[ { "id": "authors:s3eq7-k6m64", "collection": "authors", "collection_id": "s3eq7-k6m64", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170125-144353492", "type": "book_section", "title": "Microfluidic device for super-fast evaluation of membrane protein crystallization", "book_title": "8th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems", "author": [ { "family_name": "Wu", "given_name": "Hsin-Jui", "clpid": "Wu-Hsin-Jui" }, { "family_name": "Basta", "given_name": "Tamara", "clpid": "Basta-T" }, { "family_name": "Morphew", "given_name": "Mary", "clpid": "Morphew-M" }, { "family_name": "Rees", "given_name": "D. C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Stowell", "given_name": "Michael H. B.", "clpid": "Stowell-M-H-B" }, { "family_name": "Lee", "given_name": "Y. C.", "clpid": "Lee-Y-C" } ], "abstract": "Membrane proteins embedded in bi-layer lipids of cell membrane have unique functions including inter-cell communication, ions/molecules transport. And there is more than 50% of drug design emphasizes on membrane proteins specifically studying on their structure and formation. Recently we reported the structural and functional studies of membrane protein lipid nanoparticles in native biological membrane. This virus-like nanoparticle formed by a self-assembly crystallization process of membrane protein and lipids is critical to pharmaceutical industrial. These nanoparticles have a variety of potential applications in drug delivery and drug design that can carry specific the membrane protein on aim or release control. The previous studies stay on an inefficient method with a standard dialysis process that has low-throughput, time consumption, and protein sample waste. However, the interdisciplinary cooperation between in biology and Micro electro mechanical systems (MEMS) has been tremendous developed such as Bio-MEMS and Lab-on-achip technologies. Here we demonstrate a new concept with a high-throughput membraneless microfluidic device to fast produce the reconstitution of membrane protein nanoparticles. The reconstitution process in continuous micro flow dominated by convection-diffusion phenomena in microfluidic channel can be completed in seconds to form protein/lipid particles under multiple conditions applied. The controllable syringe pumps is used to test a combination of conditions rather than using inefficient hand pipette. Moreover this novel microfluidic device can save protein sample consumption down to only nanoliter or picoliter. By using this device, we have an ability to rapidly form uniform membrane protein lipid nanoparticles and we believe this new method will make a transformative impact to commercial applications in variety of areas from biology to pharmacology.", "doi": "10.1109/NEMS.2013.6559687", "isbn": "978-1-4673-6352-5", "publisher": "IEEE", "place_of_publication": "Piscataway, NJ", "publication_date": "2013-04", "pages": "84-87" }, { "id": "authors:59gt9-hc333", "collection": "authors", "collection_id": "59gt9-hc333", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170330-111026101", "type": "book_section", "title": "Nitrogenase", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Schmid", "given_name": "Benedikt", "clpid": "Schmid-B" }, { "family_name": "Chiu", "given_name": "Hsiu-Ju", "clpid": "Chiu-Hsiu-Ju" }, { "family_name": "Ramakrishnan", "given_name": "Vijay", "clpid": "Ramakrishnan-V" }, { "family_name": "Howard", "given_name": "James B.", "clpid": "Howard-J-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Nitrogenase catalyzes the enzymatic reduction of atmospheric dinitrogen to ammonia during the process of biological nitrogen fixation. Nitrogenase consists of two component metalloproteins, the iron (Fe-) protein and the molybdenum-iron (MoFe-) protein, that together mediate the ATP-hydrolysis\u2013dependent reduction of substrates to products. Crystallographic studies have established the structures of the component proteins and the associated complex metallocenters of nitrogenase, including the iron-molybdenum cofactor that provides the active site for substrate reduction and the P-cluster that participates in electron transfer between the Fe-protein and MoFe-protein. Striking parallels are evident in the interaction of the nucleotides with the Fe-protein and with a broad class of nucleotide-binding proteins involved in signal and energy transduction processes. Together with