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Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Bürger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Hérault Y, Hicks G, Hörlein A, Houghton R, Hrabé de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Kent Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Francis Stewart A, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura KI, Yoshinaga Y, Wurst W. The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 2012; 23:580-6. [PMID: 22968824 PMCID: PMC3463800 DOI: 10.1007/s00335-012-9422-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 07/20/2012] [Indexed: 11/16/2022]
Abstract
In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.
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Affiliation(s)
- Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Abdelkader Ayadi
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - James F. Battey
- National Institute on Deafness and Other Communication Disorders (NIH), Bethesda, MD 20892 USA
| | - Cindy Bell
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | - Marie-Christine Birling
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Joanna Bottomley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Steve D. Brown
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - Antje Bürger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | | | - Wendy Bushell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Christian Desaintes
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | - Brendan Doe
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Aris Economides
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | | | - Richard H. Finnell
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
- University of Texas at Austin, Austin, TX 78712 USA
| | | | - Martin Fray
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | - David Frendewey
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Roland H. Friedel
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Icahn Medical Institute, The Mount Sinai Hospital, New York, NY 10029 USA
| | - Frank G. Grosveld
- Department of Cell Biology, Center of Biomedical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Jens Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Yann Hérault
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Geoffrey Hicks
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E OV9 Canada
| | - Andreas Hörlein
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Richard Houghton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | | | - Danny Huylebroeck
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Vivek Iyer
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | | | - Cornelia Kaloff
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Karen Kennedy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Manousos Koutsourakis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - K. C. Kent Lloyd
- Mouse Biology Program, School of Veterinary Medicine, University of California, Davis, CA 95616 USA
| | - Susan Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jeremy Mason
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Colin McKerlie
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Michael P. McLeod
- The Texas A&M Institute for Genomic Medicine, College Station, TX 77843-4485 USA
| | - Harald von Melchner
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Mark Moore
- National Institutes of Health, Bethesda, MD 20205 USA
| | - Alejandro O. Mujica
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Andras Nagy
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON M5G 1X5 Canada
| | - Mikhail Nefedov
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Lauryl M. Nutter
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Guillaume Pavlovic
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | | | - Jonathan Pollock
- Division of Basic Neuroscience and Research, National Institute of Drug Abuse (NIDA), Bethesda, MD 20892-0001 USA
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Derrick E. Rancourt
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Marcello Raspa
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, 00015 Rome, Italy
| | - Jacques E. Remacle
- Infectious Diseases and Public Health, European Commission, DG Research & Innovation, 1049 Brussels, Belgium
| | | | - Barry Rosen
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Nadia Rosenthal
- European Molecular Biology Laboratory (EMBL), Monterotondo, 00015 Rome, Italy
| | - Janet Rossant
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON M5G2L3 Canada
| | - Patricia Ruiz Noppinger
- Centre for Cardiovascular Research, Department of Vertebrate Genomics, Charité, 10115 Berlin, Germany
| | - Ed Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Joel Zupicich Schick
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Frank Schnütgen
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - Paul Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG UK
| | - Claudia Seisenberger
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
| | - Mohammed Selloum
- Institut Clinique de la Souris and Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France
| | - Elizabeth M. Simpson
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child & Family Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Damian Smedley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB10 1ST UK
| | | | - A. Francis Stewart
- Biotechnology Center (BIOTEC) of the Technische Universität Dresden, 01307 Dresden, Germany
| | - Kevin Stone
- The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Kate Swan
- Genome Canada, Ottawa, ON K2P 1P1 Canada
| | | | - Lydia Teboul
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD UK
| | | | - David Valenzuela
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, NY 10591 USA
| | - Anthony P. West
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH UK
| | - Ken-ichi Yamamura
- Division of Developmental Genetics, Center for Animal Resources and Development, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, 860-0811 Japan
| | - Yuko Yoshinaga
- Children’s Hospital Oakland Research Institute (CHORI), Oakland, CA 94609 USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Technische Universität München, 85764 Neuherberg, Germany
- Max-Planck-Institute of Psychiatry, 80804 Munich, Germany
- Deutsches Zentrum fuer Neurodegenerative Erkrankungen e.V. (DZNE) Site Munich, 80336 Munich, Germany
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West AP, Diskin R, Nussenzweig MC, Bjorkman PJ. Structural basis for germline gene usage of a potent class of antibodies targeting the CD4 binding site of HIV-1 gp120. Retrovirology 2012. [PMCID: PMC3441645 DOI: 10.1186/1742-4690-9-s2-o33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Diskin R, Scheid JF, Marcovecchio PM, West AP, Klein F, Gao H, Gnanapragasam PNP, Abadir A, Seaman MS, Nussenzweig MC, Bjorkman PJ. Increasing the potency and breadth of an HIV antibody by using structure-based rational design. Science 2011; 334:1289-93. [PMID: 22033520 PMCID: PMC3232316 DOI: 10.1126/science.1213782] [Citation(s) in RCA: 311] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Antibodies against the CD4 binding site (CD4bs) on the HIV-1 spike protein gp120 can show exceptional potency and breadth. We determined structures of NIH45-46, a more potent clonal variant of VRC01, alone and bound to gp120. Comparisons with VRC01-gp120 revealed that a four-residue insertion in heavy chain complementarity-determining region 3 (CDRH3) contributed to increased interaction between NIH45-46 and the gp120 inner domain, which correlated with enhanced neutralization. We used structure-based design to create NIH45-46(G54W), a single substitution in CDRH2 that increases contact with the gp120 bridging sheet and improves breadth and potency, critical properties for potential clinical use, by an order of magnitude. Together with the NIH45-46-gp120 structure, these results indicate that gp120 inner domain and bridging sheet residues should be included in immunogens to elicit CD4bs antibodies.
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Affiliation(s)
- Ron Diskin
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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54
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Luo XM, Lei MYY, Feidi RA, West AP, Balazs AB, Bjorkman PJ, Yang L, Baltimore D. Dimeric 2G12 as a potent protection against HIV-1. PLoS Pathog 2010; 6:e1001225. [PMID: 21187894 PMCID: PMC3002980 DOI: 10.1371/journal.ppat.1001225] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 11/10/2010] [Indexed: 11/19/2022] Open
Abstract
We previously showed that broadly neutralizing anti-HIV-1 antibody 2G12 (human IgG1) naturally forms dimers that are more potent than monomeric 2G12 in in vitro neutralization of various strains of HIV-1. In this study, we have investigated the protective effects of monomeric versus dimeric 2G12 against HIV-1 infection in vivo using a humanized mouse model. Our results showed that passively transferred, purified 2G12 dimer is more potent than 2G12 monomer at preventing CD4 T cell loss and suppressing the increase of viral load following HIV-1 infection of humanized mice. Using humanized mice bearing IgG “backpack” tumors that provided 2G12 antibodies continuously, we found that a sustained dimer concentration of 5–25 µg/ml during the course of infection provides effective protection against HIV-1. Importantly, 2G12 dimer at this concentration does not favor mutations of the HIV-1 envelope that would cause the virus to completely escape 2G12 neutralization. We have therefore identified dimeric 2G12 as a potent prophylactic reagent against HIV-1 in vivo, which could be used as part of an antibody cocktail to prevent HIV-1 infection. Most successful vaccines function by eliciting antibodies that bind to the surface of pathogens of interest from the host immunologic repertoire. This should also be the case for an HIV-1 vaccine, but broadly neutralizing anti-HIV-1 antibodies have proven hard to elicit with any reagent. Thus, methods to directly administer broadly neutralizing anti-HIV-1 antibodies, such as passive transfusion, become appealing. It is therefore important to find out which antibodies, or antibody cocktails, would provide effective protection against HIV-1 before administering them. Here, we show that the dimeric fraction of 2G12, a unique monoclonal anti-HIV-1 antibody that dimerizes naturally, provides better protection against HIV-1 than its monomeric fraction. As an added bonus, although HIV-1 can evolve to completely escape antibody control, the 2G12 dimer does not favor such evolution. Our study suggests that the 2G12 dimer may be a suitable reagent for direct administration to protect people from HIV-1 infection.
