:4ytys-dce67", "collection": "authors", "collection_id": "4ytys-dce67", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150205-104036411", "type": "article", "title": "Organizing signal transduction in the postsynaptic density", "author": [ { "family_name": "Kennedy", "given_name": "Mary", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Excitatory neurons in the CNS receive thousands of synaptic contacts from other excitatory neurons. An increase in the strength of a relatively small number of these synapses can store a memory by binding connected neurons into a circuit in which all of the neurons fire each time the specific memory is evoked. An increase in synaptic strength involves addition of new glutamate receptors to the synaptic membrane, and re-arrangement of the cytoskeleton to support a larger synapse. Biochemical signaling enzymes that control this process, which is called \"activity-dependent synaptic plasticity,\" are organized near the postsynaptic membrane. The enzymes include several protein kinases, adenylyl cyclase, and regulators of Ras and Rap. Many of them are attached to a multiprotein scaffold called the \"postsynaptic density.\" At least five classes of scaffold proteins contribute to the precise orchestration of changes in synaptic strength: PSD-95 and other MAGUKS, SHANKs, Homer, AKAPs, and Densin. What we have learned thus far about the dynamic properties of the postsynaptic density reveals new ways to rapidly regulate the number and sensitivity of membrane receptors.", "issn": "0892-6638", "publisher": "Federation of American Societies for Experimental Biology", "publication": "FASEB Journal", "publication_date": "2014-04", "series_number": "1", "volume": "28", "issue": "1", "pages": "107.2" }, { "id": "authors:06fb5-6db32", "collection": "authors", "collection_id": "06fb5-6db32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130917-090325023", "type": "article", "title": "Subcellular Organization of CaMKII in Rat Hippocampal Pyramidal Neurons", "author": [ { "family_name": "Ding", "given_name": "Jin-Dong", "clpid": "Ding-Jin-Dong" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Weinberg", "given_name": "Richard J.", "clpid": "Weinberg-R-J" } ], "abstract": "Calcium/calmodulin-dependent protein kinase II (CaMKII) plays a key role in N-methyl-D-aspartate (NMDA) receptor-dependent long-term synaptic plasticity; its location is critical for signal transduction, and may provide clues that further elucidate its function. We therefore examined the subcellular localization of CaMKII in CA1 stratum radiatum of adult rat hippocampus, by using immuno-electron microscopy after chemical fixation. When tissue was fixed quickly, the concentration of CaMKII\u03b1 (assessed by pre-embedding immunogold) was significantly higher in dendritic shafts than in spine heads. However, when tissue was fixed 5 minutes after perfusion with normal saline, the density of labeling decreased in dendritic shaft while increasing in spine heads, implying rapid translocation into the spine during brief perimortem stress. Likewise, in quickly fixed tissue, CaMKII within spine heads was found at comparable concentrations in the \"proximal\" half (adjacent to the spine neck) and the \"distal\" half (containing the postsynaptic density [PSD]), whereas after delayed fixation, label density increased in the distal side of the spine head, suggesting that CaMKII within the spine head moves toward the PSD during this interval. To estimate its distribution at the synapse in vivo, we performed postembedding immunogold staining for CaMKII in quick-fixed tissue, and found that the enzyme did not concentrate primarily within the central matrix of the PSD. Instead, labeling density peaked \u223c40 nm inside the postsynaptic membrane, at the cytoplasmic fringe of the PSD. Labeling within 25 nm of the postsynaptic membrane concentrated at the lateral edge of the synapse. This lateral \"PSD core\" pool of CaMKII may play a special role in synaptic plasticity.", "doi": "10.1002/cne.23372", "pmcid": "PMC4409980", "issn": "0021-9967", "publisher": "Wiley", "publication": "Journal of Comparative Neurology", "publication_date": "2013-10", "series_number": "15", "volume": "521", "issue": "15", "pages": "3570-3583" }, { "id": "authors:fq5p7-dzr61", "collection": "authors", "collection_id": "fq5p7-dzr61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121108-110709029", "type": "conference_item", "title": "Modelling Ca2+ -dependent proteins in the spine - challenges and solutions", "author": [ { "family_name": "Stefan", "given_name": "Melanie I.", "clpid": "Stefan-M-I" }, { "family_name": "Pepke", "given_name": "Shirley", "clpid": "Pepke-S" }, { "family_name": "Mihalas", "given_name": "Stefan", "clpid": "Mihalas-S" }, { "family_name": "Bartol", "given_name": "Thomas", "clpid": "Bartol-T" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Background / Purpose:\n\nModelling post-synaptic proteins poses three technical problems: small absolute molecule numbers, large numbers of possible states, and the complex geometry of the spine, which is not a well-mixed compartment. Computational approaches are needed that solve all three of these problems.\n\nMain conclusion:\n\nStochastic simulation methods can be used for systems with small molecule numbers, agent-based methods to represent multi-state molecules, and spatial methods to simulate events in complex geometries. We used the agent-based spatial stochastic simulator MCell to model the Ca2+-dependent activation of calmodulin and Ca2+/calmodulin-dependent kinase II (CaMKII) in the spine.\n\nNext steps:\n\nNext steps will include the extension of our model to include more interaction partners, and to represent some of the regulation events in more detail.", "publisher": "Caltech Library", "publication_date": "2012-09" }, { "id": "authors:cpwj8-rax59", "collection": "authors", "collection_id": "cpwj8-rax59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120716-102059619", "type": "article", "title": "Molecular and behavioral changes associated with adult hippocampus-specific SynGAP1 knockout", "author": [ { "family_name": "Muhia", "given_name": "Mary", "clpid": "Muhia-M" }, { "family_name": "Willadt", "given_name": "Silvia", "clpid": "Willadt-S" }, { "family_name": "Yee", "given_name": "Benjamin K.", "clpid": "Yee-B-K" }, { "family_name": "Feldon", "given_name": "Joram", "clpid": "Feldon-J" }, { "family_name": "Paterna", "given_name": "Jean-Charles", "clpid": "Paterna-J-C" }, { "family_name": "Schwendener", "given_name": "Severin", "clpid": "Schwendener-S" }, { "family_name": "Vogt", "given_name": "Kaspar", "clpid": "Vogt-K" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Knuesel", "given_name": "Irene", "clpid": "Knuesel-I" } ], "abstract": "The synaptic Ras/Rap-GTPase-activating protein (SynGAP1) plays a unique role in regulating specific downstream intracellular events in response to N-methyl-D-aspartate receptor (NMDAR) activation. Constitutive heterozygous loss of SynGAP1 disrupts NMDAR-mediated physiological and behavioral processes, but the disruptions might be of developmental origin. Therefore, the precise role of SynGAP1 in the adult brain, including its relative functional significance within specific brain regions, remains unexplored. The present study constitutes the first attempt in achieving adult hippocampal-specific SynGAP1 knockout using the Cre/loxP approach. Here, we report that this manipulation led to a significant numerical increase in both small and large GluA1 and NR1 immunoreactive clusters, many of which were non-opposed to presynaptic terminals. In parallel, the observed marked decline in the amplitude of spontaneous excitatory currents (sEPSCs) and inter-event intervals supported the impression that SynGAP1 loss might facilitate the accumulation of extrasynaptic glutamatergic receptors. In addition, SynGAP1-mediated signaling appears to be critical for the proper integration and survival of newborn neurons. The manipulation impaired reversal learning in the probe test of the water maze and induced a delay-dependent impairment in spatial recognition memory. It did not significantly affect anxiety or reference memory acquisition but induced a substantial elevation in spontaneous locomotor activity in the open field test. Thus, the present study demonstrates the functional significance of SynGAP1 signaling in the adult brain by capturing several changes that are dependent on NMDAR and hippocampal integrity.", "doi": "10.1101/lm.026351.112", "issn": "1072-0502", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Learning and Memory", "publication_date": "2012-07", "series_number": "7", "volume": "19", "issue": "7", "pages": "268-281" }, { "id": "authors:ayk99-v4219", "collection": "authors", "collection_id": "ayk99-v4219", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111219-120449068", "type": "article", "title": "Deletion of Densin-180 Results in Abnormal Behaviors Associated with Mental Illness and Reduces mGluR5 and DISC1 in the Postsynaptic Density Fraction", "author": [ { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Luong", "given_name": "Tinh N.", "clpid": "Luong-T-N" }, { "family_name": "Medina-Merino", "given_name": "Andrew", "clpid": "Medina-Merino-A" }, { "family_name": "Schenker", "given_name": "Leslie", "clpid": "Schenker-L" }, { "family_name": "Khorosheva", "given_name": "Eugenia", "clpid": "Korosheva-E" }, { "family_name": "Indersmitten", "given_name": "Tim", "clpid": "Indersmitten-T" }, { "family_name": "Gunapala", "given_name": "Keith M.", "clpid": "Gunapala-K-M" }, { "family_name": "Steele", "given_name": "Andrew D.", "clpid": "Steele-A-D" }, { "family_name": "O'Dell", "given_name": "Thomas J.", "clpid": "O'Dell-T-J" }, { "family_name": "Patterson", "given_name": "Paul H.", "clpid": "Patterson-P-H" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Densin is an abundant scaffold protein in the postsynaptic density (PSD) that forms a high-affinity complex with \u03b1CaMKII and \u03b1-actinin. To assess the function of densin, we created a mouse line with a null mutation in the gene encoding it (LRRC7). Homozygous knock-out mice display a wide variety of abnormal behaviors that are often considered endophenotypes of schizophrenia and autism spectrum disorders. At the cellular level, loss of densin results in reduced levels of \u03b1-actinin in the brain and selective reduction in the localization of mGluR5 and DISC1 in the PSD fraction, whereas the amounts of ionotropic glutamate receptors and other prominent PSD proteins are unchanged. In addition, deletion of densin results in impairment of mGluR- and NMDA receptor-dependent forms of long-term depression, alters the early dynamics of regulation of CaMKII by NMDA-type glutamate receptors, and produces a change in spine morphology. These results indicate that densin influences the function of mGluRs and CaMKII at synapses and contributes to localization of mGluR5 and DISC1 in the PSD fraction. They are consistent with the hypothesis that mutations that disrupt the organization and/or dynamics of postsynaptic signaling complexes in excitatory synapses can cause behavioral endophenotypes of mental illness.", "doi": "10.1523/JNEUROSCI.5877-10.2011", "pmcid": "PMC3235477", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2011-11-09", "series_number": "45", "volume": "31", "issue": "45", "pages": "16194-16207" }, { "id": "authors:8qey9-19t18", "collection": "authors", "collection_id": "8qey9-19t18", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120613-125303676", "type": "article", "title": "Multi-Stage Modeling of the Kinetics of Activation of CaMKII", "author": [ { "family_name": "Stefan", "given_name": "Melanie I.", "clpid": "Stefan-M-I" }, { "family_name": "Pepke", "given_name": "Shirley", "clpid": "Pepke-S" }, { "family_name": "Mihalas", "given_name": "Stefan", "clpid": "Mihalas-S" }, { "family_name": "Bartol", "given_name": "Thomas", "clpid": "Bartol-T" }, { "family_name": "Sejnowski", "given_name": "Terrence J.", "orcid": "0000-0002-0622-7391", "clpid": "Sejnowski-T-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Ca 2+ /calmodulin-dependent protein kinase 2 (CaMKII) plays an important role in induction of long-term potentiation and formation of memory. It is abundant in dendritic spines, and is activated when Ca 2+ flows into the postsynaptic cytosol through open NMDA-type glutamate receptors. Its function is fine-tuned through interaction with other proteins as well as through subunit interactions and regulatory autophosphorylation. We have undertaken a multi-stage project to study the critical kinetics of activation of CaMKII in the spine by combining modeling and experimental studies. We are using computational modeling and simulations on various platforms, coupled with biochemical experiments in vitro, and eventually in vivo, to understand CaMKII regulation. The project includes the following steps: 1. Determining the parameters governing activation of a monomeric subunit. The CaMKII holoenzyme is a large dodecamer of similar, homologous subunits held together by interactions between the association domains located at the carboxyl end of each subunit. Individual, monomeric subunits can be expressed recombinantly by removing the association domain. Computer simulations of activation of monomeric CaMKII by Ca 2+ /calmodulin at both saturating and non-saturating concentrations in a test tube have helped to identify the binding parameters that are most crucial for modeling of regulation of CaMKII and thus have indicated the most useful biochemical assays to measure those parameters (Pepke et al., 2010). We are using these measurements to fine-tune our model of activation of individual catalytic subunits. 2. Building a model of the holoenzyme. Because a CaMKII holoenzyme contains 12 similar subunits, each of which can exist in several states, the holoenzyme can have a large number of state combinations. Thus, modeling the entire holoenzyme requires a computational framework that avoids the ensuing combinatorial complexity. The stochastic simulator MCell provides an elegant, rule-based way of modeling state changes in the CaMKII holoenzyme. 3. Modeling cooperativity that arises from the dodecameric structure of CaMKII. Autophosphorylation at threonine-286, which activates CaMKII subunits, is an inter-subunit event. Thus, it is greatly facilitated by the close proximity of subunits in the holoenzyme. In addition, the subunits within the holoenzyme are arranged as dimers which appears to result in cooperativity in the binding of Ca 2+ /CaM to individual subunits of the dimer (Chao et al., 2010). An accurate model of activation of subunits in the holoenzyme and their autophosphorylation will allow us to explore the effects of cooperativity on CaMKII activation on various time scales. 4. Modeling CaMKII within the context of a postsynaptic spine CaMKII interacts with a variety of other proteins, both in the postsynaptic density (PSD), close to major sources of Ca 2+ influx, and in other parts of the spine. In the fourth stage of this project we plan to implement kinetic models of activation of CaMKII in the context of an MCell model of Ca 2+ influx into a spine upon activation of NMDA-type glutamate receptors (Keller et al., 2008; Keller et al., 2011, submitted). We will explore the effects of different localization and numbers of CaMKII holoenzymes in the spine on CaMKII activation. \n\nReferences: Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). A dynamic model of interactions of Ca 2+ , calmodulin, and catalytic subunits of Ca 2+ /calmodulin-dependent protein kinase II. PLoS Comput Biol 6, e1000675. Chao, L.H., Pellicena, P., Deindl, S., Barclay, L.A., Schulman, H., and Kuriyan, J. (2010). Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation. Nat Struct Mol Biol 17, 264-272. Keller, D.X., Franks, K.M., Bartol, T.M., Jr., and Sejnowski, T.J. (2008). Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines. PLoS ONE 3, e2045. Keller, D.X., Bartol, T.M., Kinney, J.P, Kennedy, M.B., Bajaj, C., Harris, K.M., and Sejnowski, T.J. Regulation of synaptic calcium transients in reconstructed dendritic spines of hippocampal CA1 pyramidal neurons, submitted.", "doi": "10.3389/conf.fninf.2011.08.00033", "issn": "1662-5196", "publisher": "Frontiers Research Foundation", "publication": "Frontiers in Neuroinformatics", "publication_date": "2011-10-19", "pages": "Art. NO. 00033" }, { "id": "authors:s0knt-m9287", "collection": "authors", "collection_id": "s0knt-m9287", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101206-142344181", "type": "article", "title": "The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus", "author": [ { "family_name": "Marcora", "given_name": "Edoardo", "clpid": "Marcora-E" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Expansion of a polyglutamine (polyQ) tract in the Huntingtin (Htt) protein causes Huntington's disease (HD), a fatal inherited neurodegenerative disorder. Loss of the normal function of Htt is thought to be an important pathogenetic component of HD. However, the function of wild-type Htt is not well defined. Htt is thought to be a multifunctional protein that plays distinct roles in several biological processes, including synaptic transmission, intracellular transport and neuronal transcription. Here, we show with biochemical and live cell imaging studies that wild-type Htt stimulates the transport of nuclear factor \u03ba light-chain-enhancer of activated B cells (NF-\u03baB) out of dendritic spines (where NF-\u03baB is activated by excitatory synaptic input) and supports a high level of active NF-\u03baB in neuronal nuclei (where NF-\u03baB stimulates the transcription of target genes). We show that this novel function of Htt is impaired by the polyQ expansion and thus may contribute to the etiology of HD.", "doi": "10.1093/hmg/ddq358", "pmcid": "PMC2957321", "issn": "0964-6906", "publisher": "Oxford University Press", "publication": "Human Molecular Genetics", "publication_date": "2010-11-15", "series_number": "22", "volume": "19", "issue": "22", "pages": "4373-4384" }, { "id": "authors:axkxd-d9w35", "collection": "authors", "collection_id": "axkxd-d9w35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100326-111445101", "type": "article", "title": "A Dynamic Model of Interactions of Ca^(2+), Calmodulin, and Catalytic Subunits of Ca^(2+)/Calmodulin-Dependent Protein Kinase II", "author": [ { "family_name": "Pepke", "given_name": "Shirley", "clpid": "Pepke-S" }, { "family_name": "Kinzer-Ursem", "given_name": "Tamara", "clpid": "Kinzer-Ursem-T" }, { "family_name": "Mihalas", "given_name": "Stefan", "clpid": "Mihalas-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "During the acquisition of memories, influx of Ca^(2+) into the postsynaptic spine through the pores of activated N-methyl-D-aspartate-type glutamate receptors triggers processes that change the strength of excitatory synapses. The pattern of Ca^(2+) influx during the first few seconds of activity is interpreted within the Ca^(2+)-dependent signaling network such that synaptic strength is eventually either potentiated or depressed. Many of the critical signaling enzymes that control synaptic plasticity, including Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII), are regulated by calmodulin, a small protein that can bind up to 4 Ca^(2+) ions. As a first step toward clarifying how the Ca^(2+)-signaling network decides between potentiation or depression, we have created a kinetic model of the interactions of Ca^(2+), calmodulin, and CaMKII that represents our best understanding of the dynamics of these interactions under conditions that resemble those in a postsynaptic spine. We constrained parameters of the model from data in the literature, or from our own measurements, and then predicted time courses of activation and autophosphorylation of CaMKII under a variety of conditions. Simulations showed that species of calmodulin with fewer than four bound Ca^(2+) play a significant role in activation of CaMKII in the physiological regime, supporting the notion that processing ofCa^(2+) signals in a spine involves competition among target enzymes for binding to unsaturated species of CaM in an environment in which the concentration of Ca^(2+) is fluctuating rapidly. Indeed, we showed that dependence of activation on the frequency of Ca^(2+) transients arises from the kinetics of interaction of fluctuating Ca^(2+) with calmodulin/CaMKII complexes. We used parameter sensitivity analysis to identify which parameters will be most beneficial to measure more carefully to improve the accuracy of predictions. This model provides a quantitative base from which to build more complex dynamic models of postsynaptic signal transduction during learning.", "doi": "10.1371/journal.pcbi.1000675", "pmcid": "PMC2820514", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2010-02", "series_number": "2", "volume": "6", "issue": "2", "pages": "Art. No. e1000675" }, { "id": "authors:2rq43-vf544", "collection": "authors", "collection_id": "2rq43-vf544", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:CARjns08", "type": "article", "title": "SynGAP Regulates Steady-State and Activity-Dependent Phosphorylation of Cofilin", "author": [ { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Manzerra", "given_name": "Pasquale", "clpid": "Manzerra-P" }, { "family_name": "Marcora", "given_name": "Edoardo", "clpid": "Marcora-E" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP, a prominent Ras/Rap GTPase-activating protein in the postsynaptic density, regulates the timing of spine formation and trafficking of glutamate receptors in cultured neurons. However, the molecular mechanisms by which it does this are unknown. Here, we show that synGAP is a key regulator of spine morphology in adult mice. Heterozygous deletion of synGAP was sufficient to cause an excess of mushroom spines in adult brains, indicating that synGAP is involved in steady-state regulation of actin in mature spines. Both Ras- and Rac-GTP levels were elevated in forebrains from adult synGAP+/- mice. Rac is a well known regulator of actin polymerization and spine morphology. The steady-state level of phosphorylation of cofilin was also elevated in synGAP+/- mice. Cofilin, an F-actin severing protein that is inactivated by phosphorylation, is a downstream target of a pathway regulated by Rac. We show that transient regulation of cofilin by treatment with NMDA is also disrupted in synGAP mutant neurons. Treatment of wild-type neurons with 25 \u00b5M NMDA triggered transient dephosphorylation and activation of cofilin within 15 s. In contrast, neurons cultured from mice with a homozygous or heterozygous deletion of synGAP lacked the transient regulation by the NMDA receptor. Depression of EPSPs induced by a similar treatment of hippocampal slices with NMDA was disrupted in slices from synGAP+/- mice. Our data show that synGAP mediates a rate-limiting step in steady-state regulation of spine morphology and in transient NMDA-receptor-dependent regulation of the spine cytoskeleton.", "doi": "10.1523/JNEUROSCI.4695-08.200", "pmcid": "PMC2615239", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2008-12-10", "series_number": "50", "volume": "28", "issue": "50", "pages": "13673-13683" }, { "id": "authors:823pa-chb15", "collection": "authors", "collection_id": "823pa-chb15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110127-153401744", "type": "article", "title": "Conserved and Variable Regions in the Subunits of Brain Type II Ca^(2+)/Calmodulin-Dependent Protein Kinase", "author": [ { "family_name": "Bulleit", "given_name": "Robert F.", "clpid": "Bulleit-R-F" }, { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Molloy", "given_name": "Sean S.", "clpid": "Molloy-S-S" }, { "family_name": "Hurley", "given_name": "James B.", "clpid": "Hurley-J-B" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Brain type II Ca^(2+)/calmodulin-dependent protein kinase is a holoenzymecomposed of several copies each\nof three subunits, \u03b1 (50 kd), \u03b2 (60 kd), and \u03b2' (58 kd), in varying proportions. The deduced amino acid\nsequences of \u03b1 (reported here) and \u03b2 are highly similar but not identical. The major difference between\nthem is the deletion from \u03b1 of two short segments (residues 316\u2013339 and 354\u2013392 in \u03b2). cDNAs that\nappear to encode \u03b2' are identical to b except for the deletion of a segment encoding residues 378\u2013392.\nThus, the structural differences among \u03b1, \u03b2, and \u03b2' arise primarily from deletions (or insertions) in\na variable region lying immediately carboxyl to the protein kinase and calmodulin-binding domains. The\n\u03b1 and \u03b2 subunits are encoded by distinct genes expressed primarily, if not exclusively, in brain. Rather\nthan being encoded by a third gene, \u03b2' may arise by alternative splicing of the \u03b2 gene transcript.", "doi": "10.1016/j.neuron.2008.10.024", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "2008-11-06", "series_number": "3", "volume": "60", "issue": "3", "pages": "401-402" }, { "id": "authors:bnkpt-mve32", "collection": "authors", "collection_id": "bnkpt-mve32", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENn08", "type": "article", "title": "Reflections", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "In the two decades after the founding of Neuron, we witnessed the unfolding of the \"molecular biology revolution\" and its culmination in the sequencing of individual genomes. Cloning of cDNAs and rapid nucleotide sequencing were invented in the early 1970s. By the mid-1980s, \"cDNA-cloning\" was all the rage. A new breed of \"molecular neuroscientists\" began cloning and sequencing transcripts encoding neuronal receptors, ion channels, and signaling enzymes. The wealth of molecular data they generated set the stage for rigorous study of neuronal cell biology.", "doi": "10.1016/j.neuron.2008.10.024", "issn": "0896-6273", "publisher": "Cell Press", "publication": "Neuron", "publication_date": "2008-11-06", "series_number": "3", "volume": "60", "issue": "3", "pages": "401-402" }, { "id": "authors:cxn4a-7gh55", "collection": "authors", "collection_id": "cxn4a-7gh55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:LUCebj08", "type": "article", "title": "Detailed state model of CaMKII activation and autophosphorylation", "author": [ { "family_name": "Lu\u010di\u0107", "given_name": "Vladan", "clpid": "Lu\u010di\u0107-V" }, { "family_name": "Greif", "given_name": "Gabriela J.", "clpid": "Greif-G-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "By combining biochemical experiments with computer modelling of biochemical reactions we elucidated some of the currently unresolved aspects of calcium-calmodulin-dependent protein kinase II (CaMKII) activation and autophosphorylation that might be relevant for its physiological function and provided a model that incorporates in detail the mechanism of CaMKII activation and autophosphorylation at T286 that is based on experimentally determined binding constants and phosphorylation rates. To this end, we developed a detailed state model of CaMKII activation and autophosphorylation based on the currently available literature, and constrained it with data from CaMKII autophosphorylation essays. Our model takes exact phosphorylation patterns of CaMKII holoenzymes into account, and is valid at physiologically relevant conditions where the concentrations of calcium and calmodulin are not saturating. Our results strongly suggest that even when bound to less than fully calcium-bound calmodulin, CaMKII is in the active state, and indicate that the autophosphorylation of T286 by an active non-phosphorylated CaMKII subunit is significantly faster than by an autophosphorylated CaMKII subunit. These results imply that CaMKII can be efficiently activated at significantly lower calcium concentrations than previously thought, which may explain how CaMKII gets activated at calcium concentrations existing at synapses in vivo. We also investigated the significance of CaMKII holoenzyme structure on CaMKII autophosphorylation and obtained estimates of previously unknown binding constants.", "doi": "10.1007/s00249-008-0362-4", "pmcid": "PMC2801814", "issn": "0175-7571", "publisher": "Springer", "publication": "European Biophysics Journal", "publication_date": "2008-11", "series_number": "1", "volume": "38", "issue": "1", "pages": "83-98" }, { "id": "authors:rhwcm-f6j89", "collection": "authors", "collection_id": "rhwcm-f6j89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190821-104427419", "type": "book_section", "title": "Scaffold Proteins in the Postsynaptic Density", "book_title": "Structural And Functional Organization Of The Synapse", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Marcora", "given_name": "Edoardo", "clpid": "Marcora-E" }, { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" } ], "contributor": [ { "family_name": "Hell", "given_name": "Johannes W.", "clpid": "Hell-J-W" }, { "family_name": "Ehlers", "given_name": "Michael D.", "clpid": "Ehlers-M-D" } ], "abstract": "Many intractable neurological and mental diseases, including epilepsy, depression, and schizophrenia, are believed to result, in part, from derangements of regulation of synaptic transmission in the brain. For this reason, much effort has been made to discover how the delicate mechanisms of signal transduction at synapses lead to modification of synaptic strength. One fruitful area of research over the last twenty years has been the postsynaptic signaling apparatus in glutamatergic spines (8, 97, 99, 106). Spines contain clusters of receptors and signaling proteins located in a dense submembranous structure that can be seen in the electron microscope and is called the postsynaptic density or PSD (For review of early work see 98).", "doi": "10.1007/978-0-387-77232-5_14", "isbn": "978-0-387-77231-8", "publisher": "Springer", "place_of_publication": "Boston, MA", "publication_date": "2008", "pages": "407-440" }, { "id": "authors:655m3-hrp38", "collection": "authors", "collection_id": "655m3-hrp38", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-143933776", "type": "book_section", "title": "The Role of the Postsynaptic Density and the Spine\n Cytoskeleton in Synaptic Plasticity", "book_title": "Learning and Memory - A comprehensive reference", "author": [ { "family_name": "Marcora", "given_name": "Edoardo", "clpid": "Marcora-E" }, { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "contributor": [ { "family_name": "Byrne", "given_name": "John H.", "clpid": "Byrne-J-H" } ], "abstract": "N/A", "doi": "10.1016/B978-012370509-9.00036-X", "isbn": "978-0-12-370509-9", "publisher": "Academic Press", "place_of_publication": "London", "publication_date": "2008", "pages": "649-673" }, { "id": "authors:e3kgy-07e25", "collection": "authors", "collection_id": "e3kgy-07e25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-143645378", "type": "article", "title": "Interactions between the NR2B receptor and CaMKII modulate synaptic plasticity and spatial learning.", "author": [ { "family_name": "Zhou", "given_name": "Yu", "clpid": "Zhou-Yu" }, { "family_name": "Takahashi", "given_name": "Eiki", "clpid": "Takahashi-Eiki" }, { "family_name": "Li", "given_name": "Weidong", "clpid": "Li-Weidong" }, { "family_name": "Halt", "given_name": "Amy", "clpid": "Halt-Amy" }, { "family_name": "Wiltgen", "given_name": "Brian", "clpid": "Wiltgen-Brian" }, { "family_name": "Ehninger", "given_name": "Dan", "clpid": "Ehninger-Dan" }, { "family_name": "Li", "given_name": "Guo-Dong", "clpid": "Li-Guo-Dong" }, { "family_name": "Hell", "given_name": "Johannes W.", "clpid": "Hell-Johannes-W" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Silva", "given_name": "Alcino J.", "clpid": "Silva-Alcino-J" } ], "abstract": "The NR2B subunit of the NMDA receptor interacts with several prominent proteins in the postsynaptic density, including calcium/calmodulin-dependent protein kinase II (CaMKII). To determine the function of these interactions, we derived transgenic mice expressing a ligand-activated carboxy-terminal NR2B fragment (cNR2B) by fusing this fragment to a tamoxifen (TAM)-dependent mutant of the estrogen receptor ligand-binding domain LBD(G521R). Here, we show that induction by TAM allows the transgenic cNR2B fragment to bind to endogenous CaMKII in neurons. Activation of the LBD(G521R)-cNR2B transgenic protein in mice leads to the disruption of CaMKII/NR2B interactions at synapses. The disruption decreases Thr286 phosphorylation of alphaCaMKII, lowers phosphorylation of a key CaMKII substrate in the postsynaptic membrane (AMPA receptor subunit glutamate receptor 1), and produces deficits in hippocampal long-term potentiation and spatial learning. Together our results demonstrate the importance of interactions between CaMKII and NR2B for CaMKII activity, synaptic plasticity, and learning.", "doi": "10.1523/JNEUROSCI.4486-07.2007", "pmcid": "PMC6673634", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2007-12-12", "series_number": "50", "volume": "27", "issue": "50", "pages": "13843-13853" }, { "id": "authors:m88f6-kqt39", "collection": "authors", "collection_id": "m88f6-kqt39", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KORploscb06", "type": "article", "title": "Structural modeling of protein interactions by analogy : application to PSD-95", "author": [ { "family_name": "Korkin", "given_name": "Dmitry", "clpid": "Korkin-D" }, { "family_name": "Davis", "given_name": "Fred P.", "clpid": "Davis-F-P" }, { "family_name": "Alber", "given_name": "Frank", "clpid": "Alber-F" }, { "family_name": "Luong", "given_name": "Tinh", "clpid": "Luong-T" }, { "family_name": "Shen", "given_name": "Min-Yi", "clpid": "Shen-M-Y" }, { "family_name": "Lucic", "given_name": "Vladan", "clpid": "Lucic-V" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Sali", "given_name": "Andrej", "clpid": "Sali-A" } ], "abstract": "We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than comparative modeling and a higher accuracy than docking. It relies on structurally defined interactions of each of the complex components, or their homologs, with any other protein, irrespective of its fold. For each component, its known binding modes with other proteins of any fold are collected and expanded by the known binding modes of its homologs. These modes are then used to restrain conventional molecular docking, resulting in a set of binary domain complexes that are subsequently ranked by geometric complementarity and a statistical potential. The method is evaluated by predicting 20 binary complexes of known structure. It is able to correctly identify the binding mode in 70% of the benchmark complexes compared with 30% for protein docking. We applied comparative patch analysis to model the complex of the third PSD-95, DLG, and ZO-1 (PDZ) domain and the SH3-GK domains in the PSD-95 protein, whose structure is unknown. In the first predicted configuration of the domains, PDZ interacts with SH3, leaving both the GMP-binding site of guanylate kinase (GK) and the C-terminus binding cleft of PDZ accessible, while in the second configuration PDZ interacts with GK, burying both binding sites. We suggest that the two alternate configurations correspond to the different functional forms of PSD-95 and provide a possible structural description for the experimentally observed cooperative folding transitions in PSD-95 and its homologs. More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes.", "doi": "10.1371/journal.pcbi.0020153", "pmcid": "PMC1635541", "issn": "1553-734X", "publisher": "Public Library of Science", "publication": "PLoS Computational Biology", "publication_date": "2006-11", "series_number": "11", "volume": "2", "issue": "11", "pages": "e153" }, { "id": "authors:a0hxe-tkj09", "collection": "authors", "collection_id": "a0hxe-tkj09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SHIpnas06b", "type": "article", "title": "Ca2+/calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums", "author": [ { "family_name": "Shifman", "given_name": "Julia M.", "clpid": "Shifpam-J-M" }, { "family_name": "Choi", "given_name": "Mee H.", "clpid": "Choi-Mee-H" }, { "family_name": "Mihalas", "given_name": "Stefan", "clpid": "Mihalas-S" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Changes in synaptic strength that underlie memory formation in the CNS are initiated by pulses of Ca2+ flowing through NMDA-type glutamate receptors into postsynaptic spines. Differences in the duration and size of the pulses determine whether a synapse is potentiated or depressed after repetitive synaptic activity. Calmodulin (CaM) is a major Ca2+ effector protein that binds up to four Ca2+ ions. CaM with bound Ca2+ can activate at least six signaling enzymes in the spine. In fluctuating cytosolic Ca2+, a large fraction of free CaM is bound to fewer than four Ca2+ ions. Binding to targets increases the affinity of CaM's remaining Ca2+-binding sites. Thus, initial binding of CaM to a target may depend on the target's affinity for CaM with only one or two bound Ca2+ ions. To study CaM-dependent signaling in the spine, we designed mutant CaMs that bind Ca2+ only at the two N-terminal or two C-terminal sites by using computationally designed mutations to stabilize the inactivated