We propose an atomistic mechanism by which key plant processes, including seed dormancy, root elongation, secondary root proliferation, and flower and fruit produc-tion, are regulated. This regulation occurs through binding of the phytohormone abscisic acid (ABA) to the plant G protein-coupled receptor (GPCR) GCR1. This mirrors the central role of GPCRs in animal systems, where they mediate vision, taste, olfaction, pain perception, and neurotransmission. Establishing GCR1 as a bona fide GPCR in plants would represent a transformative advance in plant biology and agriculture. In particular, GCR1 would be shown to transduce ABA signals through interaction with the Gα subunit (GPA1). However, direct experimental evidence for this interaction and conformation that ABA binding to GCR1 modulates GPA1 inactivation, remains elusive. A major obstacle in testing these hypotheses is the lack of structural data on GPA1 interactions within the ABA-GCR1 complex. To address this gap, we employ molecular dynamics (MD) and metadynamics simulations based on the AMBER and CHARM31 force fields to characterize atomistically the ABA-GCR1-GPA1 ternary complex. Our MD simulations reveal an allosteric mechanism whereby GCR1-ABA binding induces a rigid-body closure of the GPA1 Ras and α-helical domains, creating a steric blockade that traps GDP in the nucleotide-binding pocket. This con-formation prevents GTP exchange and maintains GPA1 in an inactive state, effectively terminating the signaling cascade. Free energy landscape analysis further demonstrates that this closed state represents a deep energy minimum, suggesting biological relevance as a regulatory mechanism. We propose specific mutations in the ABA-binding site of GCR1 and at the GCR1-GPA1 interface that could experimentally validate (or refute) our proposed mechanism. Confirmation of this model would pave the way for designing novel agonists and inverse agonists to precisely manipulate critical plant processes.
", "doi": "10.1021/acs.jcim.5c02308", "pmcid": "PMC13080986", "issn": "1549-9596", "publisher": "American Chemical Society", "publication": "Journal of Chemical Information and Modeling", "publication_date": "2026-04-13", "series_number": "7", "volume": "66", "issue": "7", "pages": "4075-4084" }, { "id": "authors:32bqb-47283", "collection": "authors", "collection_id": "32bqb-47283", "cite_using_url": "https://authors.library.caltech.edu/records/32bqb-47283", "type": "article", "title": "Predicted molecules followed by experimental validation for protecting human neurons from oxidative stress\u2013induced cytotoxicity", "author": [ { "family_name": "Yang", "given_name": "Xuyu" }, { "family_name": "Lee", "given_name": "Joo-Youn", "orcid": "0000-0001-5685-9875", "clpid": "Lee-Joo-Youn" }, { "family_name": "Moghadam", "given_name": "Farbod", "orcid": "0009-0005-4442-2349", "clpid": "Moghadam-Farbod" }, { "family_name": "Steiner", "given_name": "Joseph" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Ganjur", "given_name": "Neha" }, { "family_name": "de Almenara", "given_name": "Adrian J.", "orcid": "0009-0007-9391-9225", "clpid": "de-Almenara-Adrian-J" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" }, { "family_name": "Loh", "given_name": "Y. Peng", "orcid": "0000-0002-5404-723X" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Alzheimer neurodegenerative disease (AD) has had a major impact worldwide, with no effective drugs for treatment. We discovered and reported earlier that neurotrophic factor-α1 (NF-α1)/carboxypeptidase E (CPE) reversed neurodegeneration and cognitive dysfunction in AD mouse models. We then predicted computationally and validated experimentally that CPE interacts with a pharmacophore of six residues on the 5-HT1E receptor (HTR1E) to activate the ERK-BCL2 signaling pathway leading to protection of human neurons against oxidative stress–induced cell death. We now report using this pharmacophore for in silico virtual screening of ~6 million small molecules to discover candidates with similar binding and neuroprotective properties as CPE. This in silico search identified a molecule (Z124) that was verified experimentally to bind to HTR1E with protective efficacy comparable to NF-α1/CPE but requiring a higher concentration. Next, we carried out R-group design optimization based on Z124 to identify 4 compounds predicted to have much better efficacy than Z124. These compounds were synthesized and tested for neuroprotective activity. All four compounds showed binding to HTLA-HTR1E cells comparable to CPE. We determined the Kd for two of these compounds: R9, 1.38 ± 0.2 nM, and R10, 2.1 ± 0.2 nM, to be over 15 times better than CPE. Furthermore, all four new compounds showed protective activity against oxidative stress–induced cytotoxicity in human HEK293 cells stably transfected with HTR1E, as well as human primary neurons. Mechanistically, R9 and R10 activated ERK phosphorylation and increased the mitochondria prosurvival protein, BCL2, making them excellent candidates for further development as a drug to treat neurodegenerative diseases.
", "doi": "10.1073/pnas.2505359122", "pmcid": "PMC12625973", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2025-11-11", "series_number": "45", "volume": "122", "issue": "45", "pages": "e2505359122" }, { "id": "authors:ddbe2-mzt46", "collection": "authors", "collection_id": "ddbe2-mzt46", "cite_using_url": "https://authors.library.caltech.edu/records/ddbe2-mzt46", "type": "article", "title": "Metabotropic GABAB Receptor Activation Induced by G Protein Coupling", "author": [ { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "G protein-coupled receptors (GPCRs) play central roles in regulating cellular responses through heterotrimeric G proteins (GP). Extensive studies have elucidated the complex cellular signaling mediated by GPCRs that accompany dynamic conformational changes upon activation. However, there has been less focus on the role of the GP on the activation process, particularly for class C GPCRs that function as obligate dimers. Herein, we report the pivotal role of GP coupling on the dynamic activation process for the metabotropic \u03b3-aminobutyric acid receptor (GABABR) based on extensive atomistic simulations. We find that GP coupling triggers drastic conformational changes in the GABABR transmembrane domain (TMD), while an agonist alone is insufficient to shift the equilibrium state from the inactive to the active states. These conformational changes induced by GP coupling destabilize the inactive TM5/TM5 interface, shifting the equilibrium toward the activated TM6/TM6 interface. This active role of the GP in activation provides fresh insights into the activation mechanism of GABABR and perhaps other class C GPCRs. These insights should aid in the development of more potent and selective drugs.", "doi": "10.1021/jacs.4c14672", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2025-01-06", "series_number": "2", "volume": "147", "issue": "2", "pages": "1911 - 1919" }, { "id": "authors:92wq3-sb827", "collection": "authors", "collection_id": "92wq3-sb827", "cite_using_url": "https://authors.library.caltech.edu/records/92wq3-sb827", "type": "article", "title": "Agonist activation to open the G\u03b1 subunit of the GPCR\u2013G protein precoupled complex defines functional agonist activation of TAS2R5", "author": [ { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Duy Mac", "given_name": "Khuong" }, { "family_name": "Strzelinski", "given_name": "Hannah R.", "orcid": "0000-0002-8461-7061" }, { "family_name": "Hoffman", "given_name": "Samantha A." }, { "family_name": "Kim", "given_name": "Donghwa", "orcid": "0000-0002-8994-8513" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Su", "given_name": "Judith", "orcid": "0000-0002-1005-1755" }, { "family_name": "Liggett", "given_name": "Stephen B.", "orcid": "0000-0002-0128-3669" }, { "family_name": "Goddard", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "G protein-coupled receptors (GPCRs) regulate multiple cellular responses and represent highly successful therapeutic targets. The mechanisms by which agonists activate the G protein are unclear for many GPCR families, including the bitter taste receptors (TAS2Rs). We ascertained TAS2R5 properties by live cell-based functional assays, direct binding affinity measurements using optical resonators, and atomistic molecular dynamics simulations. We focus on three agonists that exhibit a wide range of signal transduction in cells despite comparable ligand\u2013receptor binding energies derived from direct experiment and computation. Metadynamics simulations revealed that the critical barrier to activation is ligand-induced opening of the G protein between the \u03b1-helical (AH) and Ras-like domains of G\u03b1 subunit from a precoupled TAS2R5-G protein state to the fully activated state. A moderate agonist opens the AH-Ras cleft from 22 \u00c5 to 31 \u00c5 with an energy gain of \u22124.8 kcal mol\n \u22121\n , making GDP water-exposed for signaling. A high-potency agonist had an energy gain of \u221211.1 kcal mol\n \u22121\n . The low-potency agonist is also exothermic for G\u03b1 opening, but with an energy gain of only \u22121.4 kcal mol\n \u22121\n . This demonstrates that TAS2R5 agonist-bound functional potencies are derived from energy gains in the transition from a precoupled complex at the level of G\u03b1 opening. Our experimental and computational study provides insights into the activation mechanism of signal transduction that provide a basis for rational design of new drugs.", "doi": "10.1073/pnas.2409987121", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2024-11-26", "series_number": "48", "volume": "121", "issue": "48", "pages": "e2409987121" }, { "id": "authors:50h4n-d5n39", "collection": "authors", "collection_id": "50h4n-d5n39", "cite_using_url": "https://authors.library.caltech.edu/records/50h4n-d5n39", "type": "article", "title": "Experimental Validation of the Neurotrophic Factor-\u03b11 Binding Site on the Serotonin Receptor 1E (HTR1E) Responsible for \u03b2-Arrestin Activation and Subsequent Neuroprotection", "author": [ { "family_name": "Yang", "given_name": "Xuyu" }, { "family_name": "Lee", "given_name": "Joo-Youn", "orcid": "0000-0001-5685-9875", "clpid": "Lee-Joo-Youn" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Loh", "given_name": "Y. Peng" }, { "family_name": "Goddard", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Stress, such as neuroexcitotoxicity and oxidative stress, as well as traumatic brain injury, will result in neurodegeneration. Deciphering the mechanisms underlying neuronal cell death will facilitate the development of drugs that can promote neuronal survival and repair through neurogenesis. Many growth and trophic factors, including transforming growth factors (TGFs), insulin-like growth factors (IGFs), epidermal growth factor (EGF), fibroblast growth factor 2 (FGF2), and brain-derived neurotrophic factor (BDNF), are known to play a role in neuroprotection and neurogenesis. Neurotrophic factor-α1 (NF-α1), also known as carboxypeptidase E (CPE), has been shown experimentally to have neuroprotective activity, acting extracellularly, independent of its intracellular enzymatic function in prohormone processing. We previously reported experiments and molecular dynamics (MD) simulations showing that a 200 amino acid segment of NF-α1/CPE interacts with the serotonin receptor 1E (HTR1E) to protect human neurons against oxidative and neuroexcitotoxic stress via β-arrestin and extracellular signal-regulated kinase (ERK) signaling. We report here validation of our previously predicted binding site with a series of 16 carboxypeptidase E (CPE) mutants, identifying 3 mutants that substantially decrease the binding to HTR1E. We then carried out pERK studies to show that these 3 mutants also dramatically reduce β-arrestin activation. This was followed by MD simulations of 8 selected mutants, finding that the same 3 most dramatically reduced binding of the mutated CPE to 5-HTR1E. Then, we examined the binding of β-arrestin to these 3 (after phosphorylating the intracellular Ser and Thr) and found that the predicted binding decreased dramatically. Then, we examined the predicted activation of the β-arrestin by these 3 and found a dramatic decrease, just as in the pERK experiments. We consider that these experiments and simulations fully validate the predicted binding site for CPE, identifying the key amino acid residues critical for binding and biological activity. This provides the target for experiments and in silico computational screening to identify small molecules to replace the CPE protein as novel drugs to protect human neurons against oxidative/neuroexcitotoxic stress via β-arrestin/ERK signaling.
", "doi": "10.1021/acsomega.4c05367", "issn": "2470-1343", "publisher": "American Chemical Society", "publication": "ACS Omega", "publication_date": "2024-10-01", "series_number": "39", "volume": "9", "issue": "39", "pages": "40749\u201340758" }, { "id": "authors:zqber-vsv83", "collection": "authors", "collection_id": "zqber-vsv83", "cite_using_url": "https://authors.library.caltech.edu/records/zqber-vsv83", "type": "article", "title": "The G Protein-First Mechanism for Activation of the Class B Glucagon-like Peptide 1 Receptor Coupled to N-Terminal Domain-Mediated Conformational Progression", "author": [ { "family_name": "Li", "given_name": "Bo", "orcid": "0000-0001-5763-7262" }, { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Recently, there has been a great deal of excitement about new glucagon-like peptide 1 receptor (GLP-1R) agonists (e.g., semaglutide and tirzepatide) that have received FDA approval for type 2 diabetes and obesity. Although effective, these drugs come with side effects that limit their use. While research efforts continue to focus intensively on long-lasting, orally administered GLP-1R medications with fewer side effects, a major impediment to developing improved GLP-1R medications is that the mechanism by which an agonist activates GLP-1R to imitate signaling is not known. Here we present and validate the G protein (GP)-first mechanism for the GLP-1R supported by extensive atomistic simulations. We propose that GLP-1R is preactivated through the formation of a GLP-1R–GP precoupled complex at the cell membrane prior to ligand binding. Despite a transmembrane helix 6 (TM6)-bentout conformation characteristic of activated GLP-1R, this precoupled complex remains unactivated until an agonist binds to elicit signaling. Notably, this new hypothesis offers a unified and predictive model for the activities of a series of full and partial agonists, including the peptides ExP5, GLP-1(7-36), and GLP-1(9-36). Most surprisingly, our simulations reveal an N-terminus domain (NTD)-swing/agonist-insertion mechanism wherein the long extracellular NTD of GLP-1R tightly holds the C-terminal half of the peptide agonist and progressively shifts the N-terminal head of the peptide to facilitate insertion into the orthosteric pocket. Our findings provide novel mechanistic insights into the activation and function of class B GPCRs and should provide a realistic basis for structure-based ligand design.