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Affiliation(s)
- Xin M. Luo
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Margarida Y. Y. Lei
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Rana A. Feidi
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Anthony P. West
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Alejandro Benjamin Balazs
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Pamela J. Bjorkman
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Lili Yang
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (DB); (LY)
| | - David Baltimore
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (DB); (LY)
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55
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Yang F, West AP, Bjorkman PJ. Crystal structure of a hemojuvelin-binding fragment of neogenin at 1.8Å. J Struct Biol 2010; 174:239-44. [PMID: 20971194 PMCID: PMC3074981 DOI: 10.1016/j.jsb.2010.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/12/2010] [Accepted: 10/13/2010] [Indexed: 01/24/2023]
Abstract
Neogenin is a type I transmembrane glycoprotein with a large ectodomain containing tandem immunoglobulin-like and fibronectin type III (FNIII) domains. Closely related to the tumor suppressor gene DCC, neogenin functions in critical biological processes through binding to various ligands, including netrin, repulsive guidance molecules, and the iron regulatory protein hemojuvelin. We previously reported that neogenin binds to hemojuvelin through its membrane-proximal fifth and sixth FNIII domains (FN5-6), with domain 6 (FN6) contributing the majority of critical binding interactions. Here we present the crystal structure of FN5-6, the hemojuvelin-binding fragment of human neogenin, at 1.8Å. The two FNIII domains are orientated nearly linearly, a domain arrangement most similar to that of a tandem FNIII-containing fragment within the cytoplasmic tail of the β4 integrin. By mapping surface-exposed residues that differ between neogenin FN5-6 and the comparable domains from DCC, which does not bind hemojuvelin, we identified a potential hemojuvelin-binding site on neogenin FN6. Neogenin FN5, which does not bind hemojuvelin in isolation, exhibits a highly electropositive surface, which may be involved in interactions with negatively-charged polysaccharides or phospholipids in the membrane bilayer. The neogenin FN5-6 structure can be used to facilitate a molecular understanding of neogenin's interaction with hemojuvelin to regulate iron homeostasis and with hemojuvelin-related repulsive guidance molecules to mediate axon guidance.
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Affiliation(s)
- Fan Yang
- Graduate Option in Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Arnon TI, Kaiser JT, West AP, Olson R, Diskin R, Viertlboeck BC, Göbel TW, Bjorkman PJ. The crystal structure of CHIR-AB1: a primordial avian classical Fc receptor. J Mol Biol 2008; 381:1012-24. [PMID: 18625238 DOI: 10.1016/j.jmb.2008.06.082] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/25/2008] [Accepted: 06/26/2008] [Indexed: 01/22/2023]
Abstract
CHIR-AB1 is a newly identified avian immunoglobulin (Ig) receptor that includes both activating and inhibitory motifs and was therefore classified as a potentially bifunctional receptor. Recently, CHIR-AB1 was shown to bind the Fc region of chicken IgY and to induce calcium mobilization via association with the common gamma-chain, a subunit that transmits signals upon ligation of many different immunoreceptors. Here we describe the 1.8-A-resolution crystal structure of the CHIR-AB1 ectodomain. The receptor ectodomain consists of a single C2-type Ig domain resembling the Ig-like domains found in mammalian Fc receptors such as FcgammaRs and FcalphaRI. Unlike these receptors and other monomeric Ig superfamily members, CHIR-AB1 crystallized as a 2-fold symmetrical homodimer that bears no resemblance to variable or constant region dimers in an antibody. Analytical ultracentrifugation demonstrated that CHIR-AB1 exists as a mixture of monomers and dimers in solution, and equilibrium gel filtration revealed a 2:1 receptor/ligand binding stoichiometry. Measurement of the 1:1 CHIR-AB1/IgY interaction affinity indicates a relatively low affinity complex, but a 2:1 CHIR-AB1/IgY interaction allows an increase in apparent affinity due to avidity effects when the receptor is tethered to a surface. Taken together, these results add to the structural understanding of Fc receptors and their functional mechanisms.
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Affiliation(s)
- Tal I Arnon
- Division of Biology, 114-96 and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Yang F, West AP, Allendorph GP, Choe S, Bjorkman PJ. Neogenin interacts with hemojuvelin through its two membrane-proximal fibronectin type III domains. Biochemistry 2008; 47:4237-45. [PMID: 18335997 DOI: 10.1021/bi800036h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hemojuvelin is a recently identified iron-regulatory protein that plays an important role in affecting the expression of hepcidin, a key iron regulatory hormone. Although the underlying mechanism of this process is not clear, several hemojuvelin-binding proteins, including the cell surface receptor neogenin and bone morphogenetic protein (BMP) cytokines, have been identified. The ectodomain of neogenin is composed of four immunoglobulin-like (Ig) domains followed by six fibronectin type III-like (FNIII) domains. Here we report expression of soluble versions of hemojuvelin and neogenin for biochemical characterization of their interaction and the interaction of HJV with BMP-2. Hemojuvelin normally undergoes an autocatalytic cleavage, and as in vivo, recombinant hemojuvelin exists as a mixture of cleaved and uncleaved forms. Neogenin binds to cleaved and noncleaved hemojuvelin, as verified by its binding to an uncleaved mutant hemojuvelin. We localized the hemojuvelin binding site on neogenin to the membrane-proximal fifth and sixth FNIII domains and the juxtamembrane linker and showed that a fragment containing only this region binds 2-3 orders of magnitude more tightly than the entire neogenin ectodomain. Binding to the most membrane-proximal region of neogenin may play a role in regulating the levels of soluble and membrane-bound forms of hemojuvelin, which in turn would influence the amount of free BMP-2 available for binding to its receptors and triggering transcription of the hepcidin gene. Our finding that BMP-2 and neogenin bind simultaneously to hemojuvelin raises the possibility that neogenin is part of a multiprotein complex at the hepatocyte membrane involving BMP, its receptors, and hemojuvelin.