kinetic, spectroscopic, and synthetic model compound studies, these structures provide a framework for addressing the mechanism of substrate reduction by nitrogenase.", "doi": "10.1002/9781119951438.eibc0601", "isbn": "9781119951438", "publisher": "John Wiley and Sons, Inc.", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15", "pages": "Art. No. eibc0601" }, { "id": "authors:5hxc3-nk458", "collection": "authors", "collection_id": "5hxc3-nk458", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170403-152926110", "type": "book_section", "title": "Aldehyde Ferredoxin Oxidoreductase", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Roy", "given_name": "Roopali", "clpid": "Roy-R" }, { "family_name": "Dhawan", "given_name": "Ish K.", "clpid": "Dhawan-I-K" }, { "family_name": "Johnson", "given_name": "Michael K.", "clpid": "Johnson-M-K" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Adams", "given_name": "Michael W. W.", "clpid": "Adams-M-W-W" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Aldehyde ferredoxin oxidoreductase (AOR) is a homodimer where each subunit contains a [4Fe\u20134S] cluster and a mononuclear tungsten atom coordinated by the dithioline groups of two pterin molecules. The two subunits of the dimer are bridged by a monomeric iron site. AOR is a member of a family of five closely related tungstoenzymes found in organisms that grow at high temperatures in marine volcanic vents. The enzyme catalyzes the two-electron oxidation of its aldehyde substrate to the corresponding acid with the concomitant reduction of ferredoxin, its physiological electron acceptor. The enzyme can oxidize a wide range of aliphatic and aromatic aldehydes. The most efficient substrates for AOR are acetaldehyde, isovaleraldehyde, phenylacetaldehyde, and indoleacetaldehyde, the aldehyde derivatives of some of the most common amino acids.", "doi": "10.1002/9781119951438.eibc0607", "isbn": "9781119951438", "publisher": "Wiley", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15" }, { "id": "authors:hanew-fxw25", "collection": "authors", "collection_id": "hanew-fxw25", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170403-151722541", "type": "book_section", "title": "Formaldehyde Ferredoxin Oxidoreductase", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Roy", "given_name": "Roopali", "clpid": "Roy-R" }, { "family_name": "Dhawan", "given_name": "Ish K.", "clpid": "Dhawan-I-K" }, { "family_name": "Johnson", "given_name": "Michael K.", "clpid": "Johnson-M-K" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Adams", "given_name": "Michael W. W.", "clpid": "Adams-M-W-W" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Formaldehyde ferredoxin oxidoreductase (FOR) is a homotetramer where each subunit contains a [4Fe\u20134S] cluster and a mononuclear tungsten atom coordinated by the dithioline groups of two pterin molecules. It is a member of a family of five closely related tungstoenzymes found in organisms that grow at high temperatures in marine volcanic vents. FOR catalyzes the two-electron oxidation of its aldehyde substrate to the corresponding acid with the concomitant reduction of ferredoxin, its physiological electron acceptor. FOR oxidizes short chain C_1-C_4 aldehydes as substrates but has the highest affinity for C_4-C_6 di- and semialdehydes. The enzyme is proposed to have a role in peptide metabolism.", "doi": "10.1002/9781119951438.eibc0606", "isbn": "9781119951438", "publisher": "Wiley", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15" }, { "id": "authors:jvmxy-4z657", "collection": "authors", "collection_id": "jvmxy-4z657", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180424-134640337", "type": "book_section", "title": "Cytochrome c_(554)", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Iverson", "given_name": "Tina M.", "clpid": "Iverson-T-M" }, { "family_name": "Hendrich", "given_name": "Michael P.", "clpid": "Hendrich-M-P" }, { "family_name": "Arciero", "given_name": "David M.", "clpid": "Arciero-D-M" }, { "family_name": "Hooper", "given_name": "Alan B.", "clpid": "Hooper-A-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Cytochrome c_(554) (cyt c_(554)) is a tetra\u2010heme c\u2010type cytochrome that participates in the nitrification pathway of Nitrosomonas europaea. In this process, cyt c_(554) functions as the electron acceptor from the enzyme hydroxylamine oxidoreductase that catalyzes the oxidation of hydroxylamine