", "doi": "10.1021/jacs.4c08128", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2024-09-25", "series_number": "38", "volume": "146", "issue": "38", "pages": "26251\u201326260" }, { "id": "authors:gjjdh-16f17", "collection": "authors", "collection_id": "gjjdh-16f17", "cite_using_url": "https://authors.library.caltech.edu/records/gjjdh-16f17", "type": "article", "title": "Ligand-Dependent and G Protein-Dependent Properties for the Sweet Taste Heterodimer, TAS1R2/1R3", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Guthrie", "given_name": "Brian", "orcid": "0000-0002-3508-4625" }, { "family_name": "Goddard", "given_name": "William A.", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The heterodimeric sweet taste receptor, TAS1R2/1R3, is a class C G protein-coupled receptor (GPCR) that couples to gustducin (Gt), a G protein (GP) specifically involved in taste processing. This makes TAS1R2/1R3 a possible target for newly developing low caloric ligands that taste sweet to address obesity and diabetes. The activation of TAS1R2/1R3 involves the insertion of the GαP C-terminus of the GP into the GPCR in response to ligand binding. However, it is not known for sure whether the GP inserts into the TAS1R2 or TAS1R3 intracellular region of this GPCR dimer. Moreover, TAS1R2/1R3 can also connect to other GPs, such as Gs, Gi1, Gt3, Go, Gq, and G12. These GPs have different C-termini that may modify GPCR signaling. To understand the possible GP dependence of sweet perception, we use molecular dynamic (MD) simulations to examine the coupling of various GαP C20 termini to TAS1R2/1R3 for various steviol glycoside ligands and an artificial sweetener. Since the C20 could interact with the transmembrane domain (TMD) of either TAS1R2 (TMD2) or TAS1R3 (TMD3), we consider both cases. Without any sweetener, we find that the apo GPCR shows similar Go and Gt selectivities, while all steviol glycoside ligands increase the selectivity of Gt but decrease Go selectivity at TMD2. Interestingly, we find that high sweet rebaudioside M (RebM) and RebD ligands show better interactions of C20 at TMD3 for the Gt protein, but low sweet RebC and hydRebM ligands show better interaction of C20 at TMD2 for the Gt protein. Thus, our MD simulation suggests that TAS1R2/1R3 may couple the GP to either 1R2 or to 1R3 and that it can couple other GPs compared to Gt. This will likely lead to multimodal functions producing multiple patterns of intracellular signaling for sweet taste receptors, depending on the particular sweetener. Directing the GP to one of the other may have beneficial therapeutic outcomes.
", "doi": "10.1021/acs.jpcb.4c04610", "issn": "1520-6106", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry B", "publication_date": "2024-09-18", "series_number": "37", "volume": "128", "issue": "37", "pages": "8927\u20138932" }, { "id": "authors:c4r6a-mwp15", "collection": "authors", "collection_id": "c4r6a-mwp15", "cite_using_url": "https://authors.library.caltech.edu/records/c4r6a-mwp15", "type": "article", "title": "Methotrexate Inhibits the Binding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor Binding Domain to the Host-Cell Angiotensin-Converting Enzyme-2 (ACE-2) Receptor", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Suebka", "given_name": "Sartanee", "clpid": "Suebka-Sartanee" }, { "family_name": "Gin", "given_name": "Adley", "clpid": "Gin-Adley" }, { "family_name": "Nguyen", "given_name": "Phuong-Diem", "clpid": "Nguyen-Phuong-Diem" }, { "family_name": "Tang", "given_name": "Yisha", "orcid": "0000-0001-9267-4405", "clpid": "Tang-Yisha" }, { "family_name": "Su", "given_name": "Judith", "orcid": "0000-0002-1005-1755", "clpid": "Su-Judith" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus mutates, finding effective drugs becomes more challenging. In this study, we use ultrasensitive frequency locked microtoroid optical resonators in combination with in silico screening to search for COVID-19 drugs that can stop the virus from attaching to the human angiotensin-converting enzyme 2 (hACE2) receptor in the lungs. We found 29 promising candidates that could block the binding site and selected four of them that were likely to bind very strongly. We tested three of these candidates using frequency locked optical whispering evanescent resonator (FLOWER), a label-free sensing method based on microtoroid resonators. FLOWER has previously been used for sensing single macromolecules. Here we show, for the first time, that FLOWER can provide accurate binding affinities and sense the inhibition effect of small molecule drug candidates without labels, which can be prohibitive in drug discovery. One of the candidates, methotrexate, showed binding to the spike protein 1.8 million times greater than that to the receptor binding domain (RBD) binding to hACE2, making it difficult for the virus to enter cells. We tested methotrexate against different variants of the SARS-CoV-2 virus and found that it is effective against all four of the tested variants. People taking methotrexate for other conditions have also shown protection against the original SARS-CoV-2 virus. Normally, it is assumed that methotrexate inhibits the replication and release of the virus. However, our findings suggest that it may also block the virus from entering cells. These studies additionally demonstrate the possibility of extracting candidate ligands from large databases, followed by direct receptor–ligand binding experiments on the best candidates using microtoroid resonators, thus creating a workflow that enables the rapid discovery of new drug candidates for a variety of applications.
\nSmoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein–coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein–coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R451^(6.32) and W535^(7.55), a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position.
", "doi": "10.1073/pnas.2300919120", "pmcid": "PMC10710022", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2023-12-05", "series_number": "49", "volume": "120", "issue": "49", "pages": "e2300919120" }, { "id": "authors:w4sp9-ryv31", "collection": "authors", "collection_id": "w4sp9-ryv31", "cite_using_url": "https://authors.library.caltech.edu/records/w4sp9-ryv31", "type": "article", "title": "Discovery of 3-Phenyl Indazole-Based Novel Chemokine-like Receptor 1 Antagonists for the Treatment of Psoriasis", "author": [ { "family_name": "Ko", "given_name": "Bongki", "clpid": "Ko-Bongki" }, { "family_name": "Jang", "given_name": "Yongsoo", "clpid": "Jang-Yongsoo" }, { "family_name": "Kwak", "given_name": "Seung-hwa", "orcid": "0000-0002-1360-3412", "clpid": "Kwak-Seung-hwa" }, { "family_name": "You", "given_name": "Hyun", "clpid": "You-Hyun" }, { "family_name": "Kim", "given_name": "Jeong-hyun", "orcid": "0000-0002-6659-5292", "clpid": "Kim-Jeong-hyun" }, { "family_name": "Lee", "given_name": "Jung-Eun", "clpid": "Lee-Jung-Eun" }, { "family_name": "Park", "given_name": "Hee Dong", "orcid": "0000-0002-8768-6054", "clpid": "Park-Hee-Dong" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Han", "given_name": "Jung Hyun", "orcid": "0000-0001-7910-7406", "clpid": "Han-Jung-Hyun" }, { "family_name": "Kim", "given_name": "Yong-Chul", "orcid": "0000-0003-1520-2011", "clpid": "Kim-Yong-Chul" } ], "abstract": "Chemokine-like receptor 1 (CMKLR1)\u2500a G protein-coupled receptor\u2500has functional roles in the immune system and related diseases, including psoriasis and metabolic diseases. Psoriasis is a chronic inflammatory disease characterized by skin redness, scaliness, and itching. In this study, we sought to develop novel CMKLR1 antagonists by screening our in-house GPCR-targeting compound library. Moreover, we optimized a phenylindazole-based hit compound with antagonistic activities and evaluated its oral pharmacokinetic properties in a murine model. A structure-based design on the human CMKLR1 homology model identified S-26d as an optimized compound that serves as a potent and orally available antagonist with a pIC\u2085\u2080 value of 7.44 in hCMKLR1-transfected CHO cells. Furthermore, in the imiquimod-induced psoriasis-like mouse model, oral administration of S-26d for 1 week significantly alleviated modified psoriasis area and severity index scores (severity of erythema, scaliness, skin thickness) compared with the control group.
", "doi": "10.1021/acs.jmedchem.3c01011", "issn": "0022-2623", "publisher": "American Chemical Society", "publication": "Journal of Medicinal Chemistry", "publication_date": "2023-11-09", "series_number": "21", "volume": "66", "issue": "21", "pages": "14564-14582" }, { "id": "authors:s0zet-jvy58", "collection": "authors", "collection_id": "s0zet-jvy58", "cite_using_url": "https://authors.library.caltech.edu/records/s0zet-jvy58", "type": "article", "title": "Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist", "author": [ { "family_name": "Li", "given_name": "Bo", "orcid": "0000-0001-5763-7262", "clpid": "Li-Bo" }, { "family_name": "Maruszko", "given_name": "Krystyna", "clpid": "Maruszko-Krystyna" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Vo", "given_name": "Amy-Doan P.", "orcid": "0000-0002-6697-2713", "clpid": "Vo-Amy-Doan-P" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The glucagon-like peptide-1 receptor (GLP-1R) is a key regulator of blood glucose and a prime target for the treatment of type II diabetes and obesity with multiple public drugs. Here we present a comprehensive computational analysis of the interactions of the activated GLP-1R–Gs signaling complex with a G protein biased agonist, Exendin P5 (ExP5), which possesses a unique N-terminal sequence responsible for the signal bias. Using a refined all-atom model of the ExP5–GLP-1R–Gs complex in molecular dynamics (MD) simulations, we propose a novel mechanism of conformation transduction in which the unique interaction network of ExP5 N-terminus propagates the binding signal across an array of conserved residues at the transmembrane domain to enhance Gs protein coupling at the cytoplasmic end of the receptor. Our simulations reveal previously unobserved interactions important for activation by ExP5 toward GDP-GTP signaling, providing new insights into the mechanism of class B G protein-coupled receptor (GPCR) signaling. These findings offer a framework for the structure-based design of more effective therapeutics.