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Affiliation(s)
- Fan Yang
- Graduate Option in Chemistry, California Institute of Technology, Pasadena, California 91125, USA
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Ja WW, West AP, Delker SL, Bjorkman PJ, Benzer S, Roberts RW. Extension of Drosophila melanogaster life span with a GPCR peptide inhibitor. Nat Chem Biol 2007; 3:415-9. [PMID: 17546039 PMCID: PMC2803097 DOI: 10.1038/nchembio.2007.2] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 05/11/2007] [Indexed: 11/09/2022]
Abstract
G protein-coupled receptors (GPCRs) mediate signaling from extracellular ligands to intracellular signal transduction proteins. Methuselah (Mth) is a class B (secretin-like) GPCR, a family typified by their large, ligand-binding, N-terminal extracellular domains. Downregulation of mth increases the life span of Drosophila melanogaster; inhibitors of Mth signaling should therefore enhance longevity. We used mRNA display selection to identify high-affinity (K(d) = 15 to 30 nM) peptide ligands that bind to the N-terminal ectodomain of Mth. The selected peptides are potent antagonists of Mth signaling, and structural studies suggest that they perturb the interface between the Mth ecto- and transmembrane domains. Flies constitutively expressing a Mth antagonist peptide have a robust life span extension, which suggests that the peptides inhibit Mth signaling in vivo. Our work thus provides new life span-extending ligands for a metazoan and a general approach for the design of modulators of this important class of GPCRs.
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Affiliation(s)
- William W. Ja
- Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Silvia L. Delker
- Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Seymour Benzer
- Division of Biology, 1200 E. California Blvd. 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Richard W. Roberts
- Departments of Chemistry and Chemical Engineering, University of Southern California, Los Angeles, CA 90089, USA
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Li P, Huey-Tubman KE, Gao T, Li X, West AP, Bennett MJ, Bjorkman PJ. Erratum: The structure of a polyQ–anti-polyQ complex reveals binding according to a linear lattice model. Nat Struct Mol Biol 2007. [DOI: 10.1038/nsmb0607-568a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Li P, Huey-Tubman KE, Gao T, Li X, West AP, Bennett MJ, Bjorkman PJ. The structure of a polyQ-anti-polyQ complex reveals binding according to a linear lattice model. Nat Struct Mol Biol 2007; 14:381-7. [PMID: 17450152 DOI: 10.1038/nsmb1234] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 03/14/2007] [Indexed: 11/09/2022]
Abstract
Huntington and related neurological diseases result from expansion of a polyglutamine (polyQ) tract. The linear lattice model for the structure and binding properties of polyQ proposes that both expanded and normal polyQ tracts in the preaggregation state are random-coil structures but that an expanded polyQ repeat contains a larger number of epitopes recognized by antibodies or other proteins. The crystal structure of polyQ bound to MW1, an antibody against polyQ, reveals that polyQ adopts an extended, coil-like structure. Consistent with the linear lattice model, multimeric MW1 Fvs bind more tightly to longer than to shorter polyQ tracts and, compared with monomeric Fv, bind expanded polyQ repeats with higher apparent affinities. These results suggest a mechanism for the toxicity of expanded polyQ and a strategy to link anti-polyQ compounds to create high-avidity therapeutics.
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Affiliation(s)
- Pingwei Li
- Division of Biology 114-96, California Institute of Technology, Pasadena, California 91125, USA.
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Abstract
One of the primary physiological roles of nuclear factor-kappa B (NF-kappaB) is in the immune system. In particular, NF-kappaB family members control the transcription of cytokines and antimicrobial effectors as well as genes that regulate cellular differentiation, survival and proliferation, thereby regulating various aspects of innate and adaptive immune responses. In addition, NF-kappaB also contributes to the development and survival of the cells and tissues that carry out immune responses in mammals. This review, therefore, describes the role of the NF-kappaB pathway in the development and functioning of the immune system.
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Affiliation(s)
- M S Hayden
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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62
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Dougherty DA, Jacobs SJ, Silverman SK, Murray MM, Shultz DA, West AP, Clites JA. New Organic Polymers And Molecules With Very High Spin States. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10587259308035719] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Dennis A. Dougherty
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - S. Joshua Jacobs
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - Scott K. Silverman
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - Michael M. Murray
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - David A. Shultz
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - Anthony P. West
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
| | - Jeffrey A. Clites
- a Division of Chemistry and Chemical Engineering , California Institute of Technology , Pasadena , CA , 8758 , USA
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63
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McDermott LC, Freel JA, West AP, Bjorkman PJ, Kennedy MW. Zn-alpha2-glycoprotein, an MHC class I-related glycoprotein regulator of adipose tissues: modification or abrogation of ligand binding by site-directed mutagenesis. Biochemistry 2006; 45:2035-41. [PMID: 16475792 DOI: 10.1021/bi051881v] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zn-alpha(2)-glycoprotein (ZAG) is a soluble lipid-mobilizing factor associated with cancer cachexia and is a novel adipokine. Its X-ray crystal structure reveals a poly(ethylene glycol) molecule, presumably substituting for a higher affinity natural ligand, occupying an apolar groove between its alpha(1) and alpha(2) domain helices that corresponds to the peptide binding groove in class I MHC proteins. We previously provided evidence that the groove is a binding site for hydrophobic ligands that may relate to the protein's signaling function and that the natural ligands are probably (polyunsaturated) fatty acid-like. Using fluorescence-based binding assays and site-directed mutagenesis, we now demonstrate formally that the groove is indeed the binding site for hydrophobic ligands. We also identify amino acid positions that are involved in ligand binding and those that control the shape and exposure to solvent of the binding site itself. Some of the mutants showed minimal effects on their binding potential, one showed enhanced binding, and several were completely nonbinding. Particularly notable is Arg-73, which projects into one end of the binding groove and is the sole charged amino acid adjacent to the ligand. Replacing this amino acid with alanine abolished ligand binding and closed the groove to solvent. Arg-73 may therefore have an unexpected dual role in binding site access and anchor for an amphiphilic ligand. These data add weight to the distinctiveness of ZAG among MHC class I-like proteins in addition to providing defined binding-altered mutants for cellular signaling studies and potential medical applications.