to nitrite. Cyt c_(554) is a predominantly \u03b1\u2010helical protein with four covalently attached hemes. The four hemes are arranged in two pairs, such that the planes of the porphyrin rings are nearly parallel and overlapping at the edges. This type of heme\u2010stacking has been observed in two other nitrogen cycle proteins: hydroxylamine oxidoreductase and cytochrome c nitrite reductase, an enzyme that catalyzes the reduction of nitrite to ammonia. The relatively unusual spectral properties of cyt c_(554) may reflect interactions between these pairs of stacked hemes.", "doi": "10.1002/9781119951438.eibc0538", "isbn": "9781119951438", "publisher": "Wiley", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15", "pages": "1-12" }, { "id": "authors:rt3k6-nny83", "collection": "authors", "collection_id": "rt3k6-nny83", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180420-155706178", "type": "book_section", "title": "Nitrogenase", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Schmid", "given_name": "Benedikt", "clpid": "Schmid-B" }, { "family_name": "Chiu", "given_name": "Hsiu-Ju", "clpid": "Chiu-Hsiu-Ju" }, { "family_name": "Ramakrishnan", "given_name": "Vijay", "clpid": "Ramakrishnan-V" }, { "family_name": "Howard", "given_name": "James B.", "clpid": "Howard-J-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Nitrogenase catalyzes the enzymatic reduction of atmospheric dinitrogen to ammonia during the process of biological nitrogen fixation. Nitrogenase consists of two component metalloproteins, the iron (Fe\u2010) protein and the molybdenum\u2010iron (MoFe\u2010) protein, that together mediate the ATP\u2010hydrolysis\u2013dependent reduction of substrates to products. Crystallographic studies have established the structures of the component proteins and the associated complex metallocenters of nitrogenase, including the iron\u2010molybdenum cofactor that provides the active site for substrate reduction and the P\u2010cluster that participates in electron transfer between the Fe\u2010protein and MoFe\u2010protein. Striking parallels are evident in the interaction of the nucleotides with the Fe\u2010protein and with a broad class of nucleotide\u2010binding proteins involved in signal and energy transduction processes. Together with kinetic, spectroscopic, and synthetic model compound studies, these structures provide a framework for addressing the mechanism of substrate reduction by nitrogenase.", "doi": "10.1002/9781119951438.eibc0601", "isbn": "9781119951438", "publisher": "Wiley", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15", "pages": "1-12" }, { "id": "authors:sx99r-07g72", "collection": "authors", "collection_id": "sx99r-07g72", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170330-105823002", "type": "book_section", "title": "Cytochrome c_(554)", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Iverson", "given_name": "Tina M.", "clpid": "Iverson-T-M" }, { "family_name": "Hendrich", "given_name": "Michael P.", "clpid": "Hendrich-M-P" }, { "family_name": "Arciero", "given_name": "David M.", "clpid": "Arciero-D-M" }, { "family_name": "Hooper", "given_name": "Alan B.", "clpid": "Hooper-A-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Cytochrome c_(554) (cyt c_(554)) is a tetra-heme c-type cytochrome that participates in the nitrification pathway of Nitrosomonas europaea. In this process, cyt c_(554) functions as the electron acceptor from the enzyme hydroxylamine oxidoreductase that catalyzes the oxidation of hydroxylamine to nitrite. Cyt c_(554) is a predominantly \u03b1-helical protein with four covalently attached hemes. The four hemes are arranged in two pairs, such that the planes of the porphyrin rings are nearly parallel and overlapping at the edges. This type of heme-stacking has been observed in two other nitrogen cycle proteins: hydroxylamine oxidoreductase and cytochrome c nitrite reductase, an enzyme that catalyzes the reduction of nitrite to ammonia. The relatively unusual spectral properties of cyt c_(554) may reflect interactions between these pairs of stacked hemes.", "doi": "10.1002/9781119951438.eibc0538", "isbn": "9781119951438", "publisher": "John Wiley and Sons, Inc.", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15", "pages": "Art. No. eibc0538" }, { "id": "authors:pq0bd-hgj42", "collection": "authors", "collection_id": "pq0bd-hgj42", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180423-113156107", "type": "book_section", "title": "Formaldehyde