", "doi": "10.1021/jacs.3c05996", "pmcid": "PMC10777869", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2023-09-20", "series_number": "37", "volume": "145", "issue": "37", "pages": "20422-20431" }, { "id": "authors:n4fsz-b9e88", "collection": "authors", "collection_id": "n4fsz-b9e88", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230630-524959000.9", "type": "article", "title": "The dynamics of agonist-\u03b2\u2082-adrenergic receptor activation induced by binding of GDP-bound Gs protein", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "There is considerable uncertainty about the mechanism by which the \u03b2\u2082-adrenergic receptor (\u03b2\u2082AR) is activated. Here we use molecular metadynamics computations to predict the mechanism by which an agonist induces the activation of the \u03b2\u2082AR and its cognate Gs protein. We found that binding agonist alone to the inactive \u03b2\u2082AR does not break the ionic lock and hence does not drive the \u03b2\u2082AR towards the activated conformation. However, we found that attaching the inactive Gs protein to the agonist-bound inactive \u03b2\u2082AR (containing the ionic lock) leads to partial insertion of G\u03b1s-\u03b15 into the core of \u03b2\u2082AR, which breaks the ionic lock, leading to activation of the Gs protein coupled to \u03b2\u2082AR. Upon activation, the G\u03b1s protein undergoes a remarkable opening of the GDP binding pocket, making the GDP available for exchange or release. Concomitantly, G\u03b1s-\u03b15 undergoes a remarkable expansion in the \u03b2\u2082AR cytoplasmic region after the ionic lock is broken, inducing TM6 to displace outward by ~5\u2009\u00c5 from TM3.", "doi": "10.1038/s41557-023-01238-6", "issn": "1755-4330", "publisher": "Nature Publishing Group", "publication": "Nature Chemistry", "publication_date": "2023-07-01" }, { "id": "authors:6eyk1-dkn47", "collection": "authors", "collection_id": "6eyk1-dkn47", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230530-441187700.12", "type": "article", "title": "Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions", "author": [ { "family_name": "Nag", "given_name": "Arundhati", "orcid": "0000-0002-1328-1695", "clpid": "Nag-Arundhati" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Das", "given_name": "Samir", "clpid": "Das-Samir" }, { "family_name": "Yu", "given_name": "Mary Beth", "clpid": "Yu-Mary-Beth" }, { "family_name": "Alvarez-Villalonga", "given_name": "Belen", "clpid": "Alvarez-Villalonga-Belen" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Su", "given_name": "Yapeng", "orcid": "0000-0002-6305-8467", "clpid": "Su-Yapeng" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "Macrocycle peptides are promising constructs for imaging and inhibiting extracellular, and cell membrane proteins, but their use for targeting intracellular proteins is typically limited by poor cell penetration. We report the development of a cell-penetrant high-affinity peptide ligand targeted to the phosphorylated Ser474 epitope of the (active) Akt2 kinase. This peptide can function as an allosteric inhibitor, an immunoprecipitation reagent, and a live cell immunohistochemical staining reagent. Two cell penetrant stereoisomers were prepared and shown to exhibit similar target binding affinities and hydrophobic character but 2-3-fold different rates of cell penetration. Experimental and computational studies resolved that the ligands' difference in cell penetration could be assigned to their differential interactions with cholesterol in the membrane. These results expand the tool kit for designing new chiral-based cell-penetrant ligands.", "doi": "10.1038/s42004-023-00890-w", "pmcid": "PMC10195864", "issn": "2399-3669", "publisher": "Nature Publishing Group", "publication": "Communications Chemistry", "publication_date": "2023-05-18", "volume": "6", "pages": "Art. No. 95" }, { "id": "authors:8fqpx-swt62", "collection": "authors", "collection_id": "8fqpx-swt62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230519-1707000.18", "type": "article", "title": "Predicted structure and cell signaling of TAS2R14 reveal receptor hyper-flexibility for detecting diverse bitter tastes", "author": [ { "family_name": "Tokmakova", "given_name": "Alina", "orcid": "0000-0001-5280-7621", "clpid": "Tokmakova-Alina" }, { "family_name": "Kim", "given_name": "Donghwa", "orcid": "0000-0002-8994-8513", "clpid": "Kim-Donghwa" }, { "family_name": "Guthrie", "given_name": "Brian", "orcid": "0000-0002-3508-4625", "clpid": "Guthrie-Brian" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Liggett", "given_name": "Stephen B.", "orcid": "0000-0002-0128-3669", "clpid": "Liggett-Stephen-B" } ], "abstract": "The 25 human bitter taste receptors (TAS2Rs) are expressed on taste and extra-oral cells representing an integrated chemosensory system. The archetypal TAS2R14 is activated by > 150 topographically diverse agonists, raising the question of how this uncharacteristic accommodation is achieved for these GPCRs. We report the computationally derived structure of TAS2R14 with binding sites and energies for five highly diverse agonists. Remarkably, the binding pocket is the same for all five agonists. The energies derived from molecular dynamics are consistent with experiments determining signal transduction coefficients in live cells. TAS2R14 accommodates agonists through the breaking of a TMD3 H-bond instead of the prototypic strong salt bridge, a TMD1,2,7 interaction different from Class A GPCRs, and agonist-promoted TMD3 salt bridges for high affinity (which we confirmed by receptor mutagenesis). Thus, the broadly tuned TAS2Rs accommodate diverse agonists via a single (vs multiple) binding pocket through unique TM interactions for sensing disparate micro-environments.", "doi": "10.1016/j.isci.2023.106422", "pmcid": "PMC10121769", "issn": "2589-0042", "publisher": "Cell Press", "publication": "iScience", "publication_date": "2023-04-21", "series_number": "4", "volume": "26", "issue": "4", "pages": "Art. No. 106422" }, { "id": "authors:cj9cx-px946", "collection": "authors", "collection_id": "cj9cx-px946", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230420-612616000.1", "type": "article", "title": "Discovery and Binding Mechanism of Pyrazoloisoquinoline-Based Novel \u03b2-Arrestin Inverse Agonists of the Kappa-Opioid Receptor", "author": [ { "family_name": "Jung", "given_name": "Jae-Hoon", "clpid": "Jung-Jae-Hoon" }, { "family_name": "Jang", "given_name": "In Hee", "clpid": "Jang-In-Hee" }, { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Kim", "given_name": "Sunhong", "orcid": "0000-0002-1782-6613", "clpid": "Kim-Sunhong" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kim", "given_name": "Yong-Chul", "orcid": "0000-0003-1520-2011", "clpid": "Kim-Yong-Chul" } ], "abstract": "Chronic exposure to stress or unwanted stimuli has been known to activate kappa opioid receptor/dynorphin (KOR/DYN) systems, which could induce depressive states and develop into some psychiatric disorders. Here, we report the first discovery of pyrazoloisoquinoline-based novel KOR \u03b2-arrestin inverse agonists through synthesis, structure\u2013activity relationships, optimization, and the biological evaluations of \u03bc/\u03ba/\u03b4 opioid receptor activities with cAMP and \u03b2-arrestin recruitment assays. The optimized compound 7q shows potent and selective \u03b2-arrestin inverse agonism at KOR with an EC\u2085\u2080 value of 9.33 nM in contrast to lower activities at DOR and no activity at MOR. Moreover, we use molecular dynamics simulations to predict the binding mode of the inverse agonist and propose a mechanism for the inverse agonism. We find that the transmembrane helix 6 position of the activated state is different for the OR subtypes, leading to significantly different interactions between the receptor and \u03b2-arrestin.", "doi": "10.1021/acs.jmedchem.3c00064", "issn": "0022-2623", "publisher": "American Chemical Society", "publication": "Journal of Medicinal Chemistry", "publication_date": "2023-04-13", "series_number": "7", "volume": "66", "issue": "7", "pages": "5154-5170" }, { "id": "authors:hbrrf-tjk12", "collection": "authors", "collection_id": "hbrrf-tjk12", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230607-202651553", "type": "article", "title": "Predicted Three-Dimensional Structure of the GCR1 Putative GPCR in Arabidopsis thaliana and Its Binding to Abscisic Acid and Gibberellin A1", "author": [ { "family_name": "Hern\u00e1ndez", "given_name": "Pedro M.", "clpid": "Hern\u00e1ndez-Pedro-M" }, { "family_name": "Arango", "given_name": "Carlos A.", "orcid": "0000-0001-5920-5340", "clpid": "Arango-Carlos-A" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Jaramillo-Botero", "given_name": "Andres", "orcid": "0000-0003-2844-0756", "clpid": "Jaramillo-Botero-Andres" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "GCR1 has been proposed as a plant analogue to animal G-protein-coupled receptors that can promote or regulate several physiological processes by binding different phytohormones. For instance, abscisic acid (ABA) and gibberellin A1 (GA1) have been shown to promote or regulate germination and flowering, root elongation, dormancy, and biotic and abiotic stresses, among others. They may act through binding to GCR1, which would put GCR1 at the heart of key signaling processes of agronomic importance. Unfortunately, this GPCR function has yet to be fully validated due to the lack of an X-ray or cryo-EM 3D atomistic structure for GCR1. Here, we used the primary sequence data from Arabidopsis thaliana and the GEnSeMBLE complete sampling method to examine 13 trillion possible packings of the 7 transmembrane helical domains corresponding to GCR1 to downselect an ensemble of 25 configurations likely to be accessible to the binding of ABA or GA1. We then predicted the best binding sites and energies for both phytohormones to the best GCR1 configurations. To provide the basis for the experimental validation of our predicted ligand-GCR1 structures, we identify several mutations that should improve or weaken the interactions. Such validations could help establish the physiological role of GCR1 in plants.", "doi": "10.1021/acs.jafc.2c06846", "issn": "1520-5118", "publisher": "American Chemical Society", "publication": "Journal of Agricultural and Food Chemistry", "publication_date": "2023-04-12", "series_number": "14", "volume": "71", "issue": "14", "pages": "5770-5782" }, { "id": "authors:z8bsy-26n20", "collection": "authors", "collection_id": "z8bsy-26n20", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230607-171926973", "type": "article", "title": "Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery", "author": [ { "family_name": "Wang", "given_name": "Xudong", "orcid": "0000-0002-9686-2072", "clpid": "Wang-Xudong" }, { "family_name": "Neale", "given_name": "Chris", "orcid": "0000-0001-9912-078X", "clpid": "Neale-Chris" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Ye", "given_name": "Libin", "orcid": "0000-0003-0818-2972", "clpid": "Ye-Libin" } ], "abstract": "Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-\u03c0 lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a \"gatekeeper\" for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-\u03c0 lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.", "doi": "10.1038/s41467-023-36971-6", "pmcid": "PMC10006191", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2023-03-10", "volume": "14", "pages": "1325" }, { "id": "authors:p3k10-gqa61", "collection": "authors", "collection_id": "p3k10-gqa61", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230315-645491100.11", "type": "article", "title": "Correction to: Novel interaction between neurotrophic factor-\u03b11/carboxypeptidase E and serotonin receptor, 5-HTR1E, protects human neurons against oxidative/neuroexcitotoxic stress via \u03b2-arrestin/ERK signaling", "author": [ { "family_name": "Sharma", "given_name": "Vinay Kumar", "clpid": "Sharma-Vinay-Kumar" }, { "family_name": "Yang", "given_name": "Xuyu", "clpid": "Yang-Xuyu" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Saiz-Sanchez", "given_name": "Daniel", "orcid": "0000-0001-7002-8031", "clpid": "Saiz-Sanchez-Daniel" }, { "family_name": "Villanueva-Anguita", "given_name": "Patricia", "orcid": "0000-0002-4199-6313", "clpid": "Villanueva-Anguita-Patricia" }, { "family_name": "Xiao", "given_name": "Lan", "clpid": "Xiao-Lan" }, { "family_name": "Inoue", "given_name": "Asuka", "clpid": "Inoue-Asuka" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Loh", "given_name": "Y. Peng", "orcid": "0000-0002-5404-723X", "clpid": "Loh-Y-Peng" }, { "family_name": "Toulabi", "given_name": "Leila", "clpid": "Toulabi-Leila" } ], "abstract": "In the published article, the author name Leila Toulabi was missed during the proof stage and it has been now updated.\n\nSection on Cellular Neurobiology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, 49, Convent Drive, Bldg 49, Rm 6A\u201110, Bethesda, MD 20892, USA.