Ca2+-binding domains in the \"closed\" Ca2+-free conformation. We have measured their interactions with CaMKII, a major Ca2+/CaM target that mediates initiation of long-term potentiation. We show that CaM with two Ca2+ ions bound in its C-terminal lobe not only binds to CaMKII with low micromolar affinity but also partially activates kinase activity. Our results support the idea that competition for binding of CaM with two bound Ca2+ ions may influence significantly the outcome of local Ca2+ signaling in spines and, perhaps, in other signaling pathways.", "doi": "10.1073/pnas.0606433103", "pmcid": "PMC1599897", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2006-09-19", "series_number": "38", "volume": "103", "issue": "38", "pages": "13968-13973" }, { "id": "authors:12q8x-kbp09", "collection": "authors", "collection_id": "12q8x-kbp09", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-145108832", "type": "article", "title": "Integration of biochemical signalling in spines", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Beale", "given_name": "Holly C.", "clpid": "Beale-H-C" }, { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Washburn", "given_name": "Lorraine R.", "clpid": "Washburn-L-R" } ], "abstract": "Short-term and long-term changes in the strength of synapses in neural networks underlie working memory and long-term memory storage in the brain. These changes are regulated by many biochemical signalling pathways in the postsynaptic spines of excitatory synapses. Recent findings about the roles and regulation of the small GTPases Ras, Rap and Rac in spines provide new insights into the coordination and cooperation of different pathways to effect synaptic plasticity. Here, we present an initial working representation of the interactions of five signalling cascades that are usually studied individually. We discuss their integrated function in the regulation of postsynaptic plasticity.", "doi": "10.1038/nrn1685", "issn": "1471-003X", "publisher": "Nature Publishing Group", "publication": "Nature Reviews Neuroscience", "publication_date": "2005-06", "series_number": "6", "volume": "6", "issue": "6", "pages": "423-434" }, { "id": "authors:vwzaj-qdn75", "collection": "authors", "collection_id": "vwzaj-qdn75", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-145300780", "type": "article", "title": "Spine architecture and synaptic plasticity", "author": [ { "family_name": "Carlisle", "given_name": "Holly J.", "clpid": "Carlisle-H-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Many forms of mental retardation and cognitive disability are associated with abnormalities in dendritic spine morphology. Visualization of spines using live-imaging techniques provides convincing evidence that spine morphology is altered in response to certain forms of LTP-inducing stimulation. Thus, information storage at the cellular level appears to involve changes in spine morphology that support changes in synaptic strength produced by certain patterns of synaptic activity. Because the structure of a spine is determined by its underlying actin cytoskeleton, there has been much effort to identify signaling pathways linking synaptic activity to control of actin polymerization. This review, part of the TINS Synaptic Connectivity series, discusses recent studies that implicate EphB and NMDA receptors in the regulation of actin-binding proteins through modulation of Rho family small GTPases.", "doi": "10.1016/j.tins.2005.01.008", "issn": "0166-2236", "publisher": "Elsevier", "publication": "Trends in Neurosciences", "publication_date": "2005-04", "series_number": "4", "volume": "28", "issue": "4", "pages": "182-187" }, { "id": "authors:q6rac-2nf42", "collection": "authors", "collection_id": "q6rac-2nf42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-145452150", "type": "article", "title": "A role for synGAP in regulating neuronal apoptosis.", "author": [ { "family_name": "Knuesel", "given_name": "Irene", "clpid": "Knuesel-I" }, { "family_name": "Elliott", "given_name": "Abigail", "clpid": "Elliott-A" }, { "family_name": "Chen", "given_name": "Hong-Jung", "clpid": "Chen-H-J" }, { "family_name": "Mansuy", "given_name": "Isabelle M.", "clpid": "Mansuy-I-M" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The brain-specific Ras/Rap GTPase-activating protein synGAP is a major component of the postsynaptic density at glutamatergic synapses. It is a target for phosphorylation by Ca(2+)/calmodulin-dependent protein kinase II, which up-regulates its GTPase-activating activity. Thus, SynGAP may play an important role in coupling N-methyl-D-aspartate-type glutamate receptor activation to signaling pathways downstream of Ras or Rap. Homozygous deletion of synGAP is lethal within the first few days after birth. Therefore, to study the functions of synGAP, we used the cre/loxP recombination system to produce conditional mice mutants in which gradual loss of synGAP begins at approximately 1 week, and usually becomes maximal by 3 weeks, after birth. The resulting phenotypes fall into two groups. In a small group, the level of synGAP protein is reduced to 20-25% of wild type, and they die at 2-3 weeks of age. In a larger group, the levels remain higher than approximately 40% of wild type, and they survive and remain healthy. In all mutants, however, an abnormally high number of neurons in the hippocampus and cortex undergo apoptosis, as detected by caspase-3 activation. The effect is cell autonomous, occurring only in neuronal types in which the synGAP gene is eliminated. The level of caspase-3 activation in neurons correlates inversely with the level of synGAP protein measured at 2 and 8 weeks after birth, indicating that neuronal apoptosis is enhanced by reduction of synGAP. These data show that synGAP plays a role in regulation of the onset of apoptotic neuronal death.", "doi": "10.1111/j.1460-9568.2005.03908.x", "issn": "0953-816X", "publisher": "Wiley", "publication": "European Journal of Neuroscience", "publication_date": "2005-02", "series_number": "3", "volume": "21", "issue": "3", "pages": "611-621" }, { "id": "authors:jzd4s-m8791", "collection": "authors", "collection_id": "jzd4s-m8791", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-145649488", "type": "article", "title": "SynGAP regulates spine formation", "author": [ { "family_name": "Vazquez", "given_name": "Luis E.", "clpid": "Vazquez-Luis-E" }, { "family_name": "Chen", "given_name": "Hong-Jung", "clpid": "Chen-Hong-Jung" }, { "family_name": "Sokolova", "given_name": "Irina", "clpid": "Sokolova-Irina" }, { "family_name": "Knuesel", "given_name": "Irene", "clpid": "Knuesel-Irene" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "SynGAP is a brain-specific ras GTPase-activating protein that is an abundant component of the signaling complex associated with the NMDA-type glutamate receptor. We generated mutant mice lacking synGAP to study its physiological role. Homozygous mutant mice die in the first few days after birth; however, neurons from mutant embryos can be maintained in culture. Here, we report that spine and synapse formation are accelerated in cultured mutant neurons, and the spines of mature mutant neurons are significantly larger than those of wild type. Clusters of PSD-95 and subunits of AMPA-type and NMDA-type glutamate receptors accumulate in spines of mutant neurons by day 10 in vitro, whereas in wild-type neurons they are still mostly located in dendritic shafts. The frequency and amplitude of miniature EPSCs are larger in mutant neurons at day 10 in vitro, confirming that they have more functional synapses. At day 21 in vitro, the spines of mutant neurons remain significantly larger than those of wild type. The mutant phenotype at day 10 in vitro can be rescued by introduction of recombinant wild-type synGAP on day 9. In contrast, introduction of mutant synGAP with a mutated GAP domain or lacking the terminal domain that binds to PSD-95 does not rescue the mutant phenotype, indicating that both domains play a role in control of spine formation. Thus, the GAP activity of synGAP and its association with PSD-95 are important for normal regulation of spine and synapse formation in hippocampal neurons.", "doi": "10.1523/JNEUROSCI.3213-04.2004", "pmcid": "PMC6729942", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2004-10-06", "series_number": "40", "volume": "24", "issue": "40", "pages": "8862-8872" }, { "id": "authors:kdxdc-19b34", "collection": "authors", "collection_id": "kdxdc-19b34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:OHJjbc04", "type": "article", "title": "Regulation of the Neuron-specific Ras GTPase-activating Protein, synGAP, by Ca2+/Calmodulin-dependent Protein Kinase II", "author": [ { "family_name": "Oh", "given_name": "Jeong S.", "clpid": "Oh-Jeong-S" }, { "family_name": "Manzerra", "given_name": "Pasquale", "clpid": "Manzerra-P" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "synGAP is a neuron-specific Ras GTPase-activating protein found in high concentration in the postsynaptic density fraction from mammalian forebrain. Proteins in the postsynaptic density, including synGAP, are part of a signaling complex attached to the cytoplasmic tail of the N-methyl-D-aspartate-type glutamate receptor. synGAP can be phosphorylated by a second prominent component of the complex, Ca2+/calmodulin-dependent protein kinase II. Here we show that phosphorylation of synGAP by Ca2+/calmodulin-dependent protein kinase II increases its Ras GTPase-activating activity by 70-95%. We identify four major sites of phosphorylation, serines 1123, 1058, 750/751/756, and 764/765. These sites together with other minor phosphorylation sites in the carboxyl tail of synGAP control stimulation of GTPase-activating activity. When three of these sites and four other serines in the carboxyl tail are mutated, stimulation of GAP activity after phosphorylation is reduced to 21 \u00b1 5% compared with 70-95% for the wild type protein. We used phosphosite-specific antibodies to show that, as predicted, phosphorylation of serines 765 and 1123 is increased in cultured cortical neurons after exposure of the neurons to the agonist N-methyl-D-aspartate.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2004-04-23", "series_number": "17", "volume": "279", "issue": "17", "pages": "17980-17988" }, { "id": "authors:5ahvx-a6c66", "collection": "authors", "collection_id": "5ahvx-a6c66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111101-093208830", "type": "article", "title": "Mammalian Septins Nomenclature", "author": [ { "family_name": "Macara", "given_name": "Ian G.", "clpid": "Macara-I-G" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "There are 10 known mammalian septin genes, some of which produce multiple splice variants. The\ncurrent nomenclature for the genes and gene products is very confusing, with several different names\nhaving been given to the same gene product and distinct names given to splice variants of the same\ngene. Moreover, some names are based on those of yeast or Drosophila septins that are not the closest\nhomologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature\nsystem, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes\nwill be named SEPT1\u2013SEPT10 and Sept1\u2013Sept10, respectively. Splice variants will be designated by an\nunderscore followed by a lowercase \"v\" and a number, e.g., SEPT4_v1.", "doi": "10.1091/mbc.E02-07-0438", "pmcid": "PMC138619", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "2002-12", "series_number": "12", "volume": "13", "issue": "12", "pages": "4111-4113" }, { "id": "authors:nsy0a-2f570", "collection": "authors", "collection_id": "nsy0a-2f570", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENpnas01", "type": "article", "title": "Telling Tails", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Manzerra", "given_name": "Pat", "clpid": "Manzerra-P" } ], "abstract": "The N-methyl-D-aspartate (NMDA)-type glutamate receptor is one of three major classes of receptors for glutamate, the principle excitatory neurotransmitter in the central nervous system. It plays a key role in learning and in the formation of memories by acting as a \"coincidence detector\" that initiates changes in synaptic strength that lead to the formation of new neural networks (1). It is also an important mediator of several forms of pathological neuronal toxicity. The NMDA receptor responds at a synapse only when the presynaptic terminal releases glutamate at the same time that the postsynaptic neuron is strongly depolarized by the sum of activating influences impinging on it. In effect, it initiates the strengthening of all synapses that depolarize the same postsynaptic neuron at the same time and thus triggers formation of a new, more stable circuit. When the NMDA-receptor channel opens, it allows passage of calcium ions, as well as sodium and potassium, into the cell. The calcium ions trigger a cascade of biochemical signaling reactions catalyzed by enzymes located just underneath the postsynaptic membrane. These reactions modify other membrane channels in the synapse, ultimately leading to a change in the strength of the electrical signal produced when the synapse is activated again.", "doi": "10.1073/pnas.231486398", "pmcid": "PMC60046", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2001-10-23", "series_number": "22", "volume": "98", "issue": "22", "pages": "12323-12324" }, { "id": "authors:srvd9-9df90", "collection": "authors", "collection_id": "srvd9-9df90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141112-134213566", "type": "article", "title": "Synapses [Book Review]", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "This comprehensive overview of the current state of knowledge of the organization and function of synapses will interest both seasoned neurobiologists and newcomers to the field.", "doi": "10.1126/science.1062511", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2001-09-21", "series_number": "5538", "volume": "293", "issue": "5538", "pages": "2210-2211" }, { "id": "authors:ysrzc-hpc56", "collection": "authors", "collection_id": "ysrzc-hpc56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150610-070859430", "type": "article", "title": "Response to \"Problems with LAP nomenclature\"", "author": [ { "family_name": "Bilder", "given_name": "David", "clpid": "Bilder-D" }, { "family_name": "Birnbaum", "given_name": "Daniel", "clpid": "Birnbaum-D" }, { "family_name": "Borg", "given_name": "Jean-Paul", "clpid": "Borg-J-P" }, { "family_name": "Huibregtse", "given_name": "Jon", "clpid": "Huibregse-J" }, { "family_name": "Kennedy", "given_name": "Mary", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Labouesse", "given_name": "Michel", "clpid": "Labouesse-M" }, { "family_name": "Mechler", "given_name": "Bernard", "clpid": "Mechler-B" }, { "family_name": "Perrimon", "given_name": "Norbert", "clpid": "Perrimon-N" } ], "abstract": "In calling attention to the several biomolecular entities whose names have been abbreviated `LAP', Wilson et al. raise an important issue. Acronyms and similar abbreviations are beneficial for a term that is used repeatedly in a publication; however, the existence of multiple entities that use the same abbreviation can cause confusion. It is for this reason that the universal standard of journals calls for explicit definition of an abbreviation at its first usage in a paper. This technique serves to dispel ambiguity that might arise.", "doi": "10.1038/35070149", "issn": "1465-7392", "publisher": "Nature Publishing Group", "publication": "Nature Cell Biology", "publication_date": "2001-04", "series_number": "4", "volume": "3", "issue": "4", "pages": "E90" }, { "id": "authors:3f93s-98746", "collection": "authors", "collection_id": "3f93s-98746", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154211643", "type": "article", "title": "Presence of both constitutive and inducible forms of heat shock protein 70 in the cerebral cortex and hippocampal synapses.", "author": [ { "family_name": "Moon", "given_name": "Il Soo", "clpid": "Moon-Il-Soo" }, { "family_name": "Park", "given_name": "In Sick", "clpid": "Park-In-Sick" }, { "family_name": "Schenker", "given_name": "Leslie T.", "clpid": "Schenker-L-T" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Moon", "given_name": "Jung-Il", "clpid": "Moon-Jung-Il" }, { "family_name": "Jin", "given_name": "Ingnyol", "clpid": "Jin-Ingnyol" } ], "abstract": "Heat shock proteins serve as molecular chaperones in a protein \"holding and folding\" system. Protein sequencing, extraction and immunoblot analyses indicate that Hsc70, a constitutive form, is a major component of the rat postsynaptic density (PSD) fraction, while Hsp70, an inducible form, is present at the basal level. Immunohistochemical studies show that expression of Hsc70 is high, but that of Hsp70 is low, in the cerebral cortex and hippocampal formation. In dissociated hippocampal neurons, both Hsp70 and Hsc70 immunoreactivities are distributed throughout the soma and dendrites. In dendrites, there are many stained puncta which are mostly co-localized with PSD-95, a postsynaptic marker. Interestingly, variation in staining intensity of the puncta is significantly larger for Hsp70 than for Hsc70 in 2-week-old cultures, but becomes less significant in 5(1/2)-week-old cultures. At the electron microscopic level, both Hsp70 and Hsc70 are mainly associated with asymmetrical PSDs. However, Hsc70 is also associated with amorphous subsynaptic structures and spine apparatus-like cisternae. Our data indicate that both Hsp70 and Hsc70 are present in PSDs but are differentially distributed at subsynaptic sites, and provide a potential candidate system for a \"synaptic tag\".", "doi": "10.1093/cercor/11.3.238", "issn": "1047-3211", "publisher": "Oxford University Press", "publication": "Cerebral Cortex", "publication_date": "2001-03", "series_number": "3", "volume": "11", "issue": "3", "pages": "238-248" }, { "id": "authors:tgc1g-zf909", "collection": "authors", "collection_id": "tgc1g-zf909", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-150007753", "type": "article", "title": "Densin-180 forms a ternary complex with the \u03b1-subunit of Ca^(2+)/calmodulin-dependent protein kinase II and \u03b1-actinin", "author": [ { "family_name": "Walikonis", "given_name": "Randall S.", "clpid": "Walikonis-R-S" }, { "family_name": "Oguni", "given_name": "Asako", "clpid": "Oguni-Asako" }, { "family_name": "Khorosheva", "given_name": "Eugenia M.", "orcid": "0000-0003-3620-4884", "clpid": "Khorosheva-E-M" }, { "family_name": "Jeng", "given_name": "Chung-Jiuan", "orcid": "0000-0001-6271-5704", "clpid": "Jeng-Chung-Jiuan" }, { "family_name": "Asuncion", "given_name": "Franklin