Ferredoxin Oxidoreductase", "book_title": "Encyclopedia of Inorganic and Bioinorganic Chemistry", "author": [ { "family_name": "Roy", "given_name": "Roopali", "clpid": "Roy-R" }, { "family_name": "Dhawan", "given_name": "Ish K.", "clpid": "Dhawan-I-K" }, { "family_name": "Johnson", "given_name": "Michael K.", "clpid": "Johnson-M-K" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Adams", "given_name": "Michael W. W.", "clpid": "Adams-M-W-W" } ], "contributor": [ { "family_name": "Scott", "given_name": "Robert A.", "clpid": "Scott-R-A" } ], "abstract": "Formaldehyde ferredoxin oxidoreductase (FOR) is a homotetramer where each subunit contains a [4Fe\u20134S] cluster and a mononuclear tungsten atom coordinated by the dithioline groups of two pterin molecules. It is a member of a family of five closely related tungstoenzymes found in organisms that grow at high temperatures in marine volcanic vents. FOR catalyzes the two\u2010electron oxidation of its aldehyde substrate to the corresponding acid with the concomitant reduction of ferredoxin, its physiological electron acceptor. FOR oxidizes short chain C1\u2010C4 aldehydes as substrates but has the highest affinity for C_4\u2010C_6 di\u2010 and semialdehydes. The enzyme is proposed to have a role in peptide metabolism.", "doi": "10.1002/9781119951438.eibc0606", "isbn": "9781119951438", "publisher": "Wiley", "place_of_publication": "Hoboken, NJ", "publication_date": "2011-12-15", "pages": "1-12" }, { "id": "authors:p64mg-2sv87", "collection": "authors", "collection_id": "p64mg-2sv87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141212-144312417", "type": "book_section", "title": "Functional Analysis of Detergent-Solubilized and Membrane-Reconstituted ATP-Binding Cassette Transporters", "book_title": "Phase II Conjugation Enzymes and Transport Systems", "author": [ { "family_name": "Poolman", "given_name": "Bert", "orcid": "0000-0002-1455-531X", "clpid": "Poolman-B" }, { "family_name": "Doeven", "given_name": "Mark K.", "clpid": "Doeven-M-K" }, { "family_name": "Geertsma", "given_name": "Eric R.", "clpid": "Geertsma-E-R" }, { "family_name": "Biemans-Oldehinkel", "given_name": "Esther", "clpid": "Biemans-Oldehinkel-E" }, { "family_name": "Konings", "given_name": "Wil N.", "clpid": "Konings-W-N" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Sies", "given_name": "Helmut", "clpid": "Sies-H" }, { "family_name": "Packer", "given_name": "Lester", "clpid": "Packer-L" } ], "abstract": "ATP-binding cassette (ABC) transporters are vital to any living system and are involved in the translocation of a wide variety of substances, from ions and nutrients to high molecular weight proteins. This chapter describes methods used to purify and membrane reconstitute ABC transporters in a fully functional state. The procedures are largely based on our experience with substrate-binding protein-dependent ABC uptake systems from bacteria, but the approaches should be applicable to multisubunit membrane complexes in general. Also, we present simple methods, based on substrate binding or translocation, to follow the activity of the protein complexes in detergent-solubilized and/or membrane-reconstituted state(s).", "doi": "10.1016/S0076-6879(05)00025-X", "isbn": "978-0-12-182805-9", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "2005", "pages": "429-459" }, { "id": "authors:r4st3-vh249", "collection": "authors", "collection_id": "r4st3-vh249", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141212-145528968", "type": "book_section", "title": "Prokaryotic Mechanosensitive Channels", "book_title": "Membrane Proteins", "author": [ { "family_name": "Strop", "given_name": "Pavel", "clpid": "Strop-Pavel" }, { "family_name": "Bass", "given_name": "Randal", "clpid": "Bass-Randal-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "abstract": "Mechanosensitive ion channels are integral membrane proteins that open and close in response to mechanical stress applied either directly to the cell membrane (in the case of intrinsically mechanosensitive channels) or indirectly, through forces applied to other cytoskeletal components. Cellular phenomena mediated by mechanosensitive channels include touch, hearing, cardiovascular tone, detection of gravity, pressure sensation, pain perception, and osmoregulation. Mechanosensirive channels are quite diverse both