\n\nThe original article has been updated.", "doi": "10.1007/s00018-023-04711-0", "pmcid": "PMC9941249", "issn": "1420-682X", "publisher": "Springer", "publication": "Cellular and Molecular Life Sciences", "publication_date": "2023-03", "series_number": "3", "volume": "80", "issue": "3", "pages": "Art. No. 65" }, { "id": "authors:rx0rh-96d21", "collection": "authors", "collection_id": "rx0rh-96d21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220808-223815000", "type": "article", "title": "G protein coupling and activation of the metabotropic GABA\u2088 heterodimer", "author": [ { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Metabotropic \u03b3-aminobutyric acid receptor (GABA\u2088R), a class C G protein-coupled receptor (GPCR) heterodimer, plays a crucial role in the central nervous system. Cryo-electron microscopy studies revealed a drastic conformational change upon activation and a unique G protein (GP) binding mode. However, little is known about the mechanism for GP coupling and activation for class C GPCRs. Here, we use molecular metadynamics computations to predict the mechanism by which the inactive GP induces conformational changes in the GABA\u2088R transmembrane domain (TMD) to form an intermediate pre-activated state. We find that the inactive GP first interacts with TM3, which further leads to the TMD rearrangement and deeper insertion of the \u03b15 helix that causes the G\u03b1 subunit to open, releasing GDP, and forming the experimentally observed activated structure. This mechanism provides fresh insights into the mechanistic details of class C GPCRs activation expected to be useful for designing selective agonists and antagonists.", "doi": "10.1038/s41467-022-32213-3", "pmcid": "PMC9360005", "issn": "2041-1723", "publisher": "Nature Publishing Group", "publication": "Nature Communications", "publication_date": "2022-08-08", "volume": "13", "pages": "Art. No. 4612" }, { "id": "authors:ms6n6-fsq59", "collection": "authors", "collection_id": "ms6n6-fsq59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220425-841878300", "type": "article", "title": "The mechanism for ligand activation of the GPCR\u2013G protein complex", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "G protein\u2013coupled receptors (GPCRs) activate cellular responses ranging from odorants to neurotransmitters. Binding an agonist leads to activation of a heterotrimeric G protein (GP) that stimulates external signaling. Unfortunately, the mechanism remains unknown. We show for 15 class A GPCRs, including opioids, adrenergics, adenosines, chemokines, muscarinics, cannabinoids, serotonins, and dopamines, that interaction of an inactive GP, including Gs, Gi, Go, G11, and Gq, to the inactive GPCR, containing the intracellular ionic lock between transmembrane (TM) helices 3 and 6, evolves exothermically to form a precoupled GPCR-GP complex with an opened TM3-TM6 and the GP-\u03b15 helix partially inserted into the GPCR but not activated. We show that binding of agonist to this precoupled GPCR-GP complex causes the G\u03b1 protein to open into its active form, with the guanosine diphosphate exposed for signaling. This GP-first paradigm provides a strategy for developing selective agonists for GPCRs since it is the pharmacophore for the precoupled GPCR-GP complex that should be used to design drugs.", "doi": "10.1073/pnas.2110085119", "pmcid": "PMC9170043", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2022-04-22", "series_number": "18", "volume": "119", "issue": "18", "pages": "e2110085119" }, { "id": "authors:zts3f-f5a05", "collection": "authors", "collection_id": "zts3f-f5a05", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220112-355642683", "type": "article", "title": "Complete inhibition of a polyol nucleation by a micromolar biopolymer additive", "author": [ { "family_name": "Wen", "given_name": "Xin", "orcid": "0000-0002-2465-7870", "clpid": "Wen-Xin" }, { "family_name": "Wang", "given_name": "Sen", "clpid": "Wang-Sen" }, { "family_name": "Ramji", "given_name": "Robert", "orcid": "0000-0002-9850-7138", "clpid": "Ramji-Robert" }, { "family_name": "Butler", "given_name": "Luke O.", "clpid": "Butler-Luke-O" }, { "family_name": "Bagdagulyan", "given_name": "Yelena", "clpid": "Bagdagulyan-Yelena" }, { "family_name": "Kishishita", "given_name": "Audrey", "clpid": "Kishishita-Audrey" }, { "family_name": "Golen", "given_name": "James A.", "orcid": "0000-0002-6615-1253", "clpid": "Golen-James-A" }, { "family_name": "Rheingold", "given_name": "Arnold L.", "orcid": "0000-0003-4472-8127", "clpid": "Rheingold-Arnold-L" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Pascal", "given_name": "Tod A.", "orcid": "0000-0003-2096-1143", "clpid": "Pascal-Tod-A" } ], "abstract": "Preventing spontaneous crystallization of supersaturated solutions by additives is of critical interest to successful process design and implementation, with numerous applications in chemical, pharmaceutical, medical, pigment, and food industries, but challenges remain in laboratory and industry settings and fundamental understanding is lacking. When copresented with antifreeze proteins (AFPs), otherwise spontaneously crystallizing osmolytes are maintained at high supersaturations for months in over-wintering organisms. Thus, we here explore the inhibition phenomenon by AFPs, using persistent crystallization of a common sugar alcohol, D-mannitol, as a case study. We report experimentally that DAFP1, an insect AFP, completely inhibits D-mannitol nucleation. Computer simulations reveal a new mechanism for crystallization inhibition where the population of the crystal-forming conformers are selectively bound and randomized in solution by hydrogen bonding to the protein surface. These results highlight the advantages of using natural polymers to address crystallization inhibition challenges and suggest new strategies in controlling the nucleation processes.", "doi": "10.1016/j.xcrp.2021.100723", "pmcid": "PMC8903182", "issn": "2666-3864", "publisher": "Cell Press", "publication": "Cell Reports Physical Science", "publication_date": "2022-02-16", "series_number": "2", "volume": "3", "issue": "2", "pages": "Art. No. 100723" }, { "id": "authors:n1mc8-sxg63", "collection": "authors", "collection_id": "n1mc8-sxg63", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220117-235720695", "type": "article", "title": "Novel interaction between neurotrophic factor-\u03b11/carboxypeptidase E and serotonin receptor, 5-HTR1E, protects human neurons against oxidative/neuroexcitotoxic stress via \u03b2-arrestin/ERK signaling", "author": [ { "family_name": "Sharma", "given_name": "Vinay Kumar", "clpid": "Sharma-Vinay-Kumar" }, { "family_name": "Yang", "given_name": "Xuyu", "clpid": "Yang-Xuyu" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Saiz-Sanchez", "given_name": "Daniel", "orcid": "0000-0001-7002-8031", "clpid": "Saiz-Sanchez-Daniel" }, { "family_name": "Villanueva-Anguita", "given_name": "Patricia", "orcid": "0000-0002-4199-6313", "clpid": "Villanueva-Anguita-Patricia" }, { "family_name": "Xiao", "given_name": "Lan", "clpid": "Xiao-Lan" }, { "family_name": "Inoue", "given_name": "Asuka", "clpid": "Inoue-Asuka" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Loh", "given_name": "Y. Peng", "orcid": "0000-0002-5404-723X", "clpid": "Loh-Y-Peng" }, { "family_name": "Toulabi", "given_name": "Leila", "clpid": "Toulabi-Leila" } ], "abstract": "Protecting neurons from death during oxidative and neuroexcitotoxic stress is key for preventing cognitive dysfunction. We uncovered a novel neuroprotective mechanism involving interaction between neurotrophic factor-\u03b11 (NF-\u03b11/carboxypeptidase E, CPE) and human 5-HTR1E, a G protein-coupled serotonin receptor with no previously known neurological function. Co-immunoprecipitation and pull-down assays confirmed interaction between NF\u03b11/CPE and 5-HTR1E and 125I NF-\u03b11/CPE-binding studies demonstrated saturable, high-affinity binding to 5-HTR1E in stably transfected HEK293 cells (Kd\u2009=\u200913.82 nM). Treatment of 5-HTR1E stable cells with NF-\u03b11/CPE increased pERK 1/2 and pCREB levels which prevented a decrease in pro-survival protein, BCL2, during H\u2082O\u2082-induced oxidative stress. Cell survival assay in \u03b2-arrestin Knockout HEK293 cells showed that the NF-\u03b11/CPE-5-HTR1E-mediated protection against oxidative stress was \u03b2-arrestin-dependent. Molecular dynamics studies revealed that NF-\u03b11/CPE interacts with 5-HTR1E via 3 salt bridges, stabilized by several hydrogen bonds, independent of the serotonin pocket. Furthermore, after phosphorylating the C-terminal tail and intracellular loop 3 (ICL3) of NF-\u03b11/CPE-5-HTR1E, it recruited \u03b2-arrestin1 by forming numerous salt bridges and hydrogen bonds to ICL2 and ICL3, leading to activation of \u03b2-arrestin1. Immunofluorescence studies showed 5-HTR1E and NF-\u03b11/CPE are highly expressed and co-localized on cell surface of human hippocampal neurons. Importantly, knock-down of 5-HTR1E in human primary neurons diminished the NF-\u03b11/CPE-mediated protection of these neurons against oxidative stress and glutamate neurotoxicity-induced cell death. Thus, NF-\u03b11/CPE uniquely interacts with serotonin receptor 5-HTR1E to activate the \u03b2-arrestin/ERK/CREB/BCL2 pathway to mediate stress-induced neuroprotection.", "doi": "10.1007/s00018-021-04021-3", "pmcid": "PMC8732845", "issn": "1420-9071", "publisher": "SpringerNature", "publication": "Cellular and Molecular Life Sciences", "publication_date": "2022-01", "volume": "79", "pages": "Art. No. 24" }, { "id": "authors:z870w-e6p40", "collection": "authors", "collection_id": "z870w-e6p40", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-224624888", "type": "article", "title": "Synergic Effects in the Activation of the Sweet Receptor GPCR Heterodimer for Various Sweeteners Predicted Using Molecular Metadynamics Simulations", "author": [ { "family_name": "Jang", "given_name": "Jaewan", "orcid": "0000-0003-0595-6506", "clpid": "Jang-Jaewan" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Guthrie", "given_name": "Brian", "orcid": "0000-0002-3508-4625", "clpid": "Guthrie-Brian" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The sweet taste is elicited by activation of the TAS1R2/1R3 heterodimer G protein-coupled receptor. This is a therapeutic target for treatment of obesity and metabolic dysfunctions. Sweetener blends provide attractive strategies to lower the sugar level while preserving the attractive taste of food. To understand the synergic effect of various sweetener blend combinations of artificial and natural sweeteners, we carried out our molecular dynamics studies using predicted structures of the TAS1R2/1R3 heterodimer and predicted structures for the sweeteners. We used as a measure of activation the intracellular ionic lock distance between transmembrane helices 3 and 6 of TAS1R3. We find that full synergic combinations [rebaudioside A (Reb-A)/acesulfame K and Reb-A/sucralose] and partial synergic combinations (sucralose/acesulfame K) show significantly more negative changes in the free energy compared to single-ligand cases, while a pair known to be suppressive (saccharin and acesulfame K) shows significantly less changes than for the single-ligand case. This study provides an atomistic understanding of the mechanism for synergy and identifies new combinations of sweeteners to reduce the caloric content for treating diseases.", "doi": "10.1021/acs.jafc.1c03779", "issn": "0021-8561", "publisher": "American Chemical Society", "publication": "Journal of Agricultural and Food Chemistry", "publication_date": "2021-10-20", "series_number": "41", "volume": "69", "issue": "41", "pages": "12250-12261" }, { "id": "authors:hcmjr-sjx33", "collection": "authors", "collection_id": "hcmjr-sjx33", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211013-173908475", "type": "article", "title": "Predicted Structure of Fully Activated Tas1R3/1R3\u2032 Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Chou", "given_name": "Keng C.", "orcid": "0000-0002-8782-5253", "clpid": "Chou-Keng-C" }, { "family_name": "G\u00fcthrie", "given_name": "Brian", "clpid": "G\u00fcthrie-Brian" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The Tas1R3 G protein-coupled receptor constitutes the main component of sweet taste sensory response in humans via forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3\u2032 homodimer serves as a low-affinity sweet taste receptor, stimulating gustducin G protein (G_(Gust)) signaling in the presence of a high concentration of natural sugars. This provides an additional means to detect the taste of natural sugars, thereby differentiating the flavors between natural sugars and artificial sweeteners. We report here the predicted 3D structure of active state Tas1R3/1R3\u2032 homodimer complexed with heterotrimeric GGust and sucrose. We discovered that the G_(Gust) makes ionic anchors to intracellular loops 1 and 2 of Tas1R3 while the G\u03b1\u2013\u03b15 helix engages the cytoplasmic region extensively through salt bridge and hydrophobic interactions. We show that in the activation of this complex the Venus flytrap domains of the homodimer undergo a remarkable twist up to \u223c100\u00b0 rotation around the vertical axis to adopt a closed\u2013closed conformation while the intracellular region relaxes to an open\u2013open conformation. We find that binding of sucrose to the homodimer stabilizes a preactivated conformation with a largely open intracellular region that recruits and activates the G_(Gust). Upon activation, the G\u03b1 subunit spontaneously opens up the nucleotide-binding site, making nucleotide exchange facile for signaling. This activation of G_(Gust) promotes the interdomain twist of the Venus flytrap domains. These structures and transformations could potentially be a basis for the design of new sweeteners with higher activity and less unpleasant flavors.", "doi": "10.1021/jacs.1c08839", "issn": "0002-7863", "publisher": "American Chemical Society", "publication": "Journal of the American Chemical Society", "publication_date": "2021-10-13", "series_number": "40", "volume": "143", "issue": "40", "pages": "16824-16838" }, { "id": "authors:gry3q-whh92", "collection": "authors", "collection_id": "gry3q-whh92", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-224623544", "type": "article", "title": "Structures and Agonist Binding Sites of Bitter Taste Receptor TAS2R5 Complexed with Gi Protein and Validated against Experiment", "author": [ { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Kim", "given_name": "Donghwa", "orcid": "0000-0002-8994-8513", "clpid": "Kim-Donghwa" }, { "family_name": "Liggett", "given_name": "Stephen B.", "orcid": "0000-0002-0128-3669", "clpid": "Liggett-Stephen-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Bitter taste receptors (TAS2Rs) function in taste perception, but are also expressed in many extraoral tissues, presenting attractive therapeutic targets. TAS2R5s expressed on human airway smooth muscle cells can induce bronchodilation for treating asthma and other obstructive diseases. But TAS2R5s display low agonist affinity and the lack of a 3D structure has hindered efforts to design more active ligands. We report the structure of the activated TAS2R5 coupled to the Gi protein and bound to each of 19 agonists, using computational approaches. These agonists bind to two polar residues in TM3 that are unique for TAS2R5 among 25 TAS2R subtypes. Our predicted results correlate well with experimental results of agonist-receptor signaling coefficients, providing validation of the predicted structure. These results provide highly specific data on how agonists activate TAS2R5, how modifications of ligand structure alter receptor activation, and a guide to structure-based drug design.", "doi": "10.1021/acs.jpclett.1c02162", "pmcid": "PMC8650975", "issn": "1948-7185", "publisher": "American Chemical Society", "publication": "Journal of Physical Chemistry Letters", "publication_date": "2021-09-30", "series_number": "38", "volume": "12", "issue": "38", "pages": "9293-9300" }, { "id": "authors:bz41t-b5w45", "collection": "authors", "collection_id": "bz41t-b5w45", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211019-181528901", "type": "article", "title": "The G protein-first activation mechanism of opioid receptors by Gi protein and agonists", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "G protein-first mechanism of activation for opioid receptors and their cognate Gi protein. \u03a30: In the absence of ligand and Gi protein, the opioid receptors adopt the inactive conformation, featuring a tight hydrogen bond between the cytosolic ends of TM3 and TM6 that keeps the cytoplasmic region tightly closed. \u03a31: Before agonist binding, the inactive Gi protein tightly bound to GDP couples to inactive opioid receptor, to form a pre-coupled opioid receptor-Gi (GDP) complex. \u03a32: Interactions between inactive opioid receptor and inactive Gi (GDP) leads to breaking the TM3-TM6 hydrogen bond and opening the cytoplasmic region of the receptors to accommodate the Gi protein. As a result, the pre-activated state (\u03a32) emerges, which remains at this resting state until an agonist binds the receptor. \u03a33\u2032: agonist bound to the pre-activated state induces the Gi (GDP) to be activated. Activation of the Gi protein is associated with a remarkable opening in the cleft between AH and Ras-like domains of G\u03b1, providing an exit path for GDP release or exchange with a GTP. \u03a34\u2032: Upon GDP release of exchange, the agonist-opioid receptor-Gi protein evolves to its fully active state.", "doi": "10.1017/qrd.2021.7", "pmcid": "PMC10392629", "issn": "2633-2892", "publisher": "Cambridge University Press", "publication": "QRB Discovery", "publication_date": "2021-08-05", "series_number": "2021", "volume": "2", "issue": "2021", "pages": "e9" }, { "id": "authors:nsr10-mg844", "collection": "authors", "collection_id": "nsr10-mg844", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210606-012523434", "type": "article", "title": "Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists", "author": [ { "family_name": "Yang", "given_name": "Moon Young", "orcid": "0000-0003-4436-8010", "clpid": "Yang-Moon-Young" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Guthrie", "given_name": "Brian", "orcid": "0000-0002-3508-4625", "clpid": "Guthrie-Brian" } ], "abstract": "Bitter taste is sensed by bitter taste receptors (TAS2Rs) that belong to the G protein-coupled receptor (GPCR) superfamily. In addition to bitter taste perception, TAS2Rs have been reported recently to be expressed in many extraoral tissues and are now known to be involved in health and disease. Despite important roles of TAS2Rs in biological functions and diseases, no crystal structure is available to help understand the signal transduction mechanism or to help develop selective ligands as new therapeutic targets. We report here the three-dimensional structure of the fully activated TAS2R4 human bitter taste receptor predicted using the GEnSeMBLE complete sampling method. This TAS2R4 structure is coupled to the gustducin G protein and to each of several agonists. We find that the G protein couples to TAS2R4 by forming strong salt bridges to each of the three intracellular loops, orienting the activated G\u03b15 helix of the G\u03b1 subunit to interact extensively with the cytoplasmic region of the activated receptor. We find that the TAS2Rs exhibit unique motifs distinct from typical Class A GPCRs, leading to a distinct activation mechanism and a less stable inactive state. This fully activated bitter taste receptor complex structure provides insight into the signal transduction mechanism and into ligand binding to TAS2Rs.", "doi": "10.1017/qrd.2021.1", "pmcid": "PMC10392674", "issn": "2633-2892", "publisher": "Cambridge University Press", "publication": "QRB Discovery", "publication_date": "2021-04-08", "volume": "2", "pages": "E3" }, { "id": "authors:gpry1-7t005", "collection": "authors", "collection_id": "gpry1-7t005", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210301-120802550", "type": "article", "title": "Hedgehog proteins create a dynamic cholesterol interface", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Purohit", "given_name": "Rahul", "orcid": "0000-0001-9712-4277", "clpid": "Purohit-Rahul" }, { "family_name": "Vielmas", "given_name": "Erika", "orcid": "0000-0003-0263-7278", "clpid": "Vielmas-Erika" }, { "family_name": "Lauinger", "given_name": "Alexa R.", "orcid": "0000-0002-9820-9130", "clpid": "Lauinger-Alexa-R" }, { "family_name": "Lam", "given_name": "Brandon", "clpid": "Lam-Brandon" }, { "family_name": "Cheng", "given_name": "Yu-Shiuan", "orcid": "0000-0002-7408-7888", "clpid": "Cheng-Yu-Shiuan" }, { "family_name": "Zhang", "given_name": "Tianyi", "orcid": "0000-0001-8289-3102", "clpid": "Zhang-Tianyi" }, { "family_name": "Huang", "given_name": "Yiran", "orcid": "0000-0002-1435-6281", "clpid": "Huang-Yiran" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Ondrus", "given_name": "Alison E.", "orcid": "0000-0002-6023-3290", "clpid": "Ondrus-A-E" } ], "abstract": "During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR (\"Hog\") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.", "doi": "10.1371/journal.pone.0246814", "issn": "1932-6203", "publisher": "Public Library of Science", "publication": "PLoS ONE", "publication_date": "2021-02-25", "series_number": "2", "volume": "16", "issue": "2", "pages": "Art. No. e0246814" }, { "id": "authors:p5h6p-17d56", "collection": "authors", "collection_id": "p5h6p-17d56", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200630-070330108", "type": "article", "title": "Mechanism of \u03b2-arrestin recruitment by the \u03bc-opioid G protein-coupled receptor", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-A" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Agonists to the \u03bc-opioid G protein-coupled receptor (\u03bcOR) can alleviate pain through activation of G protein signaling, but they can also induce \u03b2-arrestin activation, leading to such side effects as respiratory depression. Biased ligands to \u03bcOR that induce G protein signaling without inducing \u03b2-arrestin signaling can alleviate pain while reducing side effects. However, the mechanism for stimulating \u03b2-arrestin signaling is not known, making it difficult to design optimum biased ligands. We use extensive molecular dynamics simulations to determine three-dimensional (3D) structures of activated \u03b2-arrestin2 stabilized by phosphorylated \u03bcOR bound to the morphine and D-Ala\u00b2, N-MePhe\u2074, Gly-ol]-enkephalin (DAMGO) nonbiased agonists and to the TRV130 biased agonist. For nonbiased agonists, we find that the \u03b2-arrestin2 couples to the phosphorylated \u03bcOR by forming strong polar interactions with intracellular loop 2 (ICL2) and either the ICL3 or cytoplasmic region of transmembrane (TM6). Strikingly, Gi protein makes identical strong bonds with these same ICLs. Thus, the Gi protein and \u03b2-arrestin2 compete for the same binding site even though their recruitment leads to much different outcomes. On the other hand, we find that TRV130 has a greater tendency to bind the extracellular portion of TM2 and TM3, which repositions TM6 in the cytoplasmic region of \u03bcOR, hindering \u03b2-arrestin2 from making polar anchors to the ICL3 or to the cytosolic end of TM6. This dramatically reduces the affinity between \u03bcOR and \u03b2-arrestin2.", "doi": "10.1073/pnas.1918264117", "pmcid": "PMC7368253", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-07-14", "series_number": "28", "volume": "117", "issue": "28", "pages": "16346-16355" }, { "id": "authors:08xff-wpz69", "collection": "authors", "collection_id": "08xff-wpz69", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201009-133620451", "type": "article", "title": "Extracellular interaction between Neurotrophic factor-\u03b11 and HTR1E serotonin receptor promotes cell survival", "author": [ { "family_name": "Sharma", "given_name": "Vinay Kumar", "clpid": "Sharma-V-K" }, { "family_name": "Xuyu", "given_name": "Yang", "clpid": "Xuyu-Yang" }, { "family_name": "Sanchez", "given_name": "Daniel-Saiz", "clpid": "Sanchez-D-S" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Loh", "given_name": "Y. Peng", "clpid": "Loh-Y-Peng" } ], "abstract": "Neurotrophic factor \u03b11 (NF\u03b11), classically known as carboxypeptidase E (CPE) has a non\u2010enzymatic role in the survival of neurons and cancer cells via binding to a putative receptor. We have identified 5\u2010Hydroxy tryptamine receptor 1E (HTR1E), a serotonin receptor with unknown function, as a binding partner that interacts with NF\u03b11/CPE extracellularly to mediate cell survival. Co\u2010immunoprecipitation using a human LN18 cells and pull\u2010down assay with NF\u03b11/CPE and HTR1E expressed in HEK293 cells confirmed interaction of these two molecules. \u00b9\u00b2\u2075I NF\u03b11/CPE binding studies demonstrated saturable, high affinity binding to HTR1E. Molecular docking studies revealed the surface interaction between NFa1/CPE and HTR1E via 3 salt bridges, further stabilized by hydrogen bonding. We also found that HTR1E was able to activate ERK/CREB signaling upon treatment with NF\u03b11/CPE. Pretreatment of HTR1E stable cells with NF\u03b11/CPE followed by H\u2082O\u2082\u2010induced oxidative stress prevented a decrease in pro\u2010survival protein BCL2 and reduced cytotoxicity. SiRNA knock\u2010down of HTR1E in U118 glioblastoma cells resulted in significant inhibition of these cancer cells survival. Immunocytochemical analysis of human hippocampus indicated co\u2010expression of HTR1E with NF\u03b11/CPE in CA1\u20103 and dentate gyrus, and cellular co\u2010localization at the cell membrane in CA3 neurons. This study has uncovered a novel role for HTR1E as a binding partner for NF\u03b11/CPE, and their interaction activates the ERK\u2010CREB\u2010BCL2 pathway to promote cell survival.", "doi": "10.1096/fasebj.2020.34.s1.01952", "issn": "0892-6638", "publisher": "Federation of American Societies for Experimental Biology", "publication": "FASEB Journal", "publication_date": "2020-04", "series_number": "S1", "volume": "34", "issue": "S1", "pages": "1-1" }, { "id": "authors:dhfb3-51c90", "collection": "authors", "collection_id": "dhfb3-51c90", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200304-085059535", "type": "article", "title": "The atomistic level structure for the activated human \u03ba-opioid receptor bound to the full Gi protein and the MP1104 agonist", "author": [ { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-A" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The kappa opioid receptor (\u03baOR) is an important target for pain therapeutics to reduce depression and other harmful side effects of existing medications. The analgesic activity is mediated by \u03baOR signaling through the adenylyl cyclase-inhibitory family of Gi protein. Here, we report the three-dimensional (3D) structure for the active state of human \u03baOR complexed with both heterotrimeric Gi protein and MP1104 agonist. This structure resulted from long molecular dynamics (MD) and metadynamics (metaMD) simulations starting from the 3.1-\u00c5 X-ray structure of \u03baOR\u2013MP1104 after replacing the nanobody with the activated Gi protein and from the 3.5-\u00c5 cryo-EM structure of \u03bcOR\u2013Gi complex after replacing the 168 missing residues. Using MD and metaMD we discovered interactions to the Gi protein with strong anchors to two intracellular loops and transmembrane helix 6 of the \u03baOR. These anchors strengthen the binding, contributing to a contraction in the binding pocket but an expansion in the cytoplasmic region of \u03baOR to accommodate G protein. These remarkable changes in \u03baOR structure reveal that the anchors are essential for activation.", "doi": "10.1073/pnas.1910006117", "pmcid": "PMC7084096", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2020-03-17", "series_number": "11", "volume": "117", "issue": "11", "pages": "5836-5843" }, { "id": "authors:87dym-vvh60", "collection": "authors", "collection_id": "87dym-vvh60", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190731-131005491", "type": "article", "title": "Discovery of Novel Biased Opioid Receptor Ligands through Structure-Based Pharmacophore Virtual Screening and Experiment", "author": [ { "family_name": "Jeong", "given_name": "Pyeonghwa", "clpid": "Jeong-Pyeonghwa" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Li", "given_name": "Quanjie", "clpid": "Li-Quanjie" }, { "family_name": "Oh", "given_name": "Su-jin", "clpid": "Oh-Su-jin" }, { "family_name": "Son", "given_name": "Seonil", "clpid": "Son-Seonil" }, { "family_name": "Chen", "given_name": "Guangju", "clpid": "Chen-Guangju" }, { "family_name": "Tan", "given_name": "Hongwei", "clpid": "Tan-Hongwei" }, { "family_name": "Kim", "given_name": "Siwon", "clpid": "Kim-Siwon" }, { "family_name": "Park", "given_name": "Jong-Hyun", "clpid": "Park-Jong-Hyun" }, { "family_name": "Park", "given_name": "Ki Duk", "clpid": "Park-Ki-Duk" }, { "family_name": "Kim", "given_name": "Yeo Ok", "clpid": "Kim-Yeo-Ok" }, { "family_name": "Yoon", "given_name": "Myung Ha", "clpid": "Yoon-Myung-Ha" }, { "family_name": "Kim", "given_name": "Yong-Chul", "clpid": "Kim-Yong-Chul" }, { "family_name": "Goddard", "given_name": "William, III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "G_i\u2010protein biased agonists with minimal \u03b2\u2010arrestin recruitment have shown opportunities for alternative safe pain treatment to overcome the serious adverse effects of human mu opioid receptor (\u03bc\u2010OR) agonists. In order to discover novel non\u2010morphine OR agonists, we applied hierarchical virtual screening of our in\u2010house database against a pharmacophore based on modeling the active conformation of ORs.We discovered Initial hit compound (4), a novel \u03bc\u2010OR agonist with pyrazoloisoquinoline scaffold. We applied computational R\u2010group screening to compound 4 and synthesized 14 derivatives predicted to be best. Of these, the new Gi\u2010protein biased compound (19) shows EC50 = 179 nM at \u03bc\u2010OR. This resulting in significant pain\u2010relief effects for mice at the phase II period in formalin tests. This study provides a new strategy to identify diverse sets of promising compounds that might prove useful for drug developments targeting other G protein\u2010coupled receptors (GPCRs).", "doi": "10.1002/cmdc.201900418", "issn": "1860-7179", "publisher": "Wiley-Blackwell", "publication": "ChemMedChem", "publication_date": "2019-10-17", "series_number": "20", "volume": "14", "issue": "20", "pages": "1783-1794" }, { "id": "authors:35dbv-tmq77", "collection": "authors", "collection_id": "35dbv-tmq77", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171222-091716111", "type": "article", "title": "The Predicted 3D Structure of Human DP Prostaglandin G Protein-Coupled Receptor Bound to CPI Antagonist", "author": [ { "family_name": "Shankar", "given_name": "Vishnu", "clpid": "Shankar-V" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" } ], "abstract": "Prostaglandins play a critical physiological role in both cardiovascular and immune systems, acting through their interactions with 9 prostanoid G protein-coupled receptors (GPCRs). These receptors are important therapeutic targets for a variety of diseases including arthritis, allergies, type 2 diabetes, and cancer. The DP prostaglandin receptor is of interest because it has unique structural and physiological properties. Most notably, DP does not have the 3\u20136 ionic lock common to Class A GPCRs. However, the lack of X-ray structures for any of the 9 prostaglandin GPCRs hampers the application of structure-based drug design methods to develop more selective and active medications to specific receptors. We predict here 3D structures for the DP prostaglandin GPCR, based on the GEnSeMBLE complete sampling with hierarchical scoring (CS-HS) methodology. This involves evaluating the energy of 13 trillion packings to finally select the best 20 that are stable enough to be relevant for binding to antagonists, agonists, and modulators. To validate the predicted structures, we predict the binding site for the Merck cyclopentanoindole (CPI) selective antagonist docked to