J.", "clpid": "Asuncion-F-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Densin-180 is a transmembrane protein that is tightly associated with the postsynaptic density in CNS neurons and is postulated to function as a synaptic adhesion molecule. Here we report the identification of the \u03b1-subunit of Ca^(2+)/calmodulin-dependent protein kinase II (CaMKII) and \u03b1-actinin-4 as potential binding partners for the densin-180 intracellular segment. We demonstrate by yeast two-hybrid and biochemical assays that the intracellular portion of densin-180, the \u03b1-subunit of CaMKII (CaMKII\u03b1), and \u03b1-actinin interact with each other at distinct binding sites and can form a ternary complex stabilized by multiple interactions. Densin-180 binds specifically to the association domain of CaMKII\u03b1 and does not bind with high affinity to holoenzymes of CaMKII that contain \u03b2-subunit. The PDZ (PSD-95, DIg, Z0-1) domain of densin contributes to its binding to \u03b1-actinin. A distinct domain of \u03b1-actinin interacts with the kinase domains of both \u03b1- and \u03b2-subunits of CaMKII. Autophosphorylation of CaMKII increases its affinity for densin-180 from an EC_(50) of >1 \u00b5m to an EC_(50) of <75-150 nM. In contrast, phosphorylation of densin-180 by CaMKII at serine-1397 only slightly decreases its affinity for CaMKII. The specific interaction of densin-180 with holoenzymes of CaMKII containing only \u03b1-subunit and the increased affinity of CaMKII for densin-180 after autophosphorylation suggest that densin-180 may be involved in localization of activated CaMKII synthesized in dendrites.", "doi": "10.1523/JNEUROSCI.21-02-00423.2001", "pmcid": "PMC6763799", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2001-01-15", "series_number": "2", "volume": "21", "issue": "2", "pages": "423-433" }, { "id": "authors:cvy49-vvy89", "collection": "authors", "collection_id": "cvy49-vvy89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-150158220", "type": "article", "title": "Signal-processing machines at the postsynaptic density", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Dendrites of individual neurons in the vertebrate central nervous system are contacted by thousands of synaptic terminals relaying information about the environment. The postsynaptic membrane at each synaptic terminal is the first place where information is processed as it converges on the dendrite. At the postsynaptic membrane of excitatory synapses, neurotransmitter receptors are attached to large protein \"signaling machines\" that delicately regulate the strength of synaptic transmission. These machines are visible in the electron microscope and are called the postsynaptic density. By changing synaptic strength in response to neural activity, the postsynaptic density contributes to information processing and the formation of memories.", "doi": "10.1126/science.290.5492.750", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "2000-10-27", "series_number": "5492", "volume": "290", "issue": "5492", "pages": "750-754" }, { "id": "authors:yjynq-mhn71", "collection": "authors", "collection_id": "yjynq-mhn71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENpnas00", "type": "article", "title": "Sticking together", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Rapid signals at the neuromuscular junction and at synapses between neurons are carried by small molecules, called neurotransmitters, that are released from the presynaptic terminal and bind to ligand-gated ion channels in the postsynaptic membrane. When transmitter binds, a small pore opens through which ions flow, resulting in a transient depolarization or hyperpolarization of the membrane and translating the chemical signal into an electrical one. The transmitters at the neuromuscular junction, and at excitatory synapses in the central nervous system, are acetylcholine and glutamate, respectively. Inhibitory signals are carried by two major transmitters: glycine, predominantly in the spinal cord, and gamma -aminobutyric acid, or GABA, predominantly in the brain.\n\nReceptors for these transmitters are important targets for drugs used to treat mental disorders, or to modulate sleep and mood. In particular, benzodiazepine-related drugs, such as Valium, Halcion, and Xanax, which are widely used for the treatment of anxiety and insomnia, appear to act by binding directly to a specific site on the GABA type A (GABAA) receptor, the principal GABA-gated ion channel (1, 2). Molecular biologists have spent much productive effort over the last decade working out the molecular structures of receptors for each of the major transmitters, while biophysicists have unraveled the detailed kinetics of transmitter binding and gating (1, 3, 4). The pharmaceutical industry concentrates enormous resources on determining the specificity and physiological consequences of binding of pharmacological agents to these receptors.", "doi": "10.1073/pnas.97.21.11135", "pmcid": "PMC34046", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2000-10-10", "series_number": "21", "volume": "97", "issue": "21", "pages": "11135-11136" }, { "id": "authors:f3j41-pyw66", "collection": "authors", "collection_id": "f3j41-pyw66", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154213661", "type": "article", "title": "Collective nomenclature for LAP proteins", "author": [ { "family_name": "Bilder", "given_name": "David", "clpid": "Bilder-D" }, { "family_name": "Birnbaum", "given_name": "Daniel", "clpid": "Birnbaum-D" }, { "family_name": "Borg", "given_name": "Jean-Paul", "clpid": "Borg-J-P" }, { "family_name": "Bryant", "given_name": "Pete", "clpid": "Bryant-P" }, { "family_name": "Huigbretse", "given_name": "Jon", "clpid": "Huigbretse-J" }, { "family_name": "Jansen", "given_name": "Erik", "clpid": "Jansen-E" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Labouesse", "given_name": "Michel", "clpid": "Labouesse-M" }, { "family_name": "Legouis", "given_name": "Renaud", "clpid": "Legouis-R" }, { "family_name": "Mechler", "given_name": "Bernard", "clpid": "Mechler-B" }, { "family_name": "Perrimon", "given_name": "Norbert", "clpid": "Perrimon-N" }, { "family_name": "Petit", "given_name": "Marleen", "clpid": "Petit-M" }, { "family_name": "Sinha", "given_name": "Pradip", "clpid": "Sinha-P" } ], "abstract": "In 1996 Mary Kennedy and colleagues isolated the protein Densin-180 from the rbat postsynaptic density. This protein had a unique structure, in that it contained a set of leucine-rich repeats (LRRs) as well as a PSD-95/Dlg/ZO-1 (PDZ) domain; these domains are thought to mediate protein\u2013protein interactions. Recently, further proteins containing both types of domain have been isolated from fly, worm, mouse and human. It seems an opportune time to select a collective name for this family of proteins.", "doi": "10.1038/35017119", "issn": "1465-7392", "publisher": "Nature Publishing Group", "publication": "Nature Cell Biology", "publication_date": "2000-07", "series_number": "7", "volume": "2", "issue": "7", "pages": "E114" }, { "id": "authors:73za0-16n13", "collection": "authors", "collection_id": "73za0-16n13", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154214639", "type": "article", "title": "C-Terminal truncation of NR2A subunits impairs synaptic but not extrasynaptic localization of NMDA receptors", "author": [ { "family_name": "Steigerwald", "given_name": "Frank", "clpid": "Steigerwald-F" }, { "family_name": "Schulz", "given_name": "Torsten W.", "clpid": "Schulz-T-W" }, { "family_name": "Schenker", "given_name": "Leslie T.", "clpid": "Schenker-L-T" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Seeburg", "given_name": "Peter H.", "clpid": "Seeburg-P-H" }, { "family_name": "K\u00f6hr", "given_name": "Georg", "clpid": "K\u00f6hr-G" } ], "abstract": "NMDA receptors interact via the extended intracellular C-terminal domain of the NR2 subunits with constituents of the postsynaptic density for purposes of retention, clustering, and functional regulation at central excitatory synapses. To examine the role of the C-terminal domain of NR2A in the synaptic localization and function of NR2A-containing NMDA receptors in hippocampal Schaffer collateral\u2013CA1 pyramidal cell synapses, we analyzed mice which express NR2A only in its C-terminally truncated form. In CA1 cell somata, the levels, activation, and deactivation kinetics of extrasynaptic NMDA receptor channels were comparable in wild-type and mutant NR2A^(\u0394C/\u0394C) mice. At CA1 cell synapses, however, the truncated receptors were less concentrated than their full-length counterparts, as indicated by immunodetection in cultured neurons, synaptosomes, and postsynaptic densities. In the mutant, the NMDA component of evoked EPSCs was reduced in a developmentally progressing manner and was even more reduced in miniature EPSCs (mEPSCs) elicited by spontaneous glutamate release. Moreover, pharmacologically isolated NMDA currents evoked by synaptic stimulation had longer latencies and displayed slower rise and decay times, even in the presence of an NR2B-specific antagonist. These data strongly suggest that the C-terminal domain of NR2A subunits is important for the precise synaptic arrangement of NMDA receptors.", "doi": "10.1523/JNEUROSCI.20-12-04573.2000", "pmcid": "PMC6772457", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2000-06-15", "series_number": "12", "volume": "20", "issue": "12", "pages": "4573-4581" }, { "id": "authors:jc9st-cs145", "collection": "authors", "collection_id": "jc9st-cs145", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-150408608", "type": "article", "title": "Identification of proteins in the postsynaptic density fraction by mass spectrometry", "author": [ { "family_name": "Walikonis", "given_name": "Randall S.", "clpid": "Walikonis-R-S" }, { "family_name": "Jensen", "given_name": "Ole N.", "clpid": "Jensen-O-N" }, { "family_name": "Mann", "given_name": "Matthias", "clpid": "Mann-M" }, { "family_name": "Provance", "given_name": "D. William, Jr.", "clpid": "Provance-D-W-Jr" }, { "family_name": "Mercer", "given_name": "John A.", "clpid": "Mercer-J-A" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Our understanding of the organization of postsynaptic signaling systems at excitatory synapses has been aided by the identification of proteins in the postsynaptic density (PSD) fraction, a subcellular fraction enriched in structures with the morphology of PSDs. In this study, we have completed the identification of most major proteins in the PSD fraction with the use of an analytical method based on mass spectrometry coupled with searching of the protein sequence databases. At least one protein in each of 26 prominent protein bands from the PSD fraction has now been identified. We found 7 proteins not previously known to be constituents of the PSD fraction and 24 that had previously been associated with the PSD by other methods. The newly identified proteins include the heavy chain of myosin-Va (dilute myosin), a motor protein thought to be involved in vesicle trafficking, and the mammalian homolog of the yeast septin protein cdc10, which is important for bud formation in yeast. Both myosin-Va and cdc10 are threefold to fivefold enriched in the PSD fraction over brain homogenates. Immunocytochemical localization of myosin-Va in cultured hippocampal neurons shows that it partially colocalizes with PSD-95 at synapses and is also diffusely localized in cell bodies, dendrites, and axons. Cdc10 has a punctate distribution in cell bodies and dendrites, with some of the puncta colocalizing with PSD-95. The results support a role for myosin-Va in transport of materials into spines and for septins in the formation or maintenance of spines.", "doi": "10.1523/JNEUROSCI.20-11-04069.2000", "pmcid": "PMC6772646", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "2000-06-01", "series_number": "11", "volume": "20", "issue": "11", "pages": "4069-4080" }, { "id": "authors:tyekn-j4994", "collection": "authors", "collection_id": "tyekn-j4994", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154215710", "type": "article", "title": "Tetanic Stimulation Leads to Increased Accumulation of Ca^(2+)/Calmodulin-Dependent Protein Kinase II via Dendritic Protein Synthesis in Hippocampal Neurons", "author": [ { "family_name": "Ouyang", "given_name": "Yannan", "clpid": "Ouyang-Yannan" }, { "family_name": "Rosenstein", "given_name": "Alan", "clpid": "Rosenstein-A" }, { "family_name": "Kreiman", "given_name": "Gabriel", "clpid": "Kreiman-G" }, { "family_name": "Schuman", "given_name": "Erin M.", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "mRNA for the \u0251-subunit of CaMKII is abundant in dendrites of neurons in the forebrain (Steward, 1997). Here we show that tetanic stimulation of the Schaffer collateral pathway causes an increase in the concentration of \u0251-CaMKII in the dendrites of postsynaptic neurons. The increase is blocked by anisomycin and is detected by both quantitative immunoblot and semiquantitative immunocytochemistry. The increase in dendritic \u0251-CaMKII can be measured 100-200 \u00b5m away from the neuronal cell bodies as early as 5 min after a tetanus. Transport mechanisms for macromolecules from neuronal cell bodies are not fast enough to account for this rapid increase in distal portions of the dendrites. Therefore, we conclude that dendritic protein synthesis must produce a portion of the newly accumulated CaMKII. The increase in concentration of dendritic CaMKII after tetanus, together with the previously demonstrated increase in autophosphorylated CaMKII (Ouyang et al., 1997), will produce a prolonged increase in steady-state kinase activity in the dendrites, potentially influencing mechanisms of synaptic plasticity that are controlled through phosphorylation by CaMKII.", "doi": "10.1523/JNEUROSCI.19-18-07823.1999", "pmcid": "PMC6782482", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1999-09-15", "series_number": "18", "volume": "19", "issue": "18", "pages": "7823-7833" }, { "id": "authors:f90jc-h2k30", "collection": "authors", "collection_id": "f90jc-h2k30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154216590", "type": "article", "title": "On beyond LTP", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1101/lm.6.5.417", "issn": "1072-0502", "publisher": "Cold Spring Harbor Laboratory Press", "publication": "Learning and Memory", "publication_date": "1999-09", "series_number": "5", "volume": "6", "issue": "5", "pages": "417-421" }, { "id": "authors:7vbnb-bd146", "collection": "authors", "collection_id": "7vbnb-bd146", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154217503", "type": "article", "title": "Citron binds to PSD-95 at glutamatergic synapses on inhibitory neurons in the hippocampus", "author": [ { "family_name": "Zhang", "given_name": "Wandong", "clpid": "Zhang-Wandong" }, { "family_name": "Vazquez", "given_name": "Luis", "clpid": "Vazquez-L" }, { "family_name": "Apperson", "given_name": "Michelle", "clpid": "Apperson-M-L" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Synaptic NMDA-type glutamate receptors are anchored to the second of three PDZ (PSD-95/Discs large/ZO-1) domains in the postsynaptic density (PSD) protein PSD-95. Here, we report that citron, a protein target for the activated form of the small GTP-binding protein Rho, preferentially binds the third PDZ domain of PSD-95. In GABAergic neurons from the hippocampus, citron forms a complex with PSD-95 and is concentrated at the postsynaptic side of glutamatergic synapses. Citron is expressed only at low levels in glutamatergic neurons in the hippocampus and is not detectable at synapses onto these neurons. In contrast to citron, p135 SynGAP, an abundant synaptic Ras GTPase-activating protein that can bind to all three PDZ domains of PSD-95, and Ca2+/calmodulin-dependent protein kinase II (CaM kinase II) are concentrated postsynaptically at glutamatergic synapses on glutamatergic neurons. CaM kinase II is not expressed and p135 SynGAP is expressed in less than half of hippocampal GABAergic neurons. Segregation of citron into inhibitory neurons does not occur in other brain regions. For example, citron is expressed at high levels in most thalamic neurons, which are primarily glutamatergic and contain CaM kinase II. In several other brain regions, citron is present in a subset of neurons that can be either GABAergic or glutamatergic and can sometimes express CaM kinase II. Thus, in the hippocampus, signal transduction complexes associated with postsynaptic NMDA receptors are different in glutamatergic and GABAergic neurons and are specialized in a way that is specific to the hippocampus.", "doi": "10.1523/JNEUROSCI.19-01-00096.1999", "pmcid": "PMC6782379", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1999-01-01", "series_number": "1", "volume": "19", "issue": "1", "pages": "96-108" }, { "id": "authors:k97b1-6hj81", "collection": "authors", "collection_id": "k97b1-6hj81", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154218718", "type": "article", "title": "Hippocampal Synaptic Plasticity in Mice Overexpressing an Embryonic Subunit of the NMDA Receptor", "author": [ { "family_name": "Okabe", "given_name": "Shigeo", "clpid": "Okabe-Shigeo" }, { "family_name": "Collin", "given_name": "Carlos", "clpid": "Collin-C" }, { "family_name": "Auerbach", "given_name": "Jonathan M.", "clpid": "Auerbach-J-M" }, { "family_name": "Meiri", "given_name": "Noam", "clpid": "Meiri-N" }, { "family_name": "Bengzon", "given_name": "Johan", "clpid": "Bengzon-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Segal", "given_name": "Menahem", "orcid": "0000-0002-1828-7682", "clpid": "Segal-M" }, { "family_name": "McKay", "given_name": "Ronald D. G.", "clpid": "McKay-R-D-G" } ], "abstract": "The effects of changing NMDA receptor subunit composition on synaptic plasticity in the hippocampus were analyzed by creating transgenic mice overexpressing NR2D, a predominantly embryonic NMDA receptor subunit. NMDA-evoked currents in the transgenic mice had smaller amplitudes and slower kinetics. The transgenics also displayed age-dependent deficits in synaptic plasticity in area CA1 of the hippocampus. Long-term depression was selectively impaired in juvenile mice when NR2D overexpression was moderate. In mature mice, overexpression of NR2D was associated with a reduction of both NR2B and Ca^(2+)-independent activity of Ca^(2+)- and calmodulin-dependent protein kinase II. These biochemical changes were correlated with a marked impairment of NMDA-dependent long-term potentiation, but spatial behavior was normal in these mice. These results show that the developmental regulation of NMDA