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Affiliation(s)
- Lindsay C McDermott
- Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
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64
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Kacskovics I, Kis Z, Mayer B, West AP, Tiangco NE, Tilahun M, Cervenak L, Bjorkman PJ, Goldsby RA, Szenci O, Hammarström L. FcRn mediates elongated serum half-life of human IgG in cattle. Int Immunol 2006; 18:525-36. [PMID: 16481343 DOI: 10.1093/intimm/dxh393] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IgG has the longest survival time in the circulation of the Ig classes and the lowest fractional catabolic rate. The neonatal Fc receptor (FcRn) plays an important role in regulating these processes. Recently, we have cloned the bovine neonatal Fc receptor (bFcRn) alpha chain and detected its expression in various epithelial cells which are mediating IgG secretion. However, its function in IgG homeostasis has not been investigated. In the current study, we analyzed the binding affinity of bovine and human IgGs to bFcRn using surface plasmon resonance and by in vitro radioreceptor binding assays. As human IgG binds stronger to the bFcRn, than bovine IgG at pH 6, we subsequently analyzed its catabolism in normal and transchromosomic calves that produce human Igs. Pharmacokinetic studies showed that human IgG had approximately 33 days serum half-life both in normal and transchromosomic calves, which is more than two times longer than its bovine counterpart. We also demonstrate FcRn expression in endothelial cells and in the kidney which are supposed to be involved in IgG metabolism. These data suggest that bFcRn is involved in IgG homeostasis in cattle and furthermore, that the transchromosomic calves producing human Igs can effectively protect their human IgGs which have implications for successful large-scale production of therapeutic antibodies.
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Affiliation(s)
- Imre Kacskovics
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary.
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65
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Hamburger ZA, Hamburger AE, West AP, Weis WI. Crystal structure of the S.cerevisiae exocyst component Exo70p. J Mol Biol 2005; 356:9-21. [PMID: 16359701 DOI: 10.1016/j.jmb.2005.09.099] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 09/29/2005] [Indexed: 11/17/2022]
Abstract
The exocyst is an evolutionarily conserved multiprotein complex required for the targeting and docking of post-Golgi vesicles to the plasma membrane. Through its interactions with a variety of proteins, including small GTPases, the exocyst is thought to integrate signals from the cell and signal that vesicles arriving at the plasma membrane are ready for fusion. Here we describe the three-dimensional crystal structure of one of the components of the exocyst, Exo70p, from Saccharomyces cerevisiae at 3.5A resolution. Exo70p binds the small GTPase Rho3p in a GTP-dependent manner with an equilibrium dissociation constant of approximately 70 microM. Exo70p is an extended rod approximately 155 angstroms in length composed principally of alpha helices, and is a novel fold. The structure provides a first view of the Exo70 protein family and provides a framework to study the molecular function of this exocyst component.
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Affiliation(s)
- Zsuzsa A Hamburger
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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66
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Zhang AS, West AP, Wyman AE, Bjorkman PJ, Enns CA. Interaction of Hemojuvelin with Neogenin Results in Iron Accumulation in Human Embryonic Kidney 293 Cells. J Biol Chem 2005; 280:33885-94. [PMID: 16103117 DOI: 10.1074/jbc.m506207200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Type 2 hereditary hemochromatosis (HH) or juvenile hemochromatosis is an early onset, genetically heterogeneous, autosomal recessive disorder of iron overload. Type 2A HH is caused by mutations in the recently cloned hemojuvelin gene (HJV; also called HFE2) (Papanikolaou, G., Samuels, M. E., Ludwig, E. H., MacDonald, M. L., Franchini, P. L., Dube, M. P., Andres, L., MacFarlane, J., Sakellaropoulos, N., Politou, M., Nemeth, E., Thompson, J., Risler, J. K., Zaborowska, C., Babakaiff, R., Radomski, C. C., Pape, T. D., Davidas, O., Christakis, J., Brissot, P., Lockitch, G., Ganz, T., Hayden, M. R., and Goldberg, Y. P. (2004) Nat. Genet. 36, 77-82), whereas Type 2B HH is caused by mutations in hepcidin. HJV is highly expressed in both skeletal muscle and liver. Mutations in HJV are implicated in the majority of diagnosed juvenile hemochromatosis patients. In this study, we stably transfected HJV cDNA into human embryonic kidney 293 cells and characterized the processing of HJV and its effect on iron homeostasis. Our results indicate that HJV is a glycosylphosphatidylinositol-linked protein and undergoes a partial autocatalytic cleavage during its intracellular processing. HJV co-immunoprecipitated with neogenin, a receptor involved in a variety of cellular signaling processes. It did not interact with the closely related receptor DCC (deleted in Colon Cancer). In addition, the HJV G320V mutant implicated in Type 2A HH did not co-immunoprecipitate with neogenin. Immunoblot analysis of ferritin levels and transferrin-55Fe accumulation studies indicated that the HJV-induced increase in intracellular iron levels in human embryonic kidney 293 cells is dependent on the presence of neogenin in the cells, thus linking these two proteins to intracellular iron homeostasis.
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Affiliation(s)
- An-Sheng Zhang
- Department of Cell and Developmental Biology, Oregon Health & Science University, Portland, Oregon 97239, USA.
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67
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Hamburger AE, West AP, Hamburger ZA, Hamburger P, Bjorkman PJ. Crystal Structure of a Secreted Insect Ferritin Reveals a Symmetrical Arrangement of Heavy and Light Chains. J Mol Biol 2005; 349:558-69. [PMID: 15896348 DOI: 10.1016/j.jmb.2005.03.074] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Revised: 03/23/2005] [Accepted: 03/25/2005] [Indexed: 10/25/2022]
Abstract
Ferritins are iron storage proteins made of 24 subunits forming a hollow spherical shell. Vertebrate ferritins contain varying ratios of heavy (H) and light (L) chains; however, known ferritin structures include only one type of chain and have octahedral symmetry. Here, we report the 1.9A structure of a secreted insect ferritin from Trichoplusia ni, which reveals equal numbers of H and L chains arranged with tetrahedral symmetry. The H/L-chain interface includes complementary features responsible for ordered assembly of the subunits. The H chain contains a ferroxidase active site resembling that of vertebrate H chains with an endogenous, bound iron atom. The L chain lacks the residues that form a putative iron core nucleation site in vertebrate L chains. Instead, a possible nucleation site is observed at the L chain 3-fold pore. The structure also reveals inter- and intrasubunit disulfide bonds, mostly in the extended N-terminal regions unique to insect ferritins. The symmetrical arrangement of H and L chains and the disulfide crosslinks reflect adaptations of insect ferritin to its role as a secreted protein.
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Affiliation(s)
- Agnes E Hamburger
- Division of Biology 114-96, California Institute of Technology, Pasadena, CA 91125, USA
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68
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Abstract
Zn-alpha2-glycoprotein (ZAG) is a 41 kDa soluble protein that is present in most bodily fluids. The previously reported 2.8 A crystal structure of ZAG isolated from human serum demonstrated the structural similarity between ZAG and class I major histocompatibility complex (MHC) molecules and revealed a non-peptidic ligand in the ZAG counterpart of the MHC peptide-binding groove. Here we present crystallographic studies to explore further the nature of the non-peptidic ligand in the ZAG groove. Comparison of the structures of several forms of recombinant ZAG, including a 1.95 A structure derived from ZAG expressed in insect cells, suggests that the non-peptidic ligand in the current structures and in the structure of serum ZAG is a polyethylene glycol (PEG), which is present in the crystallization conditions used. Further support for PEG binding in the ZAG groove is provided by the finding that PEG displaces a fluorophore-tagged fatty acid from the ZAG binding site. From these results we hypothesize that our purified forms of ZAG do not contain a bound endogenous ligand, but that the ZAG groove is capable of binding hydrophobic molecules, which may relate to its function.