physiologically and structurally and have been discovered in all fundamental branches of the phylogenetic tree, Eubacteria, Eukarya, and Archaea. Eukaryotic mechanosensitive channels include the TRPV subclass of the Transient Receptor Potential channel family: the TREK-1 and TRAAK members of the two-pore domain potassium channel family K2p; and the DEG/ENaC superfamily composed of degenerins, eptithelial sodium channels, and acid-sensing channels that have been implicated in the touch response of nematodes. Although many of these channels, including the degenerins and the yet-to-be identified channel receptors involved in hearing, appear to have an obligatory requirement for cytoskeletal coupling, others, such as the TREK-1 and TRAAK channels, exhibit intrisinic mechanosensitive activity.", "doi": "10.1016/S0065-3233(03)63008-1", "isbn": "978-0-12-034263-1", "publisher": "Elsevier", "place_of_publication": "New York, NY", "publication_date": "2003", "pages": "177-209" }, { "id": "authors:n9eg8-6cj84", "collection": "authors", "collection_id": "n9eg8-6cj84", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161206-084656751", "type": "book_section", "title": "Metalloproteins to Membrane Proteins: Biological Energy Transduction Mechanisms", "book_title": "Structures and Mechanisms", "author": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "abstract": "Structural analyses of two macromolecular systems, the metalloprotein nitrogenase and the integral membrane protein MscL (mechanosensitive channel of large conductance), are discussed within the context of energy transduction mechanisms. Nitrogenase catalyzes the ATP dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation, while MscL is a stretch activated (mechanosensitive) channel that opens and closes in response to changes in lateral tension applied to membranes. Although nitrogenase and MscL have very different structures and functions, they both mediate the coupling of two energetic processes. From these studies, it is suggested that effective coupling of two processes by transduction proteins occurs through conformational states common to each process.", "doi": "10.1021/bk-2002-0827.ch013", "isbn": "9780841237360", "publisher": "American Chemical Society", "place_of_publication": "Washington, DC", "publication_date": "2002-08-07", "pages": "202-215" }, { "id": "authors:p4f7e-kg414", "collection": "authors", "collection_id": "p4f7e-kg414", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150108-153028358", "type": "book_section", "title": "Crystallographic Analyses of Hyperthermophilic Proteins", "book_title": "Hyperthermophilic Enzymes, Part C", "author": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Adams", "given_name": "Michael W. W.", "clpid": "Adams-M-W-W" }, { "family_name": "Kelly", "given_name": "Robert M.", "clpid": "Kelly-R-M" } ], "abstract": "Following the first structure determination in 1992 of a protein from a hyperthermophilic\norganism, the rubredoxin from Pyrococcus furiosus, structures of\nhyperthermophilic proteins have appeared at an ever increasing rate, with more\nthan 50 distinct structures having been submitted to the Protein Data Bank as\nof October 1999 (Table I). These structure determinations have been undertaken\nfor many of the reasons discussed elsewhere in this volume-to understand the\nstructural basis of thermostability; to more fully characterize proteins with unusual\ncofactors or active centers; for biotechnological purposes; as homologs of eukaryotic\nproteins, especially those involved in some aspect of macromolecular biosynthesis;\nand as part of structural genomics efforts, because they either do, or do not,\nlook like some other proteins. As there is an expectation that hyperthermostable\nproteins should be more robust and potentially better suited for withstanding the\nsolution conditions and time scales of crystallization experiments, these proteins\nhave provided attractive targets for structural studies. The focus of this chapter\nis to review the status and some general implications of crystallographic studies\non hyperthermophilic proteins, with emphasis on relevant technical aspects of\nthe structure determination, quality of the crystals, and conclusions about thermal\nstability and other properties of these fascinating proteins.", "doi": "10.1016/S0076-6879(01)34484-1", "isbn": "978-0-12-182235-4", "publisher": "Academic