DP. We find that the CPI binds vertically in the 1\u20132\u20137 binding pocket, interacting favorably with residues R310^(7.40) and K76^(2.54) with additional interactions with S313^(7.43), S316^(7.46), S19^(1.35), etc. This binding site differs significantly from that of antagonists to known Class A GPCRs where the ligand binds in the 3\u20134\u20135\u20136 region. We find that the predicted binding site leads to reasonable agreement with experimental Structure\u2013Activity Relationship (SAR). We suggest additional mutation experiments including K76^(2.54), E129^(3.49), L123^(3.43), M270^(6.40), F274^(6.44) to further validate the structure, function, and activation mechanism of receptors in the prostaglandin family. Our structures and binding sites are largely consistent and improve upon the predictions by Li et al. ( J. Am. Chem. Soc. 2007, 129 (35), 10720) that used our earlier MembStruk prediction methodology.", "doi": "10.1021/acs.jctc.7b00842", "issn": "1549-9618", "publisher": "American Chemical Society", "publication": "Journal of Chemical Theory and Computation", "publication_date": "2018-03-13", "series_number": "3", "volume": "14", "issue": "3", "pages": "1624-1642" }, { "id": "authors:2rmxb-8cs16", "collection": "authors", "collection_id": "2rmxb-8cs16", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170223-110325516", "type": "article", "title": "Activation mechanism of the G protein-coupled sweet receptor heterodimer with sweeteners and allosteric agonists", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Chen", "given_name": "Yalu", "orcid": "0000-0002-0589-845X", "clpid": "Chen-Yalu" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-Ravinder" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Guthrie", "given_name": "Brian", "orcid": "0000-0002-3508-4625", "clpid": "Guthrie-Brian" } ], "abstract": "The sweet taste in humans is mediated by the TAS1R2/TAS1R3 G protein-coupled receptor (GPCR), which belongs to the class C family that also includes the metabotropic glutamate and \u03b3-aminobutyric acid receptors. We report here the predicted 3D structure of the full-length TAS1R2/TAS1R3 heterodimer, including the Venus Flytrap Domains (VFDs) [in the closed\u2013open (co) active conformation], the cysteine-rich domains (CRDs), and the transmembrane domains (TMDs) at the TM56/TM56 interface. We observe that binding of agonists to VFD2 of TAS1R2 leads to major conformational changes to form a TM6/TM6 interface between TMDs of TAS1R2 and TAS1R3, which is consistent with the activation process observed biophysically on the metabotropic glutamate receptor 2 homodimer. We find that the initial effect of the agonist is to pull the bottom part of VFD3/TAS1R3 toward the bottom part of VFD2/TAS1R2 by \u223c6 \u00c5 and that these changes get transmitted from VFD2 of TAS1R2 (where agonists bind) through the VFD3 and the CRD3 to the TMD3 of TAS1R3 (which couples to the G protein). These structural transformations provide a detailed atomistic mechanism for the activation process in GPCR, providing insights and structural details that can now be validated through mutation experiments.", "doi": "10.1073/pnas.1700001114", "pmcid": "PMC5347580", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2017-03-07", "series_number": "10", "volume": "114", "issue": "10", "pages": "2568-2573" }, { "id": "authors:rfyjc-b9w89", "collection": "authors", "collection_id": "rfyjc-b9w89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160526-095348614", "type": "article", "title": "Antifreeze proteins govern the precipitation of trehalose in a freezing-avoiding insect at low temperature", "author": [ { "family_name": "Wen", "given_name": "Xin", "orcid": "0000-0002-2465-7870", "clpid": "Wen-Xin" }, { "family_name": "Wang", "given_name": "Sen", "clpid": "Wang-Sen" }, { "family_name": "Duman", "given_name": "John G.", "clpid": "Duman-John-G" }, { "family_name": "Arifin", "given_name": "Josh Fnu", "clpid": "Arifin-Josh-Fnu" }, { "family_name": "Juwita", "given_name": "Vonny", "clpid": "Juwita-Vonny" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Rios", "given_name": "Alejandra", "orcid": "0000-0003-4881-5324", "clpid": "Rios-Alejandra" }, { "family_name": "Liu", "given_name": "Fan", "orcid": "0000-0001-5650-2809", "clpid": "Liu-Fan" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-Ravinder" }, { "family_name": "DeVries", "given_name": "Arthur L.", "clpid": "DeVries-Athrur-L" }, { "family_name": "Henling", "given_name": "Lawrence M.", "clpid": "Henling-Lawrence-M" } ], "abstract": "The remarkable adaptive strategies of insects to extreme environments are linked to the biochemical compounds in their body fluids. Trehalose, a versatile sugar molecule, can accumulate to high levels in freeze-tolerant and freeze-avoiding insects, functioning as a cryoprotectant and a supercooling agent. Antifreeze proteins (AFPs), known to protect organisms from freezing by lowering the freezing temperature and deferring the growth of ice, are present at high levels in some freeze-avoiding insects in winter, and yet, paradoxically are found in some freeze-tolerant insects. Here, we report a previously unidentified role for AFPs in effectively inhibiting trehalose precipitation in the hemolymph (or blood) of overwintering beetle larvae. We determine the trehalose level (29.6 \u00b1 0.6 mg/mL) in the larval hemolymph of a beetle, Dendroides canadensis, and demonstrate that the hemolymph AFPs are crucial for inhibiting trehalose crystallization, whereas the presence of trehalose also enhances the antifreeze activity of AFPs. To dissect the molecular mechanism, we examine the molecular recognition between AFP and trehalose crystal interfaces using molecular dynamics simulations. The theory corroborates the experiments and shows preferential strong binding of the AFP to the fast growing surfaces of the sugar crystal. This newly uncovered role for AFPs may help explain the long-speculated role of AFPs in freeze-tolerant species. We propose that the presence of high levels of molecules important for survival but prone to precipitation in poikilotherms (their body temperature can vary considerably) needs a companion mechanism to prevent the precipitation and here present, to our knowledge, the first example. Such a combination of trehalose and AFPs also provides a novel approach for cold protection and for trehalose crystallization inhibition in industrial applications.", "doi": "10.1073/pnas.1601519113", "pmcid": "PMC4914155", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences of the United States of America", "publication_date": "2016-06-14", "series_number": "24", "volume": "113", "issue": "24", "pages": "6683-6688" }, { "id": "authors:q2ss7-3zb55", "collection": "authors", "collection_id": "q2ss7-3zb55", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20160412-130650913", "type": "article", "title": "Homology modeling and molecular docking studies of Drosophila and Aedes sex peptide receptors", "author": [ { "family_name": "Kim", "given_name": "Jeong-hyun", "clpid": "Kim-Jeong-hyun" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Lee", "given_name": "Jae-Hyuk", "clpid": "Lee-Jae-Hyuk" }, { "family_name": "Kim", "given_name": "Young-Joon", "clpid": "Kim-Young-Joon" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kim", "given_name": "Yong-Chul", "clpid": "Kim-Yong-Chul" } ], "abstract": "The Drosophila melanogaster sex peptide receptor (DrmSPR), which is a G protein-coupled receptor (GPCR), is known as the specific receptor for sex peptide (SP). It is responsible for the reproductive behavior in the Drosophila model system; in particular, it is involved in the post-mating responses such as the increase in egg-laying ability and decrease in receptivity in females. In a previous study, we discovered a small molecule agonist of DrmSPR for the first time, which could not, however, activate Aedes aegypti SPR (AedesSPR). To investigate the binding mechanism of the small molecule agonist of DrmSPR, the ensemble structures of low-lying packing structures of DrmSPR and AedesSPR were assembled using the GEnSeMBLE (GPCR Ensemble of Structures in Membrane BiLayer Environment) method. The generated homology models exhibited the typical pattern of inter-helical interactions of the class A GPCRs. The docking experiments of the small molecule agonist suggest that Tyr^(5.35) and Phe^(2.67) residues may be involved in a hydrophobic interaction and that Ser^(3.25) forms a hydrogen bond with the agonist. Additionally, we found that the docking results were consistent with the experimental data of the reference compounds with variable agonistic activities. Moreover, a potential distinction of the putative binding sites in two GPCR models of DrmSPR and AedesSPR, which was determined in this study, can explain the selective action of the agonist for DrmSPR but not for AedesSPR.", "doi": "10.1016/j.jmgm.2016.03.014", "issn": "1093-3263", "publisher": "Elsevier", "publication": "Journal of Molecular Graphics and Modelling", "publication_date": "2016-05", "volume": "66", "pages": "115-122" }, { "id": "authors:6rhqa-hfp96", "collection": "authors", "collection_id": "6rhqa-hfp96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150615-153012612", "type": "article", "title": "G Protein-Coupled Odorant Receptors: from sequence to structure", "author": [ { "family_name": "de March", "given_name": "Claire", "clpid": "de-March-Claire" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Antonczak", "given_name": "Serge", "clpid": "Antonczak-Serge" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Golebiowski", "given_name": "J\u00e9r\u00f4me", "clpid": "Golebiowski-J\u00e9r\u00f4me" } ], "abstract": "Odorant receptors (ORs) are the largest sub-family within Class-A G Protein-Coupled Receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G-protein recognition.", "doi": "10.1002/pro.2717", "pmcid": "PMC4570547", "issn": "0961-8368", "publisher": "Wiley", "publication": "Protein Science", "publication_date": "2015-09", "series_number": "9", "volume": "24", "issue": "9", "pages": "1543-1548" }, { "id": "authors:tk1ey-7km50", "collection": "authors", "collection_id": "tk1ey-7km50", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150424-110101348", "type": "article", "title": "Predicted Structures for Kappa Opioid G\u2011Protein Coupled Receptor Bound to Selective Agonists", "author": [ { "family_name": "Li", "given_name": "Quanjie", "clpid": "Li-Quanjie" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chen", "given_name": "Guangju", "clpid": "Chen-Guangju" }, { "family_name": "Tan", "given_name": "Hongwei", "clpid": "Tan-Hongwei" } ], "abstract": "Human kappa opioid receptor (\u03ba-OR), a G protein-coupled receptor (GPCR), has been identified as a drug target for treatment of such human disorders as pain perception, neuroendocrine physiology, affective behavior, and cognition. In order to find more selective and active agonists, one would like to do structure based drug design. Indeed, there is an X-ray structure for an antagonist bound to \u03ba-OR, but structures for activated GPCRs are quite different from those for the inactive GPCRs. Here we predict the ensemble of 24 low-energy structures of human kappa opioid receptor (\u03ba-OR), obtained by application of the GEnSeMBLE (GPCR Ensemble of Structures in Membrane Bilayer Environment) complete sampling method, which evaluates 13 trillion combinations of tilt and rotation angles for \u03ba-OR to select the best 24. To validate these structures, we used the DarwinDock complete sampling method to predict the binding sites for five known agonists (ethylketocyclazocine, bremazocine, pentazocine, nalorphine, and morphine) bound to all 24 \u03ba-OR conformations. We find that some agonists bind selectively to receptor conformations that lack the salt bridge between transmembrane domains 3 and 6 as expected for active conformations. These 3D structures for \u03ba-OR provide a structural basis for understanding ligand binding and activation of \u03ba-OR, which should be useful for guiding subtype specific drug design.", "doi": "10.1021/ci500523z", "issn": "1549-9596", "publisher": "American Chemical Society", "publication": "Journal of Chemical Information and Modeling", "publication_date": "2015-03", "series_number": "3", "volume": "55", "issue": "3", "pages": "614-627" }, { "id": "authors:7s2jv-3k376", "collection": "authors", "collection_id": "7s2jv-3k376", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150414-145753489", "type": "article", "title": "Deciphering the odorant binding protein - olfactory receptor interactions", "author": [ { "family_name": "Viano", "given_name": "Marilyne", "clpid": "Viano-M" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William Andrew, III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "de March", "given_name": "Claire", "clpid": "de-March-C" }, { "family_name": "Golebiowski", "given_name": "J\u00e9r\u00f4me", "clpid": "Golebiowski-J" }, { "family_name": "Fiorucci", "given_name": "S\u00e9bastien", "clpid": "Fiorucci-S" } ], "abstract": "Olfactory receptors (OR) belong to the family of GPCR and\nparticipate to the recognition of odorants. Prior to the activation\nof the OR, odorants are disolved in the olfactory mucus\nby odorant binding proteins (OBP). Belonging to the family\nof lipocalins, they are small carrier proteins and are considered\nas non-specific binders. OBP would contribute to the olfaction\nprocess by carrying hydrophobic odorant molecules to the\nOR. Due to the transmembrane nature of these receptors, it\nremains a hard task to obtain their crystal structure. Molecular\nmodeling methods are perfectly suited to provide relevant\nthree-dimensional models of unknown structures to further\ngain insights on the structural features of protein-protein complexes.\nMolecular models of hOR2T4 and rORI7 have been\nbuilt using both ab initio homology modeling approaches.