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69
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Hamburger AE, West AP, Bjorkman PJ. Crystal Structure of a Polymeric Immunoglobulin Binding Fragment of the Human Polymeric Immunoglobulin Receptor. Structure 2004; 12:1925-35. [PMID: 15530357 DOI: 10.1016/j.str.2004.09.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 09/02/2004] [Accepted: 09/03/2004] [Indexed: 11/28/2022]
Abstract
The polymeric immunoglobulin receptor (pIgR) is a type I transmembrane protein that delivers dimeric IgA (dIgA) and pentameric IgM to mucosal secretions. Here, we report the 1.9 A resolution X-ray crystal structure of the N-terminal domain of human pIgR, which binds dIgA in the absence of other pIgR domains with an equilibrium dissociation constant of 300 nM. The structure of pIgR domain 1 reveals a folding topology similar to immunoglobulin variable domains, but with differences in the counterparts of the complementarity determining regions (CDRs), including a helical turn in CDR1 and a CDR3 loop that points away from the other CDRs. The unusual CDR3 loop position prevents dimerization analogous to the pairing of antibody variable heavy and variable light domains. The pIgR domain 1 structure allows interpretation of previous mutagenesis results and structure-based comparisons between pIgR and other IgA receptors.
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Affiliation(s)
- Agnes E Hamburger
- Division of Biology 114-96, California Institute of Technology, Pasadena, CA 91125, USA
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70
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West AP, Herr AB, Bjorkman PJ. The chicken yolk sac IgY receptor, a functional equivalent of the mammalian MHC-related Fc receptor, is a phospholipase A2 receptor homolog. Immunity 2004; 20:601-10. [PMID: 15142528 DOI: 10.1016/s1074-7613(04)00113-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2004] [Revised: 03/01/2004] [Accepted: 03/17/2004] [Indexed: 10/26/2022]
Abstract
In mammals, IgG is transferred from mother to young by the MHC-related receptor FcRn, which binds IgG in acidic endosomes and releases it at basic pH into blood. Maternal IgY, the avian counterpart of IgG, is transferred to embryos across yolk sac membranes. We affinity-purified the chicken yolk sac IgY receptor (FcRY) and sequenced its gene. FcRY is unrelated to MHC molecules but is a homolog of the mammalian phospholipase A(2) receptor. Analytical ultracentrifugation and truncation experiments suggest that FcRY forms a compact structure containing an IgY binding site at acidic pH but undergoes a conformational change at basic pH that disrupts the site. FcRY is thus unrelated to mammalian FcRn in both its structure and mechanism for pH-dependent binding, illustrating distinct routes utilized by evolution to transfer antibodies.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Chick Embryo
- Immunity, Maternally-Acquired
- Immunoglobulins/chemistry
- Immunoglobulins/genetics
- Immunoglobulins/immunology
- Molecular Sequence Data
- Phospholipases A/chemistry
- Phospholipases A/genetics
- Phospholipases A/immunology
- Phospholipases A2
- Polymerase Chain Reaction
- Protein Conformation
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Fc/genetics
- Receptors, Fc/immunology
- Receptors, Fc/isolation & purification
- Yolk Sac/immunology
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Affiliation(s)
- Anthony P West
- Division of Biology 114-96, California Institute of Technology, Pasadena, CA 91125, USA
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71
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Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RIS, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JGR, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ESI, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I. DNA sequence and analysis of human chromosome 9. Nature 2004; 429:369-74. [PMID: 15164053 PMCID: PMC2734081 DOI: 10.1038/nature02465] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 03/08/2004] [Indexed: 11/09/2022]
Abstract
Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
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Affiliation(s)
- S J Humphray
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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72
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Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L, Steward CA, Sims SK, Jones MC, Searle S, Scott C, Howe K, Hunt SE, Andrews TD, Gilbert JGR, Swarbreck D, Ashurst JL, Taylor A, Battles J, Bird CP, Ainscough R, Almeida JP, Ashwell RIS, Ambrose KD, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Bates K, Beasley H, Bray-Allen S, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Cahill P, Camire D, Carter NP, Chapman JC, Clark SY, Clarke G, Clee CM, Clegg S, Corby N, Coulson A, Dhami P, Dutta I, Dunn M, Faulkner L, Frankish A, Frankland JA, Garner P, Garnett J, Gribble S, Griffiths C, Grocock R, Gustafson E, Hammond S, Harley JL, Hart E, Heath PD, Ho TP, Hopkins B, Horne J, Howden PJ, Huckle E, Hynds C, Johnson C, Johnson D, Kana A, Kay M, Kimberley AM, Kershaw JK, Kokkinaki M, Laird GK, Lawlor S, Lee HM, Leongamornlert DA, Laird G, Lloyd C, Lloyd DM, Loveland J, Lovell J, McLaren S, McLay KE, McMurray A, Mashreghi-Mohammadi M, Matthews L, Milne S, Nickerson T, Nguyen M, Overton-Larty E, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter K, Rice CM, Rogosin A, Ross MT, Sarafidou T, Sehra HK, Shownkeen R, Skuce CD, Smith M, Standring L, Sycamore N, Tester J, Thorpe A, Torcasso W, Tracey A, Tromans A, Tsolas J, Wall M, Walsh J, Wang H, Weinstock K, West AP, Willey DL, Whitehead SL, Wilming L, Wray PW, Young L, Chen Y, Lovering RC, Moschonas NK, Siebert R, Fechtel K, Bentley D, Durbin R, Hubbard T, Doucette-Stamm L, Beck S, Smith DR, Rogers J. The DNA sequence and comparative analysis of human chromosome 10. Nature 2004; 429:375-81. [PMID: 15164054 DOI: 10.1038/nature02462] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 03/09/2004] [Indexed: 11/08/2022]
Abstract
The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.
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Affiliation(s)
- P Deloukas
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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73
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Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, Beare DM, Burford DC, Hunt SE, Griffiths-Jones S, Jones MC, Keenan SJ, Oliver K, Scott CE, Ainscough R, Almeida JP, Ambrose KD, Andrews DT, Ashwell RIS, Babbage AK, Bagguley CL, Bailey J, Bannerjee R, Barlow KF, Bates K, Beasley H, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burrill W, Carder C, Carter NP, Chapman JC, Clamp ME, Clark SY, Clarke G, Clee CM, Clegg SCM, Cobley V, Collins JE, Corby N, Coville GJ, Deloukas P, Dhami P, Dunham I, Dunn M, Earthrowl ME, Ellington AG, Faulkner L, Frankish AG, Frankland J, French L, Garner P, Garnett J, Gilbert JGR, Gilson CJ, Ghori J, Grafham DV, Gribble SM, Griffiths C, Hall RE, Hammond S, Harley JL, Hart EA, Heath PD, Howden PJ, Huckle EJ, Hunt PJ, Hunt AR, Johnson C, Johnson D, Kay M, Kimberley AM, King A, Laird GK, Langford CJ, Lawlor S, Leongamornlert DA, Lloyd DM, Lloyd C, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, McLaren SJ, McMurray A, Milne S, Moore MJF, Nickerson T, Palmer SA, Pearce AV, Peck AI, Pelan S, Phillimore B, Porter KM, Rice CM, Searle S, Sehra HK, Shownkeen R, Skuce CD, Smith M, Steward CA, Sycamore N, Tester J, Thomas DW, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Wilming L, Wray PW, Wright MW, Young L, Coulson A, Durbin R, Hubbard T, Sulston JE, Beck S, Bentley DR, Rogers J, Ross MT. The DNA sequence and analysis of human chromosome 13. Nature 2004; 428:522-8. [PMID: 15057823 PMCID: PMC2665288 DOI: 10.1038/nature02379] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Accepted: 01/27/2004] [Indexed: 12/14/2022]
Abstract
Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.