receptor subunit composition alters the frequency at which modification of synaptic responses occur after afferent stimulation.", "doi": "10.1523/jneurosci.18-11-04177.1998", "pmcid": "PMC6792823", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1998-06-01", "series_number": "11", "volume": "18", "issue": "11", "pages": "4177-4188" }, { "id": "authors:amxqd-89339", "collection": "authors", "collection_id": "amxqd-89339", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-150822198", "type": "article", "title": "Signal transduction molecules at the glutamatergic postsynaptic membrane", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "We have applied techniques from modern molecular biology and biochemistry to unravel the complex molecular structure of the postsynaptic membrane at glutamatergic synapses in the central nervous system. We have characterized a set of new proteins that are constituents of the postsynaptic density, including PSD-95, densin-180, citron (a rho/rac effector protein), and synaptic gp130 Ras GAP (a new Ras GTPase-activating protein). The structure of PSD-95 revealed a new protein motif, the PDZ domain, that plays an important role in the assembly of signal transduction complexes at intercellular junctions. More recently, we have used new imaging tools to observe the dynamics of autophosphorylation of CaM kinase II in intact hippocampal tissue. We have been able to detect changes in the amount of autophosphorylated CaM kinase II in dendrites, individual synapses, and somas of hippocampal neurons following induction of long-term potentiation by tetanic stimulation. In addition, we have observed a specific increase in the concentration of CaM kinase II in dendrites of neurons receiving tetanic stimulation. This increase appears to be the result of dendritic synthesis of new protein. Over the next several years we will apply similar methods to study regulatory changes that occur at the molecular level in glutamatergic synapses in the CNS as the brain processes and stores new information.", "doi": "10.1016/S0165-0173(97)00043-X", "issn": "0165-0173", "publisher": "Elsevier", "publication": "Brain Research Reviews", "publication_date": "1998-05", "series_number": "2-3", "volume": "26", "issue": "2-3", "pages": "243-257" }, { "id": "authors:5s5df-rqc22", "collection": "authors", "collection_id": "5s5df-rqc22", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-150615407", "type": "article", "title": "A Synaptic Ras-GTPase Activating Protein (p135 SynGAP) Inhibited by CaM Kinase II", "author": [ { "family_name": "Chen", "given_name": "Hong Jung", "clpid": "Chen-Hong Jung" }, { "family_name": "Rojas-Soto", "given_name": "Michelle", "clpid": "Rojas-Soto-M" }, { "family_name": "Oguni", "given_name": "Asako", "clpid": "Oguni-Asako" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Ca^(2+) influx through N-methyl-D-aspartate\u2013 (NMDA\u2013) type glutamate receptors plays a critical role in synaptic plasticity in the brain. One of the proteins activated by the increase in Ca^(2+) is CaM kinase II (CaMKII). Here, we report a novel synaptic Ras-GTPase activating protein (p135 SynGAP) that is a major component of the postsynaptic density, a complex of proteins associated with synaptic NMDA receptors. p135 SynGAP is almost exclusively localized at synapses in hippocampal neurons where it binds to and closely colocalizes with the scaffold protein PSD-95 and colocalizes with NMDA receptors. The Ras-GTPase activating activity of p135 SynGAP is inhibited by phosphorylation by CaMKII located in the PSD protein complex. Inhibition of p135 SynGAP by CaMKII will stop inactivation of GTP-bound Ras and thus could result in activation of the mitogen-activated protein (MAP) kinase pathway in hippocampal neurons upon activation of NMDA receptors.", "doi": "10.1016/S0896-6273(00)80471-7", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "1998-05", "series_number": "5", "volume": "20", "issue": "5", "pages": "895-904" }, { "id": "authors:c17xs-pkz52", "collection": "authors", "collection_id": "c17xs-pkz52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154219671", "type": "article", "title": "Characterization of calcium/calmodulin-dependent protein kinase II activity in the nervous system of the lobster, Panulirus interruptus.", "author": [ { "family_name": "Withers", "given_name": "Michelle D.", "clpid": "Withers-M-D" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Marder", "given_name": "Eve", "clpid": "Marder-E" }, { "family_name": "Griffith", "given_name": "Leslie C.", "clpid": "Griffith-L-C" } ], "abstract": "Nervous system tissue from Panulirus interruptus has an enzyme activity that behaves like calcium/calmodulin-dependent protein kinase II (CaM KII) This activity phosphorylates known targets of CaM KII, such as synapsin I and autocamtide 3. It is inhibited by a CaM KII-specific autoinhibitory domain peptide. In addition, this lobster brain activity displays calcium-independent activity after autophosphorylation, another characteristic of CaM KII. A cDNA from the lobster nervous system was amplified using polymerase chain reaction. The fragment was cloned and found to be structurally similar to CaM KII. Serum from rabbits immunized with a fusion protein containing part of this sequence immunoprecipitated a CaM KII enzyme activity and a family of phosphoproteins of the appropriate size for CaM KII subunits. Lobster CaM KII activity is found in the brain and stomatogastric nervous system including the commissural ganglia, commissures, stomatogastric ganglion and stomatogastric nerve. Immunoblot analysis of these same regions also identifies bands at an apparent molecular weight characteristic of CaM KII.", "doi": "10.1007/BF02577693", "issn": "1354-2516", "publisher": "Springer Verlag", "publication": "Invertebrate Neuroscience", "publication_date": "1998-03", "series_number": "4", "volume": "3", "issue": "4", "pages": "335-345" }, { "id": "authors:t0swn-1fp68", "collection": "authors", "collection_id": "t0swn-1fp68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154221603", "type": "article", "title": "Visualization of the distribution of autophosphorylated calcium/calmodulin-dependent protein kinase II after tetanic stimulation in the CA1 area of the hippocampus", "author": [ { "family_name": "Ouyang", "given_name": "Yannan", "clpid": "Ouyang-Yannan" }, { "family_name": "Kantor", "given_name": "David", "clpid": "Kantor-D" }, { "family_name": "Harris", "given_name": "Kristen M.", "clpid": "Harris-K-M" }, { "family_name": "Schuman", "given_name": "Erin M.", "orcid": "0000-0002-7053-1005", "clpid": "Schuman-E-M" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Autophosphorylation of calcium/calmodulin-dependent protein kinase II (CaMKII) at threonine-286 produces Ca2+-independent kinase activity and has been proposed to be involved in induction of long-term potentiation by tetanic stimulation in the hippocampus. We have used an immunocytochemical method to visualize and quantify the pattern of autophosphorylation of CaMKII in hippocampal slices after tetanization of the Schaffer collateral pathway. Thirty minutes after tetanic stimulation, autophosphorylated CaM kinase II (P-CaMKII) is significantly increased in area CA1 both in apical dendrites and in pyramidal cell somas. In apical dendrites, this increase is accompanied by an equally significant increase in staining for nonphosphorylated CaM kinase II. Thus, the increase in P-CaMKII appears to be secondary to an increase in the total amount of CaMKII. In neuronal somas, however, the increase in P-CaMKII is not accompanied by an increase in the total amount of CaMKII. We suggest that tetanic stimulation of the Schaffer collateral pathway may induce new synthesis of CaMKII molecules in the apical dendrites, which contain mRNA encoding its alpha-subunit. In neuronal somas, however, tetanic stimulation appears to result in long-lasting increases in P-CaMKII independent of an increase in the total amount of CaMKII. Our findings are consistent with a role for autophosphorylation of CaMKII in the induction and/or maintenance of long-term potentiation, but they indicate that the effects of tetanus on the kinase and its activity are not confined to synapses and may involve induction of new synthesis of kinase in dendrites as well as increases in the level of autophosphorylated kinase.", "doi": "10.1523/JNEUROSCI.17-14-05416.1997", "pmcid": "PMC6793833", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1997-07-15", "series_number": "14", "volume": "17", "issue": "14", "pages": "5416-5427" }, { "id": "authors:bm461-z3513", "collection": "authors", "collection_id": "bm461-z3513", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-151012568", "type": "article", "title": "The postsynaptic density at glutamatergic synapses", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The postsynaptic density (PSD) is a tiny, amorphous structure located beneath the postsynaptic membrane of synapses in the CNS. Until recently, the molecular composition and function of the PSD were mostly matters of speculation. With the advent of powerful new microchemical tools and molecular-genetic methods, three new classes of proteins have been identified in the PSD at glutamatergic synapses: the PSD-95 family, the NR2B subunit of the NMDA-type glutamate receptor, and densin-180. The PSD-95 family is involved in clustering of NMDA receptors. NR2B is phosphorylated by Ca^(2+)-calmodulin-dependent protein kinase type II, a prominent constituent of the PSD. Densin-180 might represent a new class of synaptic adhesion molecule. Study of these molecules is beginning to reveal the functional significance of the PSD.", "doi": "10.1016/S0166-2236(96)01033-8", "issn": "0166-2236", "publisher": "Elsevier", "publication": "Trends in Neurosciences", "publication_date": "1997-06", "series_number": "6", "volume": "20", "issue": "6", "pages": "264-268" }, { "id": "authors:tsq7e-rhy41", "collection": "authors", "collection_id": "tsq7e-rhy41", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154222584", "type": "article", "title": "Interaction of ion channels and receptors with PDZ domain proteins", "author": [ { "family_name": "Kornau", "given_name": "Hans-Christian", "clpid": "Kornau-H-C" }, { "family_name": "Seeburg", "given_name": "Peter H.", "clpid": "Seeburg-P-H" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The complex anatomy of neurons demands a high degree of functional organization. Therefore, membrane receptors and ion channels are often localized to selected subcellular sites and coupled to specific signal transduction machineries. PDZ domains have come into focus as protein interaction modules that mediate the binding of a class of submembraneous proteins to membrane receptors and ion channels and thus subserve these organizational aspects. The structures of two PDZ domains have been resolved, which has led to a structural understanding of the specificity of interactions of various PDZ domains with their respective partners. The functional implications of PDZ domain interactions are now being addressed in vitro and in vivo.", "doi": "10.1016/S0959-4388(97)80064-5", "issn": "0959-4388", "publisher": "Elsevier", "publication": "Current Opinion in Neurobiology", "publication_date": "1997-06", "series_number": "3", "volume": "7", "issue": "3", "pages": "368-373" }, { "id": "authors:1nycz-fz880", "collection": "authors", "collection_id": "1nycz-fz880", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:OMKjbc96", "type": "article", "title": "Identification of a Phosphorylation Site for Calcium/Calmodulindependent Protein Kinase II in the NR2B Subunit of the N-Methyl-D-aspartate Receptor", "author": [ { "family_name": "Omkumar", "given_name": "Ramakrishnapillai V.", "clpid": "Omkumar-R-V" }, { "family_name": "Kiely", "given_name": "Melinda J.", "clpid": "Kiely-M-J" }, { "family_name": "Rosenstein", "given_name": "Alan J.", "clpid": "Rosenstein-A-J" }, { "family_name": "Min", "given_name": "Kyung-Tai", "clpid": "Min-Kyung-Tai" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The N-methyl-D-aspartate (NMDA) subtype of excitatory glutamate receptors plays critical roles in embryonic and adult synaptic plasticity in the central nervous system. The receptor is a heteromultimer of core subunits, NR1, and one or more regulatory subunits, NR2A-D. Protein phosphorylation can regulate NMDA receptor function (Lieberman, D. N., and Mody, I. (1994) Nature 369, 235-239; Wang, Y. T., and Salter, M. W. (1994) Nature 369, 233-235; Wang, L.-Y., Orser, B. A., Brautigan, D. L., and MacDonald, J. F. (1994) Nature 369, 230-232). Here we identify a major phosphorylation site on subunit NR2B that is phosphorylated by Ca2+/calmodulin-dependent protein kinase II (CaM kinase II), an abundant protein kinase located at postsynaptic sites in glutamatergic synapses. For the initial identification of the site, we constructed a recombinant fusion protein containing 334 amino acids of the C terminus of the NR2B subunit and phosphorylated it with CaM kinase II in vitro. By peptide mapping, automated sequencing, and mass spectrometry, we identified the major site of phosphorylation on the fusion protein as Ser-383, corresponding to Ser-1303 of full-length NR2B. The Km for phosphorylation of this site in the fusion protein was ~50 nM, much lower than that of other known substrates for CaM kinase II, suggesting that the receptor is a high affinity substrate. We show that serine 1303 in the full-length NR2B and/or the cognate site in NR2A is a major site of phosphorylation of the receptor both in the postsynaptic density fraction and in living hippocampal neurons.", "doi": "10.1074/jbc.271.49.31670", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1996-12-06", "series_number": "49", "volume": "271", "issue": "49", "pages": "31670-31678" }, { "id": "authors:kprmq-rwt97", "collection": "authors", "collection_id": "kprmq-rwt97", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-151232192", "type": "article", "title": "Characterization of densin-180, a new brain-specific synaptic protein of the O-sialoglycoprotein family", "author": [ { "family_name": "Apperson", "given_name": "Michelle L.", "clpid": "Apperson-Michelle-L" }, { "family_name": "Moon", "given_name": "Ill Soo", "clpid": "Moon-Ill-Soo" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "We purified an abundant protein of apparent molecular mass 180 kDa from the postsynaptic density fraction of rat forebrain and obtained amino acid sequences of three tryptic peptides generated from the protein. The sequences were used to design a strategy for cloning the cDNA encoding the protein by polymerase chain reaction. The open reading frame of the cDNA encodes a novel protein of predicted molecular mass 167 kDa. We have named the protein densin-180. Antibodies raised against the predicted amino and carboxyl sequences of densin-180 recognize a 180 kDa band on immunoblots that is enriched in the postsynaptic density fraction. Immunocytochemical localization of densin-180 in dissociated hippocampal neuronal cultures shows that the protein is highly concentrated at synapses along dendrites. The message encoding densin-180 is brain specific and is more abundant in forebrain than in cerebellum. The sequence of densin-180 contains 17 leucine-rich repeats, a sialomucin domain, an apparent transmembrane domain, and a PDZ domain. This arrangement of domains is similar to that of several adhesion molecules, in particular GPIbalpha, which mediates binding of platelets to von Willebrand factor. We propose that densin-180 participates in specific adhesion between presynaptic and postsynaptic membranes at glutamatergic synapses.", "doi": "10.1523/JNEUROSCI.16-21-06839.1996", "pmcid": "PMC6579252", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1996-11-01", "series_number": "21", "volume": "16", "issue": "21", "pages": "6839-6852" }, { "id": "authors:j803z-ve361", "collection": "authors", "collection_id": "j803z-ve361", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154223612", "type": "article", "title": "Visualization of autophosphorylation of ^(Ca^(2+))/calmodulin ^(-dependent) protein kinase II in hippocampal slices", "author": [ { "family_name": "Kindler", "given_name": "Stefan", "clpid": "Kindler-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "We describe a method for visualizing the relative spatial distribution of autophosphorylated Ca2+/calmodulin-dependent protein kinase II (CaMKII) in neuronal subcompartments within hippocampal slices. The method employs a monoclonal antibody recognizing only autophosphorylated CaMKII, and an affinity-purified polyclonal rabbit antisera recognizing only nonphosphorylated CaMK II (Patton et al. (1993) Mol. Biol. Cell, 4: 159-172). 