\nTo understand how OBPs release odorants and participate to\nthe modulation of OR activation, state of the art protein-protein\ndocking [4] have been performed to predict OR-OBP complexes\nstructure (Figure 1). We propose models of interactions\nshowing how rOBP3 is connected to the extracellular loop 2\nof hORI7. To decipher the underlying molecular mechanism,\nmolecular dynamics simulations have been carried out to estimate\nthe octanal-rOBP3 free energy of binding. The formation\nof the OBP-OR complex destabilizes the odorant-OBP interactions\nprior to the release of the odorant.", "doi": "10.1093/chemse/bju073", "issn": "0379-864X", "publisher": "Oxford University Press", "publication": "Chemical Senses", "publication_date": "2015-03", "series_number": "3", "volume": "40", "issue": "3", "pages": "242" }, { "id": "authors:efamn-cws52", "collection": "authors", "collection_id": "efamn-cws52", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140925-084238832", "type": "article", "title": "Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Olfactory receptors (ORs) are responsible for mediating the sense of smell; they allow humans to recognize an enormous number of odors but the connection between binding and perception is not known. We predict the ensemble of low energy structures for the human OR1G1 (hOR1G1) and also for six other diverse ORs, using the G protein-coupled receptor Ensemble of Structures in Membrane BiLayer Environment complete sampling method that samples 13 trillion different rotations and tilts using four different templates to predict the 24 structures likely to be important in binding and activation. Our predicted most stable structures of hOR1G1 have a salt-bridge between the conserved D3.49 and K6.30 in the D(E)RY region, that we expect to be associated with an inactive form. The hOR1G1 structure also has specific interaction in transmembrane domains (TMD) 3-6 (E3.39 and H6.40), which is likely an important conformational feature for all hORs because of the ~94 to 98 % conservation among all hOR sequences. Of the five ligands studied (nonanal, 9-decen-1-ol, 1-nonanol, camphor, and n\u2013butanal), we find that the 4 expected to bind lead to similar binding energies with nonanol the strongest.", "doi": "10.1007/s10822-014-9793-4", "issn": "0920-654X", "publisher": "Springer", "publication": "Journal of Computer-Aided Molecular Design", "publication_date": "2014-12", "series_number": "12", "volume": "28", "issue": "12", "pages": "1175-1190" }, { "id": "authors:bhzt5-ccm72", "collection": "authors", "collection_id": "bhzt5-ccm72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150324-151114866", "type": "article", "title": "Probing the binding of antifreeze proteins to trehalose crystals", "author": [ { "family_name": "Rios", "given_name": "Alejandra", "clpid": "Rios-A" }, { "family_name": "Liu", "given_name": "Fan", "clpid": "Liu-Fan" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Wen", "given_name": "Xin", "clpid": "Wen-Xin" } ], "abstract": "Antifreeze Proteins (AFPs) refers to a class of polypeptides that allow cold-adapted organisms, such as fish\nand insects, to survive in subzero environments, by lowering the f.p. of water without affecting the m.p. This\nproject focuses on finding the binding modes of AFPs, particularly of DAFP-1 an AFP from the beetle\nDendroides canadensis, with trehalose. The binding process of this system can give a better understanding\nof the physiol. process on how theses organisms can survive at temps. below zero. It has been exptl. obsd.\nthat a trehalose dihydrate crystal has a more favorable crystal growth rate on the (-110) plane and a least\nfavorable rate on the (0-11) planeand it has been demonstrated that trehalose dihydrate f.p. changes\ndrastically in the presence of DAFP-1. Using bio software programs and mol. dynamics simulation we compare\nand contrast the interaction between DAFP-1 with (-110) and (0-11) planes of the trehalose dehydrate crystal.\nIt is of great interests to reveal the details of how do AFPs recognize the ligands and control the crystal growth\nof the substances. In addn., AFP binding conformations may yield a better understanding of the function of\nthese remarkable proteins. Crystal growth control is essential in many scientific fields including chem.,\nmaterials science, and pharmaceutical development. These recent findings greatly expanded the mol.\nrecognition repertoire of AFPs, from ice-like crystals to non-ice like crystals.", "issn": "0065-7727", "publisher": "American Chemical Society", "publication": "Abstracts of Papers of the American Chemical Society", "publication_date": "2014-08-10", "volume": "248", "pages": "81-BIOL" }, { "id": "authors:rh0av-2zr23", "collection": "authors", "collection_id": "rh0av-2zr23", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130108-114918088", "type": "article", "title": "How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case", "author": [ { "family_name": "Charlier", "given_name": "Landry", "clpid": "Charlier-Landry" }, { "family_name": "Topin", "given_name": "J\u00e9r\u00e9mie", "orcid": "0000-0003-1470-1206", "clpid": "Topin-J\u00e9r\u00e9mie" }, { "family_name": "Ronin", "given_name": "Catherine", "clpid": "Ronin-Catherine" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Efremov", "given_name": "Roman", "orcid": "0000-0002-5474-4721", "clpid": "Efremov-Roman" }, { "family_name": "Golebiowski", "given_name": "J\u00e9r\u00f4me", "orcid": "0000-0002-3675-1952", "clpid": "Golebowski-J\u00e9r\u00f4me" } ], "abstract": "The molecular features that dominate the binding mode of agonists by a broadly tuned olfactory receptor are analyzed through a joint approach combining cell biology, calcium imaging, and molecular modeling. The odorant/receptor affinities, estimated through statistics accrued during molecular dynamics simulations, are in accordance with the experimental ranking. Although in many systems receptors recognize their target through a network of oriented interactions, such as H-bonding, the binding by broadly tuned olfactory receptors is dominated by non-polar terms. We show how such a feature allows chemicals belonging to different chemical families to similarly activate the receptors through compensations of interactions within the binding site.", "doi": "10.1007/s00018-012-1116-0", "pmcid": "PMC11115053", "issn": "1420-682X", "publisher": "Springer", "publication": "Cellular and Molecular Life Sciences", "publication_date": "2012-12", "series_number": "24", "volume": "69", "issue": "24", "pages": "4205-4213" }, { "id": "authors:k3x2v-jrv21", "collection": "authors", "collection_id": "k3x2v-jrv21", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120123-110139308", "type": "article", "title": "Structure-Based Prediction of Subtype Selectivity of Histamine H_3 Receptor Selective Antagonists in Clinical Trials", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Fristrup", "given_name": "Peter", "clpid": "Fristrup-P" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Histamine receptors (HRs) are excellent drug targets for the treatment of diseases, such as schizophrenia, psychosis, depression, migraine, allergies, asthma, ulcers, and hypertension. Among them, the human H_3 histamine receptor (hH3HR) antagonists have been proposed for specific therapeutic applications, including treatment of Alzheimer's disease, attention deficit hyperactivity disorder (ADHD), epilepsy, and obesity. However, many of these drug candidates cause undesired side effects through the cross-reactivity with other histamine receptor subtypes. In order to develop improved selectivity and activity for such treatments, it would be useful to have the three-dimensional structures for all four HRs. We report here the predicted structures of four HR subtypes (H_1, H_2, H_3, and H_4) using the GEnSeMBLE (GPCR ensemble of structures in membrane bilayer environment) Monte Carlo protocol, sampling ~35 million combinations of helix packings to predict the 10 most stable packings for each of the four subtypes. Then we used these 10 best protein structures with the DarwinDock Monte Carlo protocol to sample ~50\u2009000 \u00d7 10^(20) poses to predict the optimum ligand\u2013protein structures for various agonists and antagonists. We find that E206^(5.46) contributes most in binding H3 selective agonists in agreement with experimental mutation studies. We also find that conserved E5.46/S5.43 in both of hH_(3)HR and hH_(4)HR are involved in H_(3)/ H_(4) subtype selectivity. In addition, we find that M378^(6.55) in hH_(3)HR provides additional hydrophobic interactions different from hH_(4)HR (the corresponding amino acid of T323^(6.55) in hH_(4)HR) to provide additional subtype bias. From these studies, we developed a pharmacophore model based on our predictions for known hH_(3)HR selective antagonists in clinical study [ABT-239 1, GSK-189,254 2, PF-3654746 3, and BF2.649 (tiprolisant) 4] that suggests critical selectivity directing elements are: the basic proton interacting with D114^(3.32), the spacer, the aromatic ring substituted with the hydrophilic or lipophilic groups interacting with lipophilic pockets in transmembranes (TMs) 3\u20135\u20136 and the aliphatic ring located in TMs 2\u20133\u20137. These 3D structures for all four HRs should help guide the rational design of novel drugs for the subtype selective antagonists and agonists with reduced side effects.", "doi": "10.1021/ci200435b", "pmcid": "PMC3246544", "issn": "1549-9596", "publisher": "American Chemical Society", "publication": "Journal of Chemical Information and Modeling", "publication_date": "2011-12", "series_number": "12", "volume": "51", "issue": "12", "pages": "3262-3274" }, { "id": "authors:et98x-q6g59", "collection": "authors", "collection_id": "et98x-q6g59", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120227-133905808", "type": "article", "title": "Characterizing and predicting the functional and conformational diversity of seven-transmembrane proteins", "author": [ { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Bray", "given_name": "Jenelle K.", "clpid": "Bray-J-K" }, { "family_name": "Griffith", "given_name": "Adam R.", "clpid": "Griffith-A-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "The activation of seven-transmembrane receptors (7TMRs) allows cells to sense their environment and convert extracellular signals (like hormone binding) into intracellular signals (through G protein-coupled and/or \u03b2 arrestin-coupled pathways). A single 7TMR is capable of transducing a wide spectrum of physiological responses inside a cell by coupling to these pathways. This intracellular pleiotropic action is enabled by multiple conformations exhibited by these receptors. Developments in membrane protein structure determination technologies have led to a rapid increase in crystal structures for many 7TMRs. Majority of these receptors have been crystallized in their inactive conformation and, for some, one of the many active conformations has also been crystallized. Given the topological constraints of a lipid bilayer that results in a single fold of seven almost parallel TM helices connected by mostly unstructured loops, these structures exhibit a diversity of conformations not only across the receptors but also across the different functional forms for receptors with structures for one of the functionally active conformations. Here we present a method to characterize this conformational diversity in terms of transmembrane helix topology (TMHTOP) parameters and how to use these helix orientation parameters to predict functionally-distinct multiple conformations for these receptors. The TMHTOP parameters enable a quantification of the structural changes that underlie 7TMR activation and also sheds a unique mechanistic light on the pleiotropic nature of these receptors. It provides a common language to describe the 7TMR activation mechanisms as well as differences across many receptors in terms of visually intuitive structural parameters. Protein structure prediction methods can use these parameters to describe 7TMR conformational ensembles, which coupled to experimental data can be used to develop testable hypotheses for the structural basis of 7TMR functions.", "doi": "10.1016/j.ymeth.2011.12.005", "pmcid": "PMC3286597", "issn": "1046-2023", "publisher": "Elsevier", "publication": "Methods", "publication_date": "2011-12", "series_number": "4", "volume": "55", "issue": "4", "pages": "405-414" }, { "id": "authors:y19cf-jq102", "collection": "authors", "collection_id": "y19cf-jq102", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110601-091219051", "type": "article", "title": "Predicted structures of agonist and antagonist bound complexes of adenosine A_3 receptor", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Riley", "given_name": "Lindsay", "clpid": "Riley-L" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Jacobson", "given_name": "Kenneth A.", "clpid": "Jacobson-K-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "We used the GEnSeMBLE Monte Carlo method to predict ensemble of the 20 best packings (helix rotations and tilts) based on the neutral total energy (E) from a vast number (10 trillion) of potential packings for each of the four subtypes of the adenosine G protein-coupled receptors (GPCRs), which are involved in many cytoprotective functions. We then used the DarwinDock Monte Carlo methods to predict the binding pose for the human A_3 adenosine receptor (hAA_3R) for subtype selective agonists and antagonists. We found that all four A_3 agonists stabilize the 15th lowest conformation of apo-hAA_3R while also binding strongly to the 1st and 3rd. In contrast the four A_3 antagonists stabilize the 2nd or 3rd lowest conformation. These results show that different ligands can stabilize different GPCR conformations, which will likely affect function, complicating the design of functionally unique ligands. Interestingly all agonists lead to a trans \u03c71 angle for W6.48 that experiments on other GPCRs associate with G-protein activation while all 20 apo-AA_3R conformations have a W6.48 gauche+ \u03c71 angle associated experimentally with inactive GPCRs for other systems. Thus docking calculations have identified critical ligand-GPCR structures involved with activation. We found that the predicted binding site for selective agonist Cl-IB-MECA to the predicted structure of hAA_3R shows favorable interactions to three subtype variable residues, I253^(6.58), V169^(EL2), and Q167^(EL2), while the predicted structure for hAA_(2A)R shows weakened to the corresponding amino acids: T256^(6.58), E169^(EL2), and L167^(EL2), explaining the observed subtype selectivity.", "doi": "10.1002/prot.23012", "pmcid": "PMC3092833", "issn": "0887-3585", "publisher": "Wiley", "publication": "Proteins", "publication_date": "2011-06", "series_number": "6", "volume": "79", "issue": "6", "pages": "1878-1897" }, { "id": "authors:fjytv-10a80", "collection": "authors", "collection_id": "fjytv-10a80", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110329-102438454", "type": "article", "title": "Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Li", "given_name": "Youyong", "orcid": "0000-0002-5248-2756", "clpid": "Li-Youyong" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Heo", "given_name": "Jiyoung", "clpid": "Heo-Jiyoung" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception,\n depression, migraines, hypertension, anxiety, hallucinogens, and\n gastrointestinal dysfunctions.' We report here the predicted structure\n of 5-HT2B and 5-HT2C receptors bound to highly potent and selective\n 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding\n residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)]\n determining the selectivity of binding to 5-HT2B over 5-HT2A. We also\n report structures of the endogenous agonist (5 HT) and a HT2B selective\n antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo\n [2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine\n the dynamics for the agonist-and antagonist-bound HT2B receptors in\n explicit membrane and water finding dramatically different patterns of\n water migration into the NPxxY motif and the binding site that\n correlates with the stability of ionic locks in the D(E)RY region.", "doi": "10.1021/ci100375b", "pmcid": "PMC3070210", "issn": "1549-9596", "publisher": "American