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Affiliation(s)
- A Dunham
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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74
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Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JGR, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RIS, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJR, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJF, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S. The DNA sequence and analysis of human chromosome 6. Nature 2003; 425:805-11. [PMID: 14574404 DOI: 10.1038/nature02055] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2003] [Accepted: 09/11/2003] [Indexed: 01/17/2023]
Abstract
Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.
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Affiliation(s)
- A J Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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75
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Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520-62. [PMID: 12466850 DOI: 10.1038/nature01262] [Citation(s) in RCA: 4791] [Impact Index Per Article: 217.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 10/31/2002] [Indexed: 12/18/2022]
Abstract
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
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MESH Headings
- Animals
- Base Composition
- Chromosomes, Mammalian/genetics
- Conserved Sequence/genetics
- CpG Islands/genetics
- Evolution, Molecular
- Gene Expression Regulation
- Genes/genetics
- Genetic Variation/genetics
- Genome
- Genome, Human
- Genomics
- Humans
- Mice/classification
- Mice/genetics
- Mice, Knockout
- Mice, Transgenic
- Models, Animal
- Multigene Family/genetics
- Mutagenesis
- Neoplasms/genetics
- Physical Chromosome Mapping
- Proteome/genetics
- Pseudogenes/genetics
- Quantitative Trait Loci/genetics
- RNA, Untranslated/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- Sex Chromosomes/genetics
- Species Specificity
- Synteny
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76
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Willcox BE, Thomas LM, Chapman TL, Heikema AP, West AP, Bjorkman PJ. Crystal structure of LIR-2 (ILT4) at 1.8 A: differences from LIR-1 (ILT2) in regions implicated in the binding of the Human Cytomegalovirus class I MHC homolog UL18. BMC Struct Biol 2002; 2:6. [PMID: 12390682 PMCID: PMC130215 DOI: 10.1186/1472-6807-2-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2002] [Accepted: 10/11/2002] [Indexed: 11/21/2022]
Abstract
BACKGROUND Leukocyte Immunoglobulin-like Receptor-1 (LIR-1) and LIR-2 (also known as ILT2 and ILT4 respectively) are highly related cell surface receptors that bind a broad range of class I MHC molecules with low (microM) affinities. Expressed on monocytic cells and macrophages, both molecules transmit inhibitory signals after binding ligands. In addition to binding host class I MHC, the LIR-1 molecule, which is also expressed on lymphoid tissues, binds with a high (nM) affinity to UL18, a class I MHC homolog encoded by Human Cytomegalovirus (HCMV). In comparison, LIR-2 binds UL18 only weakly (microM KD). To understand how HCMV preferentially targets the more broadly expressed LIR-1 molecule, we determined the crystal structure of a ligand-binding fragment of LIR-2, and compared this to the existing high-resolution crystal structure of LIR-1. RESULTS Recombinant LIR-2 (domains 1 and 2) was produced in E. coli and crystallized using streak seeding to optimize the crystal morphology. A data set complete to 1.8 A was collected at 100 K from a single crystal in the P4(1)2(1)2 spacegroup. The structure was solved by molecular replacement, using a search model based on the LIR-1 structure. CONCLUSIONS The overall structure of LIR-2 D1D2 resembles both LIR-1, and Killer Inhibitory Receptors, in that the A strand in each domain forms hydrogen bonds to both beta sheets, and there is a sharp angle between the two immunoglobulin-like domains. However, differences from LIR-1 are observed in each domain, with two key changes apparent in the ligand-binding domain, D1. The region corresponding to the residue 44-57 helix of LIR-1 adopts a topology distinct from that of both LIR-1 and the KIR structures, involving a shortened 310 helix. Secondly, the predicted UL18 binding region of LIR-1 is altered substantially in LIR-2: the 76-84 loop mainchain is displaced 11 A with respect to LIR-1, and Tyrosine 38 adopts an alternative rotamer conformation. In summary, the structure of LIR-2 has revealed significant differences to LIR-1, including ones that may help to explain the >1000-fold lower affinity of LIR-2 for UL18.
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Affiliation(s)
- Benjamin E Willcox
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
- Current address: Cancer Research UK Institute for Cancer Studies, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - Leonard M Thomas
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology Pasadena, California 91125, USA
| | - Tara L Chapman
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
- Current address: Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Astrid P Heikema
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology Pasadena, California 91125, USA
| | - Anthony P West
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
| | - Pamela J Bjorkman
- Division of Biology 156-29 California Institute of Technology Pasadena, California 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology Pasadena, California 91125, USA
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77
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Bennett MJ, Huey-Tubman KE, Herr AB, West AP, Ross SA, Bjorkman PJ. A linear lattice model for polyglutamine in CAG-expansion diseases. Proc Natl Acad Sci U S A 2002; 99:11634-9. [PMID: 12193654 PMCID: PMC129321 DOI: 10.1073/pnas.182393899] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Huntington's disease and several other neurological diseases are caused by expanded polyglutamine [poly(Gln)] tracts in different proteins. Mechanisms for expanded (>36 Gln residues) poly(Gln) toxicity include the formation of aggregates that recruit and sequester essential cellular proteins [Preisinger, E., Jordan, B. M., Kazantsev, A. & Housman, D. (1999) Phil. Trans. R. Soc. London B 354, 1029-1034; Chen, S., Berthelier, V., Yang, W. & Wetzel, R. (2001) J. Mol. Biol. 311, 173-182] and functional alterations, such as improper interactions with other proteins [Cummings, C. J. & Zoghbi, H. Y. (2000) Hum. Mol. Genet. 9, 909-916]. Expansion above the "pathologic threshold" ( approximately 36 Gln) has been proposed to induce a conformational transition in poly(Gln) tracts, which has been suggested as a target for therapeutic intervention. Here we show that structural analyses of soluble huntingtin exon 1 fusion proteins with 16 to 46 glutamine residues reveal extended structures with random coil characteristics and no evidence for a global conformational change above 36 glutamines. An antibody (MW1) Fab fragment, which recognizes full-length huntingtin in mouse brain sections, binds specifically to exon 1 constructs containing normal and expanded poly(Gln) tracts, with affinity and stoichiometry that increase with poly(Gln) length. These data support a "linear lattice" model for poly(Gln), in which expanded poly(Gln) tracts have an increased number of ligand-binding sites as compared with normal poly(Gln). The linear lattice model provides a rationale for pathogenicity of expanded poly(Gln) tracts and a structural framework for drug design.