50 microns sections cut from fixed 500 microns hippocampal slices are double-labeled with these antibodies bound by secondary antibodies coupled to fluorescein and Cy3, respectively. The distribution of the two antigens in identical optical sections is recorded by dual channel confocal laser scanning microscopy (CLSM). The digital images are analyzed with the program MacPhase to determine the relative levels of staining with antibodies to phosphokinase and antibodies to nonphosphokinase in subcellular domains of neurons. Comparison of data from paired control and experimental slices reveals the spatial distributions of changes in levels of autophosphorylated CaMKII produced by pharmacological treatments. We are able to detect and spatially resolve differences in levels of autophosphorylation of CaMK II between slices subjected to Ca2+ depletion (low autophosphorylation) and slices treated with a phosphatase inhibitor (high autophosphorylation).", "doi": "10.1016/0165-0270(96)00074-X", "issn": "0165-0270", "publisher": "Elsevier", "publication": "Journal of Neuroscience Methods", "publication_date": "1996-09", "series_number": "1", "volume": "68", "issue": "1", "pages": "61-70" }, { "id": "authors:rrrq5-hnp80", "collection": "authors", "collection_id": "rrrq5-hnp80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154224566", "type": "article", "title": "PSD-95 Is Associated with the Postsynaptic Density and Not with the Presynaptic Membrane at Forebrain Synapses", "author": [ { "family_name": "Hunt", "given_name": "Carol A.", "clpid": "Hunt-Carol-A" }, { "family_name": "Schenker", "given_name": "Leslie J.", "clpid": "Schenker-Leslie-J" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "PSD-95, a prominent protein component of the postsynaptic density (PSD) fraction from rat forebrain, has been localized by light microscopy to dendrites of hippocampal neurons (Cho et al., 1992) and to the presynaptic plexus of cerebellar basket cells (Kistner et al., 1993). Here we extend these studies to show that an affinity-purified antibody to PSD-95 labels the dendrites of most neurons in the forebrain and of a subset of neurons in the cerebellum. To confirm that PSD-95 is associated with the PSD at forebrain synapses and to clarify whether it is also associated with the presynaptic membrane, we employed immunogold electron microscopy of forebrain synaptosomes. Gold-labeled antibodies to PSD-95 labeled postsynaptic densities in both intact and lysed forebrain synaptosomes but did not label presynaptic terminals or the presynaptic membrane. The asymmetric distribution of PSD-95 at synapses contrasts with that of its homologs, disks-large and ZO-1, which are arranged symmetrically at septate and tight junctions, respectively.", "doi": "10.1523/JNEUROSCI.16-04-01380.1996", "pmcid": "PMC6578559", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1996-02-15", "series_number": "4", "volume": "16", "issue": "4", "pages": "1380-1388" }, { "id": "authors:40x4j-80008", "collection": "authors", "collection_id": "40x4j-80008", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-151520271", "type": "article", "title": "Domain interaction between NMDA receptor subunits and the postsynaptic density protein PSD-95", "author": [ { "family_name": "Kornau", "given_name": "Hans-Christian", "clpid": "Kornau-H-C" }, { "family_name": "Schenker", "given_name": "Leslie T.", "clpid": "Schenker-L-T" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Seeburg", "given_name": "Peter H.", "clpid": "Seeburg-P-H" } ], "abstract": "The N-methyl-D-aspartate (NMDA) receptor subserves synaptic glutamate-induced transmission and plasticity in central neurons. The yeast two-hybrid system was used to show that the cytoplasmic tails of NMDA receptor subunits interact with a prominent postsynaptic density protein PSD-95. The second PDZ domain in PSD-95 binds to the seven-amino acid, COOH-terminal domain containing the terminal tSXV motif (where S is serine, X is any amino acid, and V is valine) common to NR2 subunits and certain NR1 splice forms. Transcripts encoding PSD-95 are expressed in a pattern similar to that of NMDA receptors, and the NR2B subunit co-localizes with PSD-95 in cultured rat hippocampal neurons. The interaction of these proteins may affect the plasticity of excitatory synapses.", "doi": "10.1126/science.7569905", "issn": "0036-8075", "publisher": "American Association for the Advancement of Science", "publication": "Science", "publication_date": "1995-09-22", "series_number": "5231", "volume": "269", "issue": "5231", "pages": "1737-1740" }, { "id": "authors:q65j6-w1y33", "collection": "authors", "collection_id": "q65j6-w1y33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154225409", "type": "article", "title": "Origin of PDZ (DHR, GLGF) domains", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1016/S0968-0004(00)89074-X", "issn": "0968-0004", "publisher": "Elsevier", "publication": "Trends in Biochemical Sciences", "publication_date": "1995-09", "series_number": "9", "volume": "20", "issue": "9", "pages": "350-350" }, { "id": "authors:symfz-he520", "collection": "authors", "collection_id": "symfz-he520", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120307-084000522", "type": "article", "title": "The Biochemistry of Synaptic Regulation in the Central Nervous System", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1146/annurev.bi.63.070194.003035", "issn": "0066-4154", "publisher": "Annual Reviews", "publication": "Annual Review of Biochemistry", "publication_date": "1994-07", "volume": "63", "pages": "571-600" }, { "id": "authors:hx7yg-tys08", "collection": "authors", "collection_id": "hx7yg-tys08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154226349", "type": "article", "title": "The major tyrosine-phosphorylated protein in the postsynaptic density fraction is N-methyl-D-aspartate receptor subunit 2B", "author": [ { "family_name": "Moon", "given_name": "Il Soo", "clpid": "Moon-Il-Soo" }, { "family_name": "Apperson", "given_name": "Michelle L.", "clpid": "Apperson-M-L" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The postsynaptic density (PSD) is a specialization of the submembranous cytoskeleton that is visible in the electron microscope on the cytoplasmic face of the postsynaptic membrane. A subcellular fraction enriched in structures with the morphology of PSDs contains signal-transduction molecules thought to regulate receptor localization and function in the central nervous system. We have purified a prominent tyrosine-phosphorylated glycoprotein of apparent molecular mass 180 kDa, termed PSD-gp180, that is highly enriched in the rat forebrain PSD fraction. The sequences of four tryptic peptides generated from the protein reveal that it is the 2B subunit of the N-methyl-D-aspartate (NMDA) type glutamate receptor. We have confirmed the identity of PSD-gp180 by showing that it reacts with antibodies raised against a unique fragment of the 2B subunit of the NMDA receptor. We also show that the 2B subunit is the most prominently tyrosine-phosphorylated protein in the PSD fraction based upon recognition by an anti-phosphotyrosine antibody. Two types of NMDA receptor subunits have been identified by molecular cloning [Nakanishi, S. (1992) Science 258, 597-603]. The single type 1 subunit is expressed throughout the brain and is necessary for formation of the receptor channel. The four type 2 subunits (2A, 2B, 2C, and 2D) are expressed in discrete brain regions, contain unusually long unique C termini, and confer distinct kinetic properties on NMDA receptors that contain them. Our findings suggest that, in the forebrain, NMDA receptor subunit 2B may serve to anchor NMDA receptors at the postsynaptic membrane through its interaction with the PSD. The prominent presence of tyrosine phosphate further suggests that the NMDA receptor may be regulated by tyrosine phosphorylation or that it may participate in signaling through tyrosine phosphorylation and through its ion channel.", "doi": "10.1073/pnas.91.9.3954", "pmcid": "PMC43701", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1994-04-26", "series_number": "9", "volume": "91", "issue": "9", "pages": "3954-3958" }, { "id": "authors:babac-gfy54", "collection": "authors", "collection_id": "babac-gfy54", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154227302", "type": "article", "title": "The postsynaptic density", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The postsynaptic density is a specialization of the nerve cell's submembrane cytoskeleton that is hypothesized to participate in the regulation of synaptic adhesion, transmitter receptor clustering, and modulation of receptor sensitivity. Until recently, many of the major proteins in the highly insoluble postsynaptic density fraction remained uncharacterized. Modern immunological and microsequencing methods now make it possible to define more precisely the molecular composition and function of this intriguing organelle.", "doi": "10.1016/0959-4388(93)90145-O", "issn": "0959-4388", "publisher": "Elsevier", "publication": "Current Opinion in Neurobiology", "publication_date": "1993-10", "series_number": "5", "volume": "3", "issue": "5", "pages": "732-737" }, { "id": "authors:6ak7n-ksy98", "collection": "authors", "collection_id": "6ak7n-ksy98", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:PATmbc93", "type": "article", "title": "Autophosphorylation of type II CaM kinase in hippocampal neurons: localization of phospho- and dephosphokinase with complementary phosphorylation site-specific antibodies", "author": [ { "family_name": "Patton", "given_name": "Bruce L.", "clpid": "Patton-B-L" }, { "family_name": "Molloy", "given_name": "Sean S.", "clpid": "Molloy-S-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "We have visualized the distribution of autophosphorylated type II CaM kinase in neural tissue with the use of two complementary antibodies: a monoclonal antibody that binds to the alpha and beta subunits of the kinase only when they are autophosphorylated at threonine-286 (287 in beta) and affinity-purified rabbit antibodies that bind to both subunits only when they are not phosphorylated at these residues. We used these antibodies to double-label organotypic hippocampal cultures, detecting the mouse monoclonal antibody with rhodamine and the rabbit polyclonal antibodies with fluorescein. In double-exposed photographs, the ratios of intensities of the two fluorophores revealed the relative proportion of autophosphorylated and nonphosphorylated kinase in individual neurons throughout the cultures. We found that autophosphorylated and nonphosphorylated kinase are colocalized throughout most neurons rather than segregated within distinct cells or subcellular domains. However, the variations in intensity of the two fluorophores indicated that the proportion of autophosphorylated kinase is consistently higher in neuronal somas than in the neuropil. Incubation of the cultures in Ca2+ free medium dramatically reduced both the level of autophosphorylated kinase detected biochemically and the relative intensity of fluorescent staining with the phosphokinase specific monoclonal antibody. These results support the hypothesis that regulation of Ca(2+)-independent CaM kinase activity in vivo occurs by a dynamic equilibrium between autophosphorylation and dephosphorylation and that this equilibrium is maintained, at varying steady-state levels, in all parts of neurons.", "doi": "10.1091/mbc.4.2.159", "pmcid": "PMC300912", "issn": "1059-1524", "publisher": "American Society for Cell Biology", "publication": "Molecular Biology of the Cell", "publication_date": "1993-02", "series_number": "2", "volume": "4", "issue": "2", "pages": "159-172" }, { "id": "authors:gfz1g-yn863", "collection": "authors", "collection_id": "gfz1g-yn863", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-151657008", "type": "article", "title": "The rat brain postsynaptic density fraction contains a homolog of the Drosophila discs-large tumor suppressor protein", "author": [ { "family_name": "Cho", "given_name": "Kyung-Ok", "clpid": "Cho-Kyung-Ok" }, { "family_name": "Hunt", "given_name": "Carol A.", "clpid": "Hunt-C-A" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "In CNS synapses, the synaptic junctional complex with associated postsynaptic density is presumed to contain proteins responsible for adhesion between pre- and postsynaptic membranes and for postsynaptic signal transduction. We have found that a prominent, brain-specific protein (PSD-95) enriched in the postsynaptic density fraction from rat brain is highly similar to the Drosophila lethal(1)discs-large-1 (dlg) tumor suppressor protein. The dlg protein is associated with septate junctions in developing flies and contains a guanylate kinase domain that is required for normal control of cell division. The sequence similarity between dlg and PSD-95 suggests that molecular mechanisms critical for growth control in developing organisms may also regulate synapse formation, stabilization, or function in the adult brain.", "doi": "10.1016/0896-6273(92)90245-9", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "1992-11", "series_number": "5", "volume": "9", "issue": "5", "pages": "929-942" }, { "id": "authors:25pfh-z6186", "collection": "authors", "collection_id": "25pfh-z6186", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154228152", "type": "article", "title": "The Pierian Spring", "author": [ { "family_name": "Morris", "given_name": "Richard G. M.", "clpid": "Morris-R-G-M" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1016/0960-9822(92)90001-Q", "issn": "0960-9822", "publisher": "Cell Press", "publication": "Current Biology", "publication_date": "1992-10", "series_number": "10", "volume": "2", "issue": "10", "pages": "511-514" }, { "id": "authors:bk0tm-e3k71", "collection": "authors", "collection_id": "bk0tm-e3k71", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154229132", "type": "article", "title": "The \u0251 subunit of type II Ca^(2+)/calmodulin-dependent protein kinase is highly conserved in Drosophila", "author": [ { "family_name": "Cho", "given_name": "Kyung-Ok", "clpid": "Cho-Kyung-Ok" }, { "family_name": "Wall", "given_name": "John B.", "clpid": "Wall-J-B" }, { "family_name": "Pugh", "given_name": "Phyllis C.", "clpid": "Pugh-P-C" }, { "family_name": "Ito", "given_name": "Masamichi", "clpid": "Ito-Masamichi" }, { "family_name": "Mueller", "given_name": "Shelley A.", "clpid": "Mueller-S-A" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "A monoclonal antibody against rat brain type II Ca^(2+)/calmodulin-dependent protein kinase (CaM kinase) precipitates three proteins from Drosophila heads with apparent molecular weights similar to those of the subunits of the rat brain kinase. Fly heads also contain a CaM kinase activity that becomes partially independent of Ca^(2+) after autophosphorylation, as does the rat brain kinase. We have isolated a Drosophila cDNA encoding an amino acid sequence that is 77% identical to the sequence of the rat alpha subunit. All known autophosphorylation sites are conserved, including the site that controls Ca^(2+)-independent activity. The gene encoding the cDNA is located between 102E and F on the fourth chromosome. The protein product of this gene is expressed at much higher levels in the fly head than in the body. Thus, both the amino acid sequence and the tissue specificity of the mammalian kinase are highly conserved in Drosophila.", "doi": "10.1016/0896-6273(91)90296-C", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "1991-09", "series_number": "3", "volume": "7", "issue": "3", "pages": "439-450" }, { "id": "authors:1t65f-jt952", "collection": "authors", "collection_id": "1t65f-jt952", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154230067", "type": "article", "title": "Autophosphorylation of type II Ca^(2+)/calmodulin-dependent protein kinase in cultures of postnatal rat hippocampal slices.", "author": [ { "family_name": "Molloy", "given_name": "Sean S.", "clpid": "Molloy-S-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Autophosphorylation of Thr^(286) on type II Ca^(2+)/calmodulin-dependent protein kinase (CaM kinase) in vitro causes kinase activity to become partially independent of Ca^(2+). Here we report that Thr^(286) is the major CaM kinase autophosphorylation site occupied in situ in \"organotypic\" hippocampal cultures. Measurement of Ca^(2+)-independent CaM kinase activity revealed that approximately one-third of the kinase is autophosphorylated in situ when the basal Ca^(2+) concentration is 15-43 nM. This proportion was substantially reduced 30 min after removal of extracellular Ca^(2+) or treatment of the cultures with protein kinase inhibitors and was increased by treatment with okadaic acid. Therefore, the high proportion of autophosphorylated kinase at basal Ca^(2+) concentrations appears to be maintained by Ca^(2+)-dependent autophosphorylation. Homogenates of intact hippocampi also contain a high proportion of Ca^(2+)-independent type II CaM kinase, 13-23% depending on developmental age. Thus, in hippocampal neurons, an important function of the autophosphorylation mechanism may be to produce a relatively high level of CaM kinase activity, even at basal Ca^(2+) concentrations, permitting both upward and downward local regulation by physiological agents.", "doi": "10.1073/pnas.88.11.4756", "pmcid": "PMC51745", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1991-06-01", "series_number": "11", "volume": "88", "issue": "11", "pages": "4756-4760" }, { "id": "authors:r1hbw-gsf80", "collection": "authors", "collection_id": "r1hbw-gsf80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154231046", "type": "article", "title": "Phosphorylation of smooth muscle myosin by type II Ca^(2+)/calmodulin-dependent protein kinase.", "author": [ { "family_name": "Edelman", "given_name": "Arthur M.", "clpid": "Edelman-A-M" }, { "family_name": "Lin", "given_name": "Wei-Hsung", "clpid": "Lin-Wei-Hsung" }, { "family_name": "Osterhout", "given_name": "Donna J.", "clpid": "Osterhout-D-J" }, { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Krebs", "given_name": "Edwin G.", "clpid": "Krebs-E-G" } ], "abstract": "Brain type II Ca^(2+)/calmodulin-dependent protein kinase was found to phosphorylate smooth muscle myosin, incorporating maximally ~ 2 mol of phosphoryl per mol of myosin, exclusively on the 20,000 dalton light chain subunit. After maximal phosphorylation of myosin or the isolated 20,000 dalton light chain subunit by myosin light chain kinase, the addition of type II Ca^(2+)/calmodulin-dependent protein kinase led to no further incorporation indicating the two kinases phosphorylated a common site. This conclusion was supported by two dimensional mapping of tryptic digests of myosin phosphorylated by the two kinases. By phosphoamino acid analysis the phosphorylated residue was identified as a serine. The phosphorylation by type II Ca^(2+)/calmodulin-dependent protein kinase of myosin resulted in enhancement of its actin-activated Mg^(2+)-ATPase activity. Taken together, these data strongly support the conclusion that type II Ca^(2+)/calmodulin-dependent protein kinase phosphorylates the same amino acid residue on the 20,000 dalton light chain subunit of smooth muscle myosin as is phosphorylated by myosin light chain kinase and suggest an alternative mechanism for the regulation of actin-myosin interaction.", "doi": "10.1007/BF00231704", "issn": "0300-8177", "publisher": "Springer Verlag", "publication": "Molecular and cellular biochemistry", "publication_date": "1990-09-03", "series_number": "1", "volume": "97", "issue": "1", "pages": "87-98" }, { "id": "authors:bv4cj-9vd08", "collection": "authors", "collection_id": "bv4cj-9vd08", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154232058", "type": "article", "title": "Activation of type II calcium/calmodulin-dependent protein kinase by Ca^(2+)/calmodulin is inhibited by autophosphorylation of threonine within the calmodulin-binding domain", "author": [ { "family_name": "Patton", "given_name": "Bruce L.", "clpid": "Patton-B-L" }, { "family_name": "Miller", "given_name": "Stephen G.", "clpid": "Miller-S-G" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "It is now well established that autophosphorylation of a threonine residue located next to each calmodulin-binding domain in the subunits of type II Ca^(2+)/calmodulin-dependent protein kinase causes the kinase to remain active, although at a reduced rate, after Ca^(2+) is removed from the reaction. This autophosphorylated form of the kinase is still sensitive to Ca2+/calmodulin, which is required for a maximum catalytic rate. After removal of Ca^(2+), new sites are autophosphorylated by the partially active kinase. Autophosphorylation of these sites abolishes sensitivity of the kinase to Ca^(2+)/calmodulin (Hashimoto, Y., Schworer, C. M., Colbran, R. J., and Soderling, T. R. (1987) J. Biol. Chem. 262, 8051-8055). We have identified two pairs of homologous residues, Thr^(305) and Ser^(314) in the alpha subunit and Thr^(306) and Ser^(315) in the beta subunit, that are autophosphorylated only after removal of Ca^(2+) from an autophosphorylation reaction. The sites were identified by direct sequencing of labeled tryptic phosphopeptides isolated by reverse-phase high pressure liquid chromatography. Thr^(305-306) is rapidly dephosphorylated by purified protein phosphatases 1 and 2A, whereas Ser^(314-315) is resistant to dephosphorylation. We have shown by selective dephosphorylation that the presence of phosphate on Thr^(305-306) blocks sensitivity of the kinase to Ca^(2+)/calmodulin. In contrast, the presence of phosphate on Ser^(314-315) is associated with an increase in the Kact for Ca^(2+)/calmodulin of only about 2-fold, producing a relatively small decrease in sensitivity to Ca^(2+)/calmodulin.