Press", "place_of_publication": "San Diego, CA", "publication_date": "2001", "pages": "423-437" }, { "id": "authors:4kz77-25d78", "collection": "authors", "collection_id": "4kz77-25d78", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180405-140056548", "type": "book_section", "title": "Crystal Structures of the Iron Protein and Molybdenum-Iron Protein of Nitrogenase", "author": [ { "family_name": "Rees", "given_name": "D. C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Kim", "given_name": "J.", "clpid": "Kim-J" }, { "family_name": "Georgiadis", "given_name": "M. M.", "clpid": "Georgiadis-M-M" }, { "family_name": "Komiya", "given_name": "H.", "clpid": "Komiya-H" }, { "family_name": "Chirino", "given_name": "A. J.", "clpid": "Chirino-A-J" }, { "family_name": "Woo", "given_name": "D.", "clpid": "Woo-D" }, { "family_name": "Schlessman", "given_name": "J.", "clpid": "Schlessman-J" }, { "family_name": "Chan", "given_name": "M. K.", "clpid": "Chan-M-K" }, { "family_name": "Joshua-Tor", "given_name": "L.", "clpid": "Joshua-Tor-L" }, { "family_name": "Santillan", "given_name": "G.", "clpid": "Santillan-G" }, { "family_name": "Chakrabarti", "given_name": "P.", "clpid": "Chakrabarti-P" }, { "family_name": "Hsu", "given_name": "B. T.", "clpid": "Hsu-B-T" } ], "abstract": "Three-dimensional structures of the nitrogenase iron protein and molybdenum-iron protein from Azotobacter vinelandii have been determined by x-ray crystallography. The iron protein contains a single 4Fe:4S cluster symmetrically liganded by two identical subunits. The molybdenum-iron protein is an \u03b1_2\u03b2_2 tetramer, where the homologous \u03b1 and \u03b2 subunits surround two different types of metal centers: the FeMo-cofactor and the P-cluster pair. Both centers are constructed from two bridged clusters; the FeMo-cofactor has 4Fe:3S and 1Mo:3Fe:3S cluster bridged by three non-protein ligands, while the P-cluster pair contains two 4Fe:4S clusters bridged by two cysteine ligands located at the \u03b1\u03b2 subunit interface. Docking studies between the iron protein and molybdenum iron protein suggest a possible interaction mode between these two proteins.", "doi": "10.1021/bk-1993-0535.ch011", "publisher": "American Chemical Society", "publication_date": "1993-07-26" }, { "id": "authors:rq4nt-pws29", "collection": "authors", "collection_id": "rq4nt-pws29", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150209-103752426", "type": "book_section", "title": "Solvation Energy Contributions to Binding Energies", "book_title": "Protein structure, folding, and design 2", "author": [ { "family_name": "Eisenberg", "given_name": "D.", "clpid": "Eisenberg-D" }, { "family_name": "Wesson", "given_name": "M.", "clpid": "Wesson-M" }, { "family_name": "Goodsell", "given_name": "D.", "clpid": "Goodsell-D" }, { "family_name": "Wilcox", "given_name": "W.", "clpid": "Wilcox-W" }, { "family_name": "Gribskov", "given_name": "M.", "clpid": "Gribskov-M" }, { "family_name": "Altschuh", "given_name": "D.", "clpid": "Altschuh-D" }, { "family_name": "Rees", "given_name": "D. C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "contributor": [ { "family_name": "Oxender", "given_name": "Dale L.", "clpid": "Oxender-D-L" } ], "abstract": "Binding affinities for the association\nof protein chains, and for the association of a drug\nto DNA, are examined with atomic salvation parameters\n(ASPs). ASPs permit an estimate of the solvation free\nenergy of binding in aqueous solution, starting from\nknown atomic coordinates. ASPs are semiempirical\ncoefficients, giving the free energy change per unit\nsurface area for the transfer of each type of chemical\ngroup from a relatively apolar environment, such as\nthe interior of a protein, to the aqueous surface.\nFor this estimate of free energy, the accessible\nsurface area of an atomic group is computed, first for\nthe free ligand and macromolecule, and then for the\ncomplex. The change in surface area is multiplied by\nthe ASP for the group and summed with terms for all\nother groups to give the standard free energy change.\nTests of the procedure are described for: (a) The\ntetramerization of melittin; (b) The formation of a\nDNA-drug complex; (c) The polymerization of tobacco\nmosaic protein subunits; and (d) The rotational isomerization of butane.", "isbn": "9780845126684", "publisher": "Liss", "place_of_publication": "New York, NY", "publication_date": "1987", "pages": "203-213" } ]