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Affiliation(s)
- Melanie J Bennett
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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78
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79
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80
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Pascal RA, West AP, Van Engen D. Synthesis and structure of an in-phosphaphane: enforced interaction of a phosphine and an aromatic ring. J Am Chem Soc 2002. [DOI: 10.1021/ja00173a044] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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81
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82
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West AP, Smyth N, Kraml CM, Ho DM, Pascal RA. Synthesis, molecular structure, and properties of in-phosphaphanes with substituted basal aromatic rings. J Org Chem 2002. [DOI: 10.1021/jo00065a009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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83
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West AP, Giannetti AM, Herr AB, Bennett MJ, Nangiana JS, Pierce JR, Weiner LP, Snow PM, Bjorkman PJ. Mutational analysis of the transferrin receptor reveals overlapping HFE and transferrin binding sites. J Mol Biol 2001; 313:385-97. [PMID: 11800564 DOI: 10.1006/jmbi.2001.5048] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The transferrin receptor (TfR) binds two proteins critical for iron metabolism: transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. Previous results demonstrated that Tf and HFE compete for binding to TfR, suggesting that Tf and HFE bind to the same or an overlapping site on TfR. TfR is a homodimer that binds one Tf per polypeptide chain (2:2, TfR/Tf stoichiometry), whereas both 2:1 and 2:2 TfR/HFE stoichiometries have been observed. In order to more fully characterize the interaction between HFE and TfR, we determined the binding stoichiometry using equilibrium gel-filtration and analytical ultracentrifugation. Both techniques indicate that a 2:2 TfR/HFE complex can form at submicromolar concentrations in solution, consistent with the hypothesis that HFE competes for Tf binding to TfR by blocking the Tf binding site rather than by exerting an allosteric effect. To determine whether the Tf and HFE binding sites on TfR overlap, residues at the HFE binding site on TfR were identified from the 2.8 A resolution HFE-TfR co-crystal structure, then mutated and tested for their effects on HFE and Tf binding. The binding affinities of soluble TfR mutants for HFE and Tf were determined using a surface plasmon resonance assay. Substitutions of five TfR residues at the HFE binding site (L619A, R629A, Y643A, G647A and F650Q) resulted in significant reductions in Tf binding affinity. The findings that both HFE and Tf form 2:2 complexes with TfR and that mutations at the HFE binding site affect Tf binding support a model in which HFE and Tf compete for overlapping binding sites on TfR.
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Affiliation(s)
- A P West
- Division of Biology 156-29 , California Institute of Technology, Pasadena, CA 91125, USA
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84
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Abstract
The neonatal Fc receptor (FcRn) transports immunoglobulin G (IgG) across epithelia, binding IgG in acidic vesicles (pH < or = 6.5) and releasing IgG in the blood at pH 7.4. Well-ordered FcRn/Fc crystals are prevented by the formation of "oligomeric ribbons" of FcRn dimers bridged by Fc homodimers, thus we crystallized a 1:1 complex between rat FcRn and a heterodimeric Fc containing only one FcRn binding site. The 2.8 A complex structure demonstrates that FcRn uses its alpha2 and beta2-microglobulin domains and carbohydrate to interact with the Fc C(gamma)2-C(gamma)3 interface. The structure reveals conformational changes in Fc and three titratable salt bridges that confer pH-dependent binding, and can be used to guide rational design of therapeutic IgGs with longer serum half-lives.
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Affiliation(s)
- W L Martin
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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85
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West AP, Llamas LL, Snow PM, Benzer S, Bjorkman PJ. Crystal structure of the ectodomain of Methuselah, a Drosophila G protein-coupled receptor associated with extended lifespan. Proc Natl Acad Sci U S A 2001; 98:3744-9. [PMID: 11274391 PMCID: PMC31123 DOI: 10.1073/pnas.051625298] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2000] [Indexed: 11/18/2022] Open
Abstract
The Drosophila mutant methuselah (mth) was identified from a screen for single gene mutations that extended average lifespan. Mth mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage. The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family. Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site. Here we report the 2.3-A resolution crystal structure of the Mth extracellular region, revealing a folding topology in which three primarily beta-structure-containing domains meet to form a shallow interdomain groove containing a solvent-exposed tryptophan that may represent a ligand binding site. The Mth structure is analyzed in relation to predicted Mth homologs and potential ligand binding features.
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Affiliation(s)
- A P West
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
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86
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West AP, Bennett MJ, Sellers VM, Andrews NC, Enns CA, Bjorkman PJ. Comparison of the interactions of transferrin receptor and transferrin receptor 2 with transferrin and the hereditary hemochromatosis protein HFE. J Biol Chem 2000; 275:38135-8. [PMID: 11027676 DOI: 10.1074/jbc.c000664200] [Citation(s) in RCA: 184] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The transferrin receptor (TfR) interacts with two proteins important for iron metabolism, transferrin (Tf) and HFE, the protein mutated in hereditary hemochromatosis. A second receptor for Tf, TfR2, was recently identified and found to be functional for iron uptake in transfected cells (Kawabata, H., Germain, R. S., Vuong, P. T., Nakamaki, T., Said, J. W., and Koeffler, H. P. (2000) J. Biol. Chem. 275, 16618-16625). TfR2 has a pattern of expression and regulation that is distinct from TfR, and mutations in TfR2 have been recognized as the cause of a non-HFE linked form of hemochromatosis (Camaschella, C., Roetto, A., Cali, A., De Gobbi, M., Garozzo, G., Carella, M., Majorano, N., Totaro, A., and Gasparini, P. (2000) Nat. Genet. 25, 14-15). To investigate the relationship between TfR, TfR2, Tf, and HFE, we performed a series of binding experiments using soluble forms of these proteins. We find no detectable binding between TfR2 and HFE by co-immunoprecipitation or using a surface plasmon resonance-based assay. The affinity of TfR2 for iron-loaded Tf was determined to be 27 nm, 25-fold lower than the affinity of TfR for Tf. These results imply that HFE regulates Tf-mediated iron uptake only from the classical TfR and that TfR2 does not compete for HFE binding in cells expressing both forms of TfR.