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1990-07-05", "series_number": "19", "volume": "265", "issue": "19", "pages": "11204-11212" }, { "id": "authors:ms4j0-1qh24", "collection": "authors", "collection_id": "ms4j0-1qh24", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154234958", "type": "article", "title": "Hippocampal Neurons Predisposed to Neurofibrillary Tangle Formation Are Enriched in Type II Calcium/Calmodulin-Dependent Protein Kinase", "author": [ { "family_name": "McKee", "given_name": "Ann C.", "clpid": "McKee-A-C" }, { "family_name": "Kosik", "given_name": "Kenneth S.", "clpid": "Kosik-K-S" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Kowall", "given_name": "Neil W.", "clpid": "Kowall-N-W" } ], "abstract": "The microtubule-associated phosphoprotein, tau, is an integral component of paired helical filaments in Alzheimer neurofibrillary tangles (NFT). The mechanism of NFT formation is unknown but aberrant phosphorylation of tau may be contributory. Calcium/calmodulin-dependent protein kinase type II (CaM kinase II), the most abundant kinase in the brain, phosphorylates tau in vitro. We found CaM kinase II immunoreactivity concentrated in human hippocampal pyramidal neurons of CA1 and the subiculum. In Alzheimer's disease (AD) staining intensity of CA1 and subicular neurons is strikingly increased despite NFT formation and neuronal depletion. Enhanced CaM kinase II activity, possibly a result of deafferentation, may contribute to phosphorylation of tau protein leading to NFT deposition and neuronal death in AD.", "doi": "10.1097/00005072-199001000-00006", "issn": "0022-3069", "publisher": "Lippincott, Williams & Wilkins", "publication": "Journal of Neuropathology and Experimental Neurology", "publication_date": "1990-01", "series_number": "1", "volume": "49", "issue": "1", "pages": "49-63" }, { "id": "authors:zj7ke-her87", "collection": "authors", "collection_id": "zj7ke-her87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154234009", "type": "article", "title": "Structure and Regulation of Type II Calcium/Calmodulin-dependent Protein Kinase in Central Nervous System Neurons", "author": [ { "family_name": "Kennedy", "given_name": "M. B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Bennett", "given_name": "M. K.", "clpid": "Bennett-M-K" }, { "family_name": "Bulleit", "given_name": "R. F.", "clpid": "Bulleit-R-F" }, { "family_name": "Erondu", "given_name": "N. E.", "clpid": "Erondu-N-E" }, { "family_name": "Jennings", "given_name": "V. R.", "clpid": "Jennings-V-R" }, { "family_name": "Miller", "given_name": "S. G.", "clpid": "Miller-S-G" }, { "family_name": "Molloy", "given_name": "S. S.", "clpid": "Molloy-S-S" }, { "family_name": "Patton", "given_name": "B. L.", "clpid": "Patton-B-L" }, { "family_name": "Schenker", "given_name": "L. J.", "clpid": "Schenker-L-J" } ], "abstract": "N/A", "doi": "10.1101/SQB.1990.055.01.013", "issn": "0091-7451", "publisher": "Cold Spring Harbor Laboratory", "publication": "Cold Spring Harbor Symposia on Quantitative Biology", "publication_date": "1990", "volume": "55", "pages": "101-110" }, { "id": "authors:g6c95-1wk21", "collection": "authors", "collection_id": "g6c95-1wk21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154237552", "type": "article", "title": "Do activity-dependent changes in expression of regulatory proteins play a role in the progression of central nervous system neural degeneration?", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Cellular responses to the environment are initiated through membrane receptors that are\nactivated by hormones or other extracellular agents. Activated receptors communicate to\nmolecular machinery within the cell either by changing the flux of ions across the membrane\nor by altering the synthesis or degradation of second messengers such as CAMP,\ncalcium ion, or diacylglycerol. One major mechanism through which these messengers\ncontrol cell function is the activation of protein kinases. It seems increasingly clear that\ncoordinated control over many cell processes at once is often exerted by networks of\nprotein kinases, perhaps tailored specifically for each cell type. We have only begun to\nglimpse how these networks might be organized. Most current research is still aimed at\nthe important goal of identifying and thoroughly characterizing the key regulatory proteins\n(often protein kinases) that mediate regulation by each second messenger in each specialized\ncell.", "doi": "10.1111/j.1749-6632.1989.tb12508.x", "issn": "0077-8923", "publisher": "New York Academy of Sciences", "publication": "Annals of the New York Academy of Sciences", "publication_date": "1989-12-29", "volume": "568", "pages": "193-197" }, { "id": "authors:63tf1-naw52", "collection": "authors", "collection_id": "63tf1-naw52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154235802", "type": "article", "title": "Regulation of synaptic transmission in the central nervous system: long-term potentiation", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1016/0092-8674(89)90601-6", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1989-12-01", "series_number": "5", "volume": "59", "issue": "5", "pages": "777-787" }, { "id": "authors:n06n0-m1x33", "collection": "authors", "collection_id": "n06n0-m1x33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154236693", "type": "article", "title": "Regulation of neuronal function by calcium", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "In the classical picture of brain function, electrical impulses are initiated in sensory organs and spread rapidly down axons, jumping synaptic clefts by neurochemical transmission. Patterns of electrical activity generated in this way integrate information throughout the brain and result in coordinated motor output. Even as this picture of the central role of electrical transmission was emerging in the mid-20th century, the more speculative neuroscientists reasoned that there must be more to it. In order to store information and adapt to a changing environment, neurons must be able to alter their own properties or those of their neighbors, in highly controlled ways, sometimes permanently.", "doi": "10.1016/0166-2236(89)90089-1", "issn": "0166-2236", "publisher": "Elsevier", "publication": "Trends in Neurosciences", "publication_date": "1989-11", "series_number": "11", "volume": "12", "issue": "11", "pages": "417-420" }, { "id": "authors:0edac-g9749", "collection": "authors", "collection_id": "0edac-g9749", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154238383", "type": "article", "title": "Synaptic memory molecules", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "N/A", "doi": "10.1038/335770a0", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "1988-10-27", "series_number": "6193", "volume": "335", "issue": "6193", "pages": "770-772" }, { "id": "authors:mp8t2-1gn96", "collection": "authors", "collection_id": "mp8t2-1gn96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154239342", "type": "article", "title": "Sequences of autophosphorylation sites in neuronal type II CaM kinase that control Ca^(2+)-independent activity", "author": [ { "family_name": "Miller", "given_name": "Stephen G.", "clpid": "Miller-S-G" }, { "family_name": "Patton", "given_name": "Bruce L.", "clpid": "Patton-B-L" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "After initial activation by Ca^(2+), the catalytic activity of type II Ca^(2+)/calmodulin-dependent protein kinase rapidly becomes partially independent of Ca^(2+). The transition is caused by autophosphorylation of a few subunits in the dodecameric holoenzyme, which is composed of varying proportions of two homologous types of subunits, alpha (50 kd) and beta (58-60 kd). We have identified one site in the alpha subunit (Thr286) and two in the beta subunit (Thr287 and Thr382) that are rapidly autophosphorylated. We show that phosphorylation of alpha-Thr286 and beta-Thr287, which are located immediately adjacent to the calmodulin binding domain, controls Ca^(2+)-independent activity. In contrast, phosphorylation of beta-Thr382 is not required to maintain Ca2+ independence. It is absent in the alpha subunit and is selectively removed from the minor beta' subunit, apparently by alternative splicing. Regulation of the presence of beta-Thr382 in the holoenzyme by both differential gene expression and alternative splicing suggests that it may have an important but highly specialized function.", "doi": "10.1016/0896-6273(88)90108-0", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "1988-09", "series_number": "7", "volume": "1", "issue": "7", "pages": "593-604" }, { "id": "authors:by0sh-zm911", "collection": "authors", "collection_id": "by0sh-zm911", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154241333", "type": "article", "title": "Conserved and Variable Regions in the Subunits of Brain Type II Ca^(2+)/Calmodulin-Dependent Protein Kinase", "author": [ { "family_name": "Bulleit", "given_name": "Robert F.", "clpid": "Bulleit-R-F" }, { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Molloy", "given_name": "Sean S.", "clpid": "Molloy-S-S" }, { "family_name": "Hurley", "given_name": "James B.", "clpid": "Hurley-J-B" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Brain type II Ca2+/calmodulin-dependent protein kinase is a holoenzyme composed of several copies each of three subunits, alpha (50 kd), beta (60 kd), and beta' (58 kd), in varying proportions. The deduced amino acid sequences of alpha (reported here) and beta are highly similar but not identical. The major difference between them is the deletion from alpha of two short segments (residues 316-339 and 354-392 in beta). cDNAs that appear to encode beta' are identical to beta except for the deletion of a segment encoding residues 378-392. Thus, the structural differences among alpha, beta, and beta' arise primarily from deletions (or insertions) in a variable region lying immediately carboxyl to the protein kinase and calmodulin-binding domains. The alpha and beta subunits are encoded by distinct genes expressed primarily, if not exclusively, in brain. Rather than being encoded by a third gene, beta' may arise by alternative splicing of the beta gene transcript.", "doi": "10.1016/0896-6273(88)90210-3", "issn": "0896-6273", "publisher": "Elsevier", "publication": "Neuron", "publication_date": "1988-03", "series_number": "1", "volume": "1", "issue": "1", "pages": "63-72" }, { "id": "authors:70dgj-1gc36", "collection": "authors", "collection_id": "70dgj-1gc36", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154242537", "type": "article", "title": "Molecules underlying memory", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "n/a", "doi": "10.1038/329015a0", "issn": "0028-0836", "publisher": "Nature Publishing Group", "publication": "Nature", "publication_date": "1987-09-03", "series_number": "6134", "volume": "329", "issue": "6134", "pages": "15-16" }, { "id": "authors:5m3s6-2x208", "collection": "authors", "collection_id": "5m3s6-2x208", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:BENpnas87", "type": "article", "title": "Deduced Primary Structure of the \u03b2 Subunit of Brain Type II Ca2+/calmodulin-dependent Protein Kinase Determined by Molecular Cloning", "author": [ { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "cDNA clones coding for the \u03b2 subunit of rat brain type II Ca2+/calmodulin-dependent protein kinase were isolated and sequenced. The clones, including one containing the entire coding region, hybridize at high stringency to a single band of poly(A)+ RNA of length 4.8 kilobases. The subunit coded for by the clones was identified by in vitro transcription of the cDNA followed by translation of the resulting RNA. The DNA sequence of the clones contains a single long open reading frame (1626 nucleotides) coding for a protein of 542 amino acids with a molecular weight of 60,333, the amino-terminal half of which is homologous to several other protein kinases. Potential ATP- and calmodulin-binding domains were identified. Two independent clones contain an identical 45-nucleotide deletion, relative to the clones described above, resulting in a shorter open reading frame coding for a protein of molecular weight 58,000. This suggests that the minor, 58-kDa \u03b2' subunit of the type II Ca2+/calmodulin-dependent kinase may be synthesized on a separate message.", "pmcid": "PMC304527", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1987-04-01", "series_number": "7", "volume": "84", "issue": "7", "pages": "1794-1798" }, { "id": "authors:qfmg6-4ht80", "collection": "authors", "collection_id": "qfmg6-4ht80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154243496", "type": "article", "title": "Regulation of Brain Type II Ca^(2+)/Calmodulin-Dependent Protein Kinase by Autophosphorylation: A Ca^(2+)-Triggered Molecular Switch", "author": [ { "family_name": "Miller", "given_name": "Stephen G.", "clpid": "Miller-S-G" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Calcium/calmodulin-stimulated autophosphorylation of a prominent brain calmodulin-dependent protein kinase (Type II CaM kinase) produces dramatic changes in its enzymatic activity. These changes suggest a mechanism by which the kinase could act as a calcium-triggered molecular switch. Incorporation of 3-12 of a possible total of 30 phosphate groups per holoenzyme causes kinase activity toward exogenous substrates as well as autophosphorylation itself to become independent of calcium. Thus, kinase activity could be prolonged beyond the duration of an initial activating calcium signal. The calcium-independent autophosphorylation could further prolong the active state by opposing dephosphorylation by cellular phosphatases.", "doi": "10.1016/0092-8674(86)90008-5", "issn": "0092-8674", "publisher": "Elsevier", "publication": "Cell", "publication_date": "1986-03-28", "series_number": "6", "volume": "44", "issue": "6", "pages": "861-870" }, { "id": "authors:s60c7-qer05", "collection": "authors", "collection_id": "s60c7-qer05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:HENpnas86", "type": "article", "title": "Immunoreactivity for a calmodulin-dependent protein kinase is selectively increased in macaque striate cortex after monocular deprivation", "author": [ { "family_name": "Hendry", "given_name": "S. H. C.", "clpid": "Hendry-S-H-C" }, { "family_name": "Kennedy", "given_name": "M. B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Immunocytochemical methods were used to localize type II Ca2+/calmodulin-dependent protein kinase in the macaque primary visual cortex. Neurons that stain for the kinase include both pyramidal and nonpyramidal cells and they appear to form a subset of cortical neurons. They are densely packed in layers II and IVB, somewhat more sparse in layers III, IVC\u00df, and VI, and nearly absent in layer V. In normal animals the distribution of kinase-positive cells within each layer is relatively uniform. However, in animals in which one eye is removed 7-14 days before sacrifice or sutured shut for 9 or 11 weeks, the cells in layer IVC\u00df are divided into alternating lightly and darkly stained bands. Comparison of immunocytochemically stained sections with adjacent sections stained for the mitochondrial enzyme, cytochrome oxidase, reveals that the kinase staining increases in ocular dominance columns originally driven by the removed or closed eye. These findings suggest that either the concentration of type II Ca2+/calmodulin-dependent protein kinase or its accessibility to the antibody probe increases dramatically and selectively in neurons of macaque primary visual cortex that have been deprived of their normal visual input. This may indicate that changing levels of activity in cortical neurons can alter their regulatory machinery.", "doi": "10.1073/pnas.83.5.1536", "pmcid": "PMC323112", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1986-03-01", "series_number": "5", "volume": "83", "issue": "5", "pages": "1536-1540" }, { "id": "authors:d4kzx-vkw15", "collection": "authors", "collection_id": "d4kzx-vkw15", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154244445", "type": "article", "title": "Regional distribution of type II Ca^(2+)/calmodulin-dependent protein kinase in rat brain", "author": [ { "family_name": "Erondu", "given_name": "Ngozi E.", "clpid": "Erondu-N-E" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "The distribution of type II Ca^(2+)/calmodulin-dependent protein kinase has been mapped in rat brain by immunochemical and immunohistochemical methods using an antibody against its alpha-subunit. The concentration of the kinase, measured by radioimmunoassay, varies markedly in different brain regions. It is most highly concentrated in the telencephalon where it comprises approximately 2% of the total hippocampal protein, 1.3% of cortical protein, and 0.7% of striatal protein. It is less concentrated in lower brain structures, ranging from about 0.3% of hypothalamic protein to 0.1% of protein in the pons/medulla. The gradient of staining intensity observed in brain sections by immunohistochemistry corroborates this distribution. Neurons and neuropil of the hippocampus are densely stained, whereas little staining is observed in lower brain regions such as the superior colliculus. Within the diencephalon and midbrain, dense staining is observed only in thalamic nuclei and the substantia nigra. The skewed