Chemical Society", "publication": "Journal of Chemical Information and Modeling", "publication_date": "2011-02", "series_number": "2", "volume": "51", "issue": "2", "pages": "420-433" }, { "id": "authors:tkxtf-khb86", "collection": "authors", "collection_id": "tkxtf-khb86", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101026-081332237", "type": "article", "title": "Prediction of the Three-Dimensional Structure for the Rat Urotensin\u2005II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic Simulations", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Li", "given_name": "Youyong", "orcid": "0000-0002-5248-2756", "clpid": "Li-Youyong" }, { "family_name": "Park", "given_name": "Changmoon", "clpid": "Park-Changmoon" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "abstract": "Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known. Thus, a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders. However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in preclinical animal disease models. ACT058362 is a selective antagonist for the human U-II receptor (hUT2R) with a reported K_d value of \u223c4 nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with a K_d value of \u223c1\u2009500 nM. In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (K_d=\u223c9 nM) and rUT2R (K_d=\u223c21 nM). To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 in both hUT2R and rUT2R to explain the dramatically lower (\u223c400-fold) affinity of ACT058362 for rUT2R and the similar affinity (\u223c10 nM) of SB706375 for both UT2Rs. These studies used MembStruk and MSCDock to predict the UT2R structure and the binding site of ACT058362 and SB706375. Based on binding energies, we found two binding modes each with D130^(3.32) as the crucial anchoring point (Ballesteros\u2013Weinstein numbering given in superscript). We predict that ACT058362 (an aryl\u2013amine\u2013aryl or ANA ligand) binds in the transmembrane (TM) 3456 region, while SB706375 (an aryl\u2013aryl\u2013amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding of the ANA ligand to rat and human receptors, while explaining the similar binding of the AAN compound to rat and human receptors. Moreover the predictions explain currently available structure\u2013activity relationship (SAR) data. To further validate the predicted binding sites of these ligands in hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses between UT2R of different species, potentially indicating novel UT2R antagonists with cross-species high affinity.", "doi": "10.1002/cmdc.201000175", "pmcid": "PMC3517062", "issn": "1860-7179", "publisher": "Wiley-Blackwell", "publication": "ChemMedChem", "publication_date": "2010-09-03", "series_number": "9", "volume": "5", "issue": "9", "pages": "1594-1608" }, { "id": "authors:02w9z-f8d89", "collection": "authors", "collection_id": "02w9z-f8d89", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100407-143528745", "type": "article", "title": "Predicted 3D structures for adenosine receptors bound to ligands: Comparison to the crystal structure", "author": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Li", "given_name": "Youyong", "orcid": "0000-0002-5248-2756", "clpid": "Li-Youyong" }, { "family_name": "Trzaskowski", "given_name": "Bartosz", "clpid": "Trzaskowski-B" }, { "family_name": "Griffith", "given_name": "Adam R.", "clpid": "Griffith-A-R" }, { "family_name": "Abrol", "given_name": "Ravinder", "orcid": "0000-0001-7333-6793", "clpid": "Abrol-R" } ], "abstract": "G protein-coupled receptors (GPCRs) are therapeutic targets for many diseases, but progress in developing active and selective therapeutics has been severely hampered by the difficulty in obtaining accurate structures. We have been developing methods for predicting the structures for GPCR ligand complexes, but validation has been hampered by a lack of experimental structures with which to compare our predictions. We report here the predicted structures of the human adenosine GPCR subtypes (A_1, A_(2A), A_(2B), and A_3) and the binding sites for adenosine agonist and eight antagonists to this predicted structure, making no use of structural data, and compare with recent experimental crystal structure for ZM241385 bound human A_(2A) receptor. The predicted structure correctly identifies 9 of the 12 crystal binding site residues. Moreover, the predicted binding energies of eight antagonists to the predicted structure of A_(2A) correlate quite well with experiment. These excellent predictions resulted when we used Monte Carlo techniques to optimize the loop structures, particularly the cysteine linkages. Ignoring these linkages led to a much worse predicted binding site (identifying only 3 of the 12 important residues).\nThese results indicate that computational methods can predict the three-dimensional structure of GPCR membrane proteins sufficiently accurately for use in designing subtype selective ligands for important GPCR therapeutics targets.", "doi": "10.1016/j.jsb.2010.01.001", "issn": "1047-8477", "publisher": "Elsevier", "publication": "Journal of Structural Biology", "publication_date": "2010-04", "series_number": "1", "volume": "170", "issue": "1", "pages": "10-20" }, { "id": "authors:fbh1t-egc62", "collection": "authors", "collection_id": "fbh1t-egc62", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20090922-131933657", "type": "article", "title": "A spatially resolved study of photoelectric heating and [C II] cooling in the LMC", "author": [ { "family_name": "Rubin", "given_name": "D.", "clpid": "Rubin-D-M" }, { "family_name": "Hony", "given_name": "S.", "clpid": "Hony-S" }, { "family_name": "Madden", "given_name": "S. C.", "clpid": "Madden-S-C" }, { "family_name": "Tielens", "given_name": "A. G. G. M.", "clpid": "Tielens-A-G-G-M" }, { "family_name": "Meixner", "given_name": "M.", "clpid": "Meixner-M" }, { "family_name": "Indebetouw", "given_name": "R.", "clpid": "Indebetouw-R" }, { "family_name": "Reach", "given_name": "W.", "orcid": "0000-0001-8362-4094", "clpid": "Reach-W-T" }, { "family_name": "Ginsburg", "given_name": "A.", "orcid": "0000-0001-6431-9633", "clpid": "Ginsburg-A" }, { "family_name": "Kim", "given_name": "S.", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Mochizuki", "given_name": "K.", "clpid": "Mochizuki-K" }, { "family_name": "Babler", "given_name": "B.", "clpid": "Babler-B-L" }, { "family_name": "Block", "given_name": "M.", "clpid": "Block-M" }, { "family_name": "Bracker", "given_name": "S. B.", "clpid": "Bracker-S-B" }, { "family_name": "Engelbracht", "given_name": "C. W.", "clpid": "Engelbracht-C-W" }, { "family_name": "For", "given_name": "B.-Q.", "clpid": "For-Bi-Qing" }, { "family_name": "Gordon", "given_name": "K.", "clpid": "Gordon-K-D" }, { "family_name": "Hora", "given_name": "J. L.", "orcid": "0000-0002-5599-4650", "clpid": "Hora-J-L" }, { "family_name": "Leitherer", "given_name": "C.", "orcid": "0000-0003-2685-4488", "clpid": "Leitherer-C" }, { "family_name": "Meade", "given_name": "M.", "clpid": "Meade-M-R" }, { "family_name": "Misselt", "given_name": "K.", "clpid": "Misselt-K-A" }, { "family_name": "Sewilo", "given_name": "M.", "orcid": "0000-0003-2248-6032", "clpid": "Sewilo-M" }, { "family_name": "Vijh", "given_name": "U.", "clpid": "Vijh-U-P" }, { "family_name": "Whitney", "given_name": "B.", "clpid": "Whitney-B-A" } ], "abstract": "Context. Photoelectric heating is a dominant heating mechanism for many phases of the interstellar medium. We study this mechanism throughout the Large Magellanic Cloud (LMC).\nAims. We aim to quantify the importance of the [C II] cooling line and the photoelectric heating process of various environments in the LMC and to investigate which parameters control the extent of photoelectric heating.\nMethods. We use the BICE [C II] map and the Spitzer/SAGE infrared maps. We examine the spatial variations in the efficiency of photoelectric heating: photoelectric heating rate over power absorbed by grains, i.e. the observed [C II] line strength over the integrated infrared emission. We correlate the photoelectric heating efficiency and the emission from various dust constituents and study the variations as a function of H emission, dust temperatures, and the total infrared luminosity. The observed variations are interpreted in a theoretical framework. From this we estimate radiation field, gas temperature, and electron density.\nResults. We find systematic variations in photoelectric efficiency. The highest efficiencies are found in the diffuse medium, while the lowest coincide with bright star-forming regions (~1.4 times lower). The [C II] line emission constitutes 1.32% of the far infrared luminosity across the whole of the LMC. We find correlations between the [C II] emission and ratios of the mid infrared and far infrared bands, which comprise various dust constituents. The correlations are interpreted in light of the spatial variations of the dust abundance and by the local environmental conditions that affect the dust emission properties. As a function of the total infrared surface brightness, S_(TIR), the [C II] surface brightness can be described as: S_([C II]) = 1.25 S^(0.69)_(TIR)[10^(-3) erg s^(-1)\u2009cm^(-2)\u2009sr^(-1)], for S_(TIR) \u2273 3.2 x 10^(-4) erg s^(-1)\u2009cm^(-2)\u2009sr^(-1). We provide a simple model of the photoelectric efficiency as a function of the total infrared luminosity. We find a power-law relation between radiation field and electron density, consistent with other studies. The [C II] emission is well-correlated with the 8 \u00b5m emission, suggesting that the polycyclic aromatic hydrocarbons play a dominant role in the photoelectric heating process.", "doi": "10.1051/0004-6361:200810968", "issn": "0004-6361", "publisher": "EDP Sciences", "publication": "Astronomy and Astrophysics", "publication_date": "2009-02", "series_number": "2", "volume": "494", "issue": "2", "pages": "647-661" }, { "id": "authors:jm0h8-7a527", "collection": "authors", "collection_id": "jm0h8-7a527", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170201-111306968", "type": "article", "title": "Three-Dimensional Quantitative Structure\u2212Activity Relationship of Nucleosides Acting at the A_3 Adenosine Receptor: Analysis of Binding and Relative Efficacy", "author": [ { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Jacobson", "given_name": "Kenneth A.", "clpid": "Jacobson-K-A" } ], "abstract": "The binding affinity and relative maximal efficacy of human A_3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure\u2212activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used as training sets a series of 91 structurally diverse adenosine analogues with modifications at the N^6 and C2 positions of the adenine ring and at the 3', 4', and 5' positions of the ribose moiety. The CoMFA and CoMSIA models yielded significant cross-validated q^2 values of 0.53 (r^2 = 0.92) and 0.59 (r^2 = 0.92), respectively, and were further validated by an external test set (25 adenosine derivatives), resulting in the best predictive r^2 values of 0.84 and 0.70 in each model. Both the CoMFA and the CoMSIA maps for steric or hydrophobic, electrostatic, and hydrogen-bonding interactions well reflected the nature of the putative binding site previously obtained by molecular docking. A conformationally restricted bulky group at the N^6 or C2 position of the adenine ring and a hydrophilic and/or H-bonding group at the 5' position were predicted to increase A_3AR binding affinity. A small hydrophobic group at N^6 promotes receptor activation. A hydrophilic and hydrogen-bonding moiety at the 5' position appears to contribute to the receptor activation process, associated with the conformational change of transmembrane domains 5, 6, and 7. The 3D-CoMFA/CoMSIA model correlates well with previous receptor-docking results, current data of A_3AR agonists, and the successful conversion of the A_3AR agonist into antagonists by substitution (at N^6) or conformational constraint (at 5'-N-methyluronamide).", "doi": "10.1021/ci600501z", "issn": "1549-9596", "publisher": "American Chemical Society", "publication": "Journal of Chemical Information and Modeling", "publication_date": "2007-05", "series_number": "3", "volume": "47", "issue": "3", "pages": "1225-1233" }, { "id": "authors:70549-vch46", "collection": "authors", "collection_id": "70549-vch46", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:SCAjbc07", "type": "article", "title": "Multiple Residues in the Second Extracellular Loop Are Critical for M3 Muscarinic Acetylcholine Receptor Activation", "author": [ { "family_name": "Scarselli", "given_name": "Marco", "clpid": "Scarselli-M" }, { "family_name": "Li", "given_name": "Bo", "orcid": "0000-0002-8019-8891", "clpid": "Li-Bo" }, { "family_name": "Kim", "given_name": "Soo-Kyung", "orcid": "0000-0002-4498-5441", "clpid": "Kim-Soo-Kyung" }, { "family_name": "Wess", "given_name": "J\u00fcrgen", "clpid": "Wess-J" } ], "abstract": "Recent studies suggest that the second extracellular loop (o2 loop) of bovine rhodopsin and other class I G protein-coupled receptors (GPCRs) targeted by biogenic amine ligands folds deeply into the transmembrane receptor core where the binding of cis-retinal and biogenic amine ligands is known to occur. In the past, the potential role of the o2 loop in agonist-dependent activation of biogenic amine GPCRs has not been studied systematically. To address this issue, we used the M3 muscarinic acetylcholine receptor (M3R), a prototypic class I GPCR, as a model system. Specifically, we subjected the o2 loop of the M3R to random mutagenesis and subsequently applied a novel yeast genetic screen to identity single amino acid substitutions that interfered with M3R function. This screen led to the recovery of about 20 mutant M3Rs containing single amino acid changes in the o2 loop that were inactive in yeast. In contrast, application of the same strategy to the extracellular N-terminal domain of the M3R did not yield any single point mutations that disrupted M3R function. Pharmacological characterization of many of the recovered mutant M3Rs in mammalian cells, complemented by site-directed mutagenesis studies, indicated that the presence of several o2 loop residues is important for efficient agonist-induced M3R activation. Besides the highly conserved Cys220 residue, Gln207, Gly211, Arg213, Gly218, Ile222, Phe224, Leu225, and Pro228 were found to be of particular functional importance. In general, mutational modification of these residues had little effect on agonist binding affinities. Our findings are therefore consistent with a model in which multiple o2 loop residues are involved in stabilizing the active state of the M3R. Given the high degree of structural homology found among all biogenic amine GPCRs, our findings should be of considerable general relevance.", "doi": "10.1074/jbc.M610394200", "issn": "0021-9258", "publisher": "American Society for Biochemistry and Molecular Biology", "publication": "Journal of Biological Chemistry", "publication_date": "2007-03-09", "series_number": "10", "volume": "282", "issue": "10", "pages": "7385-7396" } ]