distribution of alpha-subunit appears to be due in part to the occurrence in the cerebellum and pons/medulla of forms of the kinase with a high ratio of beta- to alpha-subunits. However, most of the variation is due to the extremely high concentration of the kinase in particular neurons, especially those of the hippocampus, cortex and striatum. The unusually high expression of the kinase in these neurons is likely to confer upon them specialized responses to calcium ion that are different from those of neurons in lower brain regions.", "pmcid": "PMC6565219", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1985-12", "series_number": "12", "volume": "5", "issue": "12", "pages": "3270-3277" }, { "id": "authors:0w030-66j35", "collection": "authors", "collection_id": "0w030-66j35", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154245416", "type": "article", "title": "Distinct forebrain and cerebellar isozymes of type II Ca^(2+)/calmodulin-dependent protein kinase associate differently with the postsynaptic density fraction", "author": [ { "family_name": "Miller", "given_name": "Stephen G.", "clpid": "Miller-S-G" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Forebrain and cerebellar Type II Ca2+/calmodulin-dependent protein kinases have different subunit compositions. The forebrain holoenzyme, characterized in our laboratory, is a 650-kDa holoenzyme composed of 50-kDa alpha-subunits and 60-kDa beta-subunits assembled in approximately a 3:1 ratio (Bennett, M. K., Erondu, N. E., and Kennedy, M. B. (1983) J. Biol. Chem. 258, 12735-12744). The cerebellar isozyme is a 500-kDa holoenzyme composed of alpha-subunits and beta-subunits assembled in almost the converse ratio, approximately four beta-subunits for each alpha-subunit. When compared by tryptic peptide mapping and by immunochemical techniques, the beta-subunits from the two brain regions are indistinguishable and the alpha-subunits appear closely related. The specific activities, substrate specificities, and catalytic constants of the cerebellar and forebrain isozymes are similar, suggesting that the alpha- and beta-subunits contain similar catalytic sites. However, two differences in the properties of the isozymes may result in functional differences between them in vivo. First, the apparent affinity of the cerebellar kinase for Ca2+/calmodulin is 2-fold higher than that of the forebrain kinase. Second, the two isozymes appear to associate differently with subcellular structures. Approximately 85% of the cerebellar kinase and 50% of the forebrain kinase remain in the particulate fraction after homogenization under standard conditions. However, they are present in different amounts in postsynaptic density fractions. Postsynaptic densities prepared from forebrain contain the forebrain isozyme. Immunochemical measurements show that it comprises approximately 16% of their total protein. In contrast, postsynaptic densities prepared from cerebellum contain the cerebellar isozyme, but it comprises only approximately 1-2% of their total protein. Thus, the alpha-subunit may play a role in anchoring Type II Ca2+/calmodulin-dependent protein kinase to postsynaptic densities.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1985-07-25", "series_number": "15", "volume": "260", "issue": "15", "pages": "9039-9046" }, { "id": "authors:v9vh6-7gh79", "collection": "authors", "collection_id": "v9vh6-7gh79", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENpnas83", "type": "article", "title": "Biochemical and immunochemical evidence that the \"major postsynaptic density protein\" is a subunit of a calmodulin-dependent protein kinase", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Erondu", "given_name": "Ngozi E.", "clpid": "Erondu-N-E" } ], "abstract": "By three criteria, two biochemical and one immunochemical, the major postsynaptic density protein (mPSDp) is indistinguishable from the 50-kilodalton (kDa) \u03b1 subunit of a brain calmodulin-dependent protein kinase. First, the two proteins comigrate on NaDodSO4/polyacrylamide gels. Second, iodinated tryptic peptide maps of the two are identical. Finally, a monoclonal antibody (6G9) that was raised against the protein kinase binds on immunoblots to a single 50 kDa band in crude brain homogenates and to both the subunit of the purified kinase and the mPSDp from postsynaptic density fractions. The purified kinase holoenzyme also contains a 60-kDa subunit termed \u00df.A comparison of the peptide map of \u00df with the maps of 60-kDa proteins from the postsynaptic density fraction suggests that \u00df is present there but is not the only protein present in this molecular weight range. These results indicate that the calmodulin-dependent protein kinase is a major constituent of the postsynaptic density fraction and thus may be a component of type I postsynaptic densities.", "pmcid": "PMC390054", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1983-12-01", "series_number": "23", "volume": "80", "issue": "23", "pages": "7357-7361" }, { "id": "authors:eawaf-vws21", "collection": "authors", "collection_id": "eawaf-vws21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154250659", "type": "article", "title": "Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain", "author": [ { "family_name": "Bennett", "given_name": "Mark K.", "clpid": "Bennett-M-K" }, { "family_name": "Erondu", "given_name": "Ngozi E.", "clpid": "Erondu-N-E" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "A calcium and calmodulin-dependent protein kinase has been purified from rat brain. It was monitored during the purification by its ability to phosphorylate the synaptic vesicle-associated protein, synapsin I. A 300-fold purification was sufficient to produce kinase that is 90-95% pure as determined by scans of stained sodium dodecyl sulfate-polyacrylamide gels and has a specific activity of 2.9 mumol of 32P transferred per min/mg of protein. Thus, the kinase is a relatively abundant brain enzyme, perhaps comprising as much as 0.3% of the total brain protein. The Stokes radius (95 A) and sedimentation coefficient (16.4 S) of the kinase indicate a holoenzyme molecular weight of approximately 650,000. The holoenzyme is composed of three subunits as judged by their co-migration with kinase activity during the purification steps and co-precipitation with kinase activity by a specific anti-kinase monoclonal antibody. The three subunits have molecular weights of 50,000, 58,000, and 60,000, and have been termed alpha, beta', and beta, respectively. The alpha- and beta-subunits are distinct peptides, however, beta' may have been generated from beta by proteolysis. All three of these subunits bind calmodulin in the presence of calcium and are autophosphorylated under conditions in which the kinase is active. The subunits are present in a ratio of about 3 alpha-subunits to 1 beta/beta'-subunit. We therefore postulate that the 650,000-Da holoenzyme consists of approximately 9 alpha-subunits and 3 beta/beta'-subunits. The abundance of this calmodulin-dependent protein kinase indicates that its activation is likely to be an important biochemical response to increases in calcium ion concentration in neuronal tissue.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1983-10-25", "series_number": "20", "volume": "258", "issue": "20", "pages": "12735-12744" }, { "id": "authors:90wf0-r6p31", "collection": "authors", "collection_id": "90wf0-r6p31", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154251882", "type": "article", "title": "A calcium/calmodulin-dependent protein kinase from mammalian brain that phosphorylates Synapsin I: partial purification and characterization", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "McGuinness", "given_name": "Teresa", "clpid": "McGuinness-T" }, { "family_name": "Greengard", "given_name": "Paul", "clpid": "Greengard-P" } ], "abstract": "A calcium/calmodulin-dependent protein kinase, which phosphorylates a synaptic vesicle-associated protein designated Synapsin I, has been shown to be present in both soluble and particulate fractions of rat brain homogenates. In the present study, the particulate activity was solubilized by washing with a low ionic strength solution, and the enzymes from the two fractions were partially purified by ion exchange chromatography and calmodulin-Sepharose affinity chromatography. By each of several criteria, the partially purified enzymes from the two sources were indistinguishable. These criteria included specificity for various substrate proteins, concentration dependence of activation by calcium and calmodulin, pH dependence, and apparent affinities for the substrates Synapsin I and ATP. The mild conditions that released the particulate enzyme indicated that it was not tightly bound to the membrane and suggested that it may exist in a dynamic equilibrium between soluble and particulate-bound states. The partially purified enzyme preparations from both the soluble and particulate fractions contained three proteins that were phosphorylated in the presence of calcium and calmodulin, a 50-kilodalton (Kd) protein and two proteins in the 60-Kd region. When compared by phosphopeptide mapping and two-dimensional gel electrophoresis, the proteins were indistinguishable from three proteins of corresponding molecular weights that were shown by Schulman and Greengard (Schulman, H., and P. Greengard (1978) Nature 271: 478-479) to be prominent substrates for calcium/calmodulin-dependent protein kinase in a crude particulate preparation from rat brain. The 50-Kd substrate was the major Coomassie blue staining protein in both partially purified enzyme preparations. The peak of this protein coincided with that of enzyme activity during DEAE-cellulose and calmodulin-Sepharose chromatography. These results suggest that the 50-Kd phosphoprotein may be an autophosphorylatable subunit of the Synapsin I Kinase or may exist in a complex with it.", "doi": "10.1523/jneurosci.03-04-00818.1983", "pmcid": "PMC6564459", "issn": "0270-6474", "publisher": "Society for Neuroscience", "publication": "Journal of Neuroscience", "publication_date": "1983-04", "series_number": "4", "volume": "3", "issue": "4", "pages": "818-831" }, { "id": "authors:rfhb8-rtd11", "collection": "authors", "collection_id": "rfhb8-rtd11", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENarn83", "type": "article", "title": "Experimental approaches to understanding the role of protein phosphorylation in the regulation of neuronal function", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Studies by Earl Sutherland and his colleagues on hormonal regulation of the breakdown of glycogen in liver resulted in the discovery that the first step in the action of many hormones is to increase the synthesis of cAMP by activating adenylate cyclase (Raft et al 1957, Sutherland & Rall 1958, Robison et al 1968). It was later established that cAMP exerts its effects by stimulating protein kinases that catalyze the phosphorylation of specific functional proteins and thereby regulate their activity (Walsh et al 1968, Kuo & Greengard 1969, Krebs & Beavo 1979). The discovery that the brain contains a high concentration of cAMP-dependent protein kinase led to the proposal that protein phosphorylation might play an important role in regulation of neuronal properties by neurotransmitters and neurohormones (Miyamoto et al 1969). In particular, it seemed that protein phosphorylation, which usually takes place on a time scale of hundreds of milliseconds or longer, might be a mechanism underlying relatively long-lasting changes in neuronal properties such as \"slow\" changes in post-synaptic potentials (McAfee & Greengard 1972), changes in the rate of transmitter synthesis (Morgenroth et al 1975), or changes in gene expression (Klein & Berg 1970). The biochemists and neurobiologists who took up the study of brain protein phosphorylation hoped to gain insight into some of the mechanisms underlying changes in neuronal excitability and synaptic efficacy and also, perhaps, into processes that govern the development of various neuronal types during the formation of the nervous system. This line of research was bolstered by the findings that the brain contains not only high concentrations of protein kinases, but also protein phosphatases, adenylate cyclase, and phosphodiesterase (Greengard 1976), and also by the discovery that several neurotransmitters stimulate the synthesis of second messengers such as cyclic AMP and cyclic GMP by binding to specific receptors on the surfaces of neurons (for reviews see Nathanson 1977, Greengard 1981).", "doi": "10.1146/annurev.ne.06.030183.002425", "issn": "0147-006X", "publisher": "Annual Reviews", "publication": "Annual Review of Neuroscience", "publication_date": "1983-03", "volume": "6", "pages": "493-525" }, { "id": "authors:ccwvr-4ds59", "collection": "authors", "collection_id": "ccwvr-4ds59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:KENpnas81", "type": "article", "title": "Two calcium/calmodulin-dependent protein kinases, which are highly concentrated in brain, phosphorylate protein I at distinct sites", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Greengard", "given_name": "Paul", "clpid": "Greengard-P" } ], "abstract": "Two calcium-stimulated protein kinase activities (ATP:protein phosphotransferase, EC 2.7.1.37) that phosphorylate protein I, a specific synaptic protein, have been identified in homogenates of rat brain. One of these is found in both the particulate and cytosolic fractions and phosphorylates a region of protein I that is phosphorylated in intact synaptosomes in response to calcium but not to cyclic AMP. The stimulation by calcium of the particulate enzyme and of the partially purified cytosolic enzyme requires the addition of calmodulin. It is not yet known whether the particulate and cytosolic enzymes are related. A second calcium-stimulated protein I kinase is found only in the cytosol and phosphorylates a region of protein I that is phosphorylated in intact synaptosomes in response to either calcium or cyclic AMP. The calcium stimulation of this latter kinase is probably mediated by calmodulin, judging from its inhibition by low concentrations of trifluoperazine. Both of the calcium-stimulated protein I kinases are more highly concentrated in brain than in other tissues. The two cytosolic kinases are distinguishable from each other and from myosin light chain kinase and phosphorylase b kinase by their substrate specificities and their chromatographic behavior on DEAE-cellulose.", "pmcid": "PMC319995", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "1981-02", "series_number": "2", "volume": "78", "issue": "2", "pages": "1293-1297" }, { "id": "authors:d8q3f-53a83", "collection": "authors", "collection_id": "d8q3f-53a83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154252993", "type": "article", "title": "Lysophosphatidyl choline facilitates labeling of CNS projections with horseradish peroxidase", "author": [ { "family_name": "Frank", "given_name": "Eric", "clpid": "Franck-E" }, { "family_name": "Harris", "given_name": "William A.", "clpid": "Harris-W-A" }, { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" } ], "abstract": "Previously, it has been difficult to label sensory terminations in the CNS by back-filling peripheral sensory nerves with horseradish peroxidase (HRP), apparently because the amount of HRP transported along the axons is insufficient. Labeling of central sensory projections in axolotls and frogs can be improved by agents known to disrupt membranes. Of those tested, L-alpha-lysophosphatidyl choline is the most effective. The addition of this detergent ot the HRP solution dramatically increases both the number of axons labeled and the density of label within single axons.", "doi": "10.1016/0165-0270(80)90059-X", "issn": "0165-0270", "publisher": "Elsevier", "publication": "Journal of Neuroscience Methods", "publication_date": "1980-04", "series_number": "2", "volume": "2", "issue": "2", "pages": "183-189" }, { "id": "authors:2h13z-5ek30", "collection": "authors", "collection_id": "2h13z-5ek30", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120424-154253948", "type": "article", "title": "Characterization of the extracellular lipase of Bacillus subtilis and its relationship to a membrane-bound lipase found in a mutant strain", "author": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Lennarz", "given_name": "W. J.", "clpid": "Lennarz-W-J" } ], "abstract": "Bacillus subtilis CMK33 is a mutant that is more osmotically fragile than the wild type when it is converted to the protoplast form. The protoplasts of this mutant contain a membrane-bound lipase, which is not found in protoplasts of the wild type. Hydrolysis of the membrane lipid of mutant protoplasts by the lipase is the cause of their fragility. A protein found in the wild type organism specifically inhibits the lipase (Kent, C., and Lennarz, W. J. (1972) Proc. Natl. Acad. Sci. U. S. A. 69, 2793-2797). This paper reports that cultures of both mutant and wild type cells contain an extracellular lipase which accumulates during the logarithmic phase of growth. The extracellular activity appears to be induced by a component of the growth medium. The membrane-bound lipase of the mutant has been partially purified and its properties have been compared to those of the extracellular lipase of the wild type. Their properties and sensitivity to the wild type inhibitor are similar, which suggests that the two molecules are closely related. The subcellular location of the lipase in the mutant has been investigated and compared to the location of the membrane-bound portion of the lipase inhibitor in the wild type. The lipase is located almost exclusively in the cytoplasmic membrane and not in mesosomal vesicles. In contrast, the lipase inhibitor is located in both types of membranes and is more concentrated in mesosomal vesicles. Under appropriate conditions, the appearance of new extracellular lipase activity in mutant cultures is paralleled by the loss of an equivalent amount of lipase activity from protoplasts prepared from the cells. This suggests that the membrane-bound lipase may be an intermediate in the secretion of the extracellular lipase. Because of the mutation in B. subtilis CMK33, which results in the absence of the lipase inhibitor, this intermediate can be found in protoplasts of the mutant, although it is not detectable in the wild type. Consequently, the mutant may be useful in studies of the mechanism of secretion of exoenzymes by Bacilli.", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "1979-02-25", "series_number": "4", "volume": "254", "issue": "4", "pages": "1080-1089" } ]