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Affiliation(s)
- A P West
- Division of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
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87
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Ramalingam TS, West AP, Lebrón JA, Nangiana JS, Hogan TH, Enns CA, Bjorkman PJ. Binding to the transferrin receptor is required for endocytosis of HFE and regulation of iron homeostasis. Nat Cell Biol 2000; 2:953-7. [PMID: 11146662 DOI: 10.1038/35046611] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HFE, the protein that is mutated in hereditary haemochromatosis, binds to the transferrin receptor (TfR). Here we show that wild-type HFE and TfR localize in endosomes and at the basolateral membrane of a polarized duodenal epithelial cell line, whereas the primary haemochromatosis HFE mutant, and another mutant with impaired TfR-binding ability accumulate in the ER/Golgi and at the basolateral membrane, respectively. Levels of the iron-storage protein ferritin are greatly reduced and those of TfR are slightly increased in cells expressing wild-type HFE, but not in cells expressing either mutant. Addition of an endosomal-targeting sequence derived from the human low-density lipoprotein receptor (LDLR) to the TfR-binding-impaired mutant restores its endosomal localization but not ferritin reduction or TfR elevation. Thus, binding to TfR is required for transport of HFE to endosomes and regulation of intracellular iron homeostasis, but not for basolateral surface expression of HFE.
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Affiliation(s)
- T S Ramalingam
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA
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88
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Abstract
LIR-1 is an inhibitory receptor that recognizes class I MHC molecules and the human cytomegalovirus class I homolog UL18. Here, we report the 2.1 A resolution crystal structure of the ligand binding portion of LIR-1 (domains 1 and 2 [D1D2]) and localize the binding region for UL18. LIR-1 D1D2 is composed of two immunoglobulin-like domains arranged at an acute angle to form a bent structure resembling the structures of natural killer inhibitory receptors (KIRs). The LIR-1 binding site comprises a portion of D1 distant from the interdomain hinge region that constitutes the KIR binding site, consistent with differences in LIR-1 and KIR recognition properties and functions.
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Affiliation(s)
- T L Chapman
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
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89
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West AP, Bjorkman PJ. Crystal structure and immunoglobulin G binding properties of the human major histocompatibility complex-related Fc receptor(,). Biochemistry 2000; 39:9698-708. [PMID: 10933786 DOI: 10.1021/bi000749m] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The neonatal Fc receptor (FcRn) performs two distinct but related functions: transport of maternal immunoglobulin G (IgG) to pre- or neonatal mammals, thus providing passive immunity, and protection of IgG from normal serum protein catabolism. FcRn is related to class I MHC proteins but lacks a functional peptide binding groove. The crystal structure of human FcRn has been determined at 2.7 A resolution and compared to the previously described structure of rat FcRn [Burmeister et al. (1994) Nature 372, 336-343] and to the structures of MHC and MHC-related proteins. Human FcRn is structurally similar to the rat receptor but does not form receptor dimers in the crystals as observed in crystals of rat FcRn. The interaction between human FcRn and IgG was characterized by determining the binding stoichiometry using equilibrium gel filtration and by deriving binding affinities for the different human IgG subclasses using a surface plasmon resonance assay. Like rat and mouse FcRn, human FcRn interacts with IgG with a 2:1 receptor:ligand stoichiometry. The binding of human FcRn to the four human IgG subclasses shows subclass and allotype variations but no clear subclass affinity differences that correlate with serum half-lives. The structure of human FcRn and studies of its ligand binding are relevant to current efforts to use FcRn-mediated regulation of IgG half-life in serum to increase the lifetimes of antibody-based therapeutics.
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Affiliation(s)
- A P West
- Division of Biology 156-29 and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA
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Abstract
HFE is a class I major histocompatibility complex (MHC)-related protein that is mutated in patients with the iron overload disease hereditary hemochromatosis. HFE binds to transferrin receptor (TfR), the receptor used by cells to obtain iron in the form of diferric transferrin (Fe-Tf). Previous studies demonstrated that HFE and Fe-Tf can bind simultaneously to TfR to form a ternary complex, and that membrane-bound or soluble HFE binding to cell surface TfR results in a reduction in the affinity of TfR for Fe-Tf. We studied the inhibition by soluble HFE of the interaction between soluble TfR and Fe-Tf using radioactivity-based and biosensor-based assays. The results demonstrate that HFE inhibits the TfR:Fe-Tf interaction by binding at or near the Fe-Tf binding site on TfR, and that the Fe-Tf:TfR:HFE ternary complex consists of one Fe-Tf and one HFE bound to a TfR homodimer.
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Affiliation(s)
- J A Lebrón
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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91
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Abstract
Populations of Anoplodiscus cirrusspiralis were monitored for 1 year on tagged individual snapper in experimental cages kept in a large on-shore pond with flow-through filtered sea water. The cages were stocked with small and large fish at either low or high initial density. Irrespective of size and density, snapper with light initial infections maintained light infections, whereas fish with heavy initial infections showed fluctuations in parasite population size throughout the year. These data indicate that some snapper have an innate resistance to infection by A. cirrusspiralis, with little evidence for acquired immunity induced by heavy infection. Parasite longevity was greater on the pectoral fin than caudal fin, and greater on large than small fish irrespective of fish density; longevity was greater on susceptible fish than on resistant fish. Recruitment and mortality rates were greater on the pectoral fin and in low density cages, but were influenced by fork length.
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Affiliation(s)
- A P West
- Fisheries Research Institute, Cronulla, N.S.W., Australia
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92
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West AP, Bjorkman PJ, Dougherty DA, Lester HA. Expression and circular dichroism studies of the extracellular domain of the alpha subunit of the nicotinic acetylcholine receptor. J Biol Chem 1997; 272:25468-73. [PMID: 9325259 DOI: 10.1074/jbc.272.41.25468] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
To provide material suitable for structural studies of the nicotinic acetylcholine receptor, we have expressed and purified the NH2-terminal extracellular domain of the mouse muscle alpha subunit. Several constructs were initially investigated using Xenopus oocytes as a convenient small scale expression system. A fusion protein (alpha210GPI) consisting of the 210 NH2-terminal amino acids of the alpha subunit and a glycosylphosphatidylinositol anchorage sequence conferred surface alpha-bungarotoxin binding in oocytes. Coexpression of alpha210GPI with an analogous construct made from the delta subunit showed no evidence of heterodimer formation. The alpha210GPI protein was chosen for large scale expression in transfected Chinese hamster ovary cells. The alpha210GPI protein was cleaved from these cells and purified on an immunoaffinity column. Gel and column chromatography show that the purified protein is processed as expected and exists as a monomer. The purified protein also retains the two distinct, conformation-specific binding sites expected for the correctly folded alpha subunit. Circular dichroism studies of alpha210GPI suggest that this region of the receptor includes considerable beta-sheet secondary structure, with a small proportion of alpha-helix.
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Affiliation(s)
- A P West
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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94
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Mecozzi S, West AP, Dougherty DA. Cation-pi interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide. Proc Natl Acad Sci U S A 1996; 93:10566-71. [PMID: 8855218 PMCID: PMC38193 DOI: 10.1073/pnas.93.20.10566] [Citation(s) in RCA: 463] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The cation-pi interaction is an important, general force for molecular recognition in biological receptors. Through the sidechains of aromatic amino acids, novel binding sites for cationic ligands such as acetylcholine can be constructed. We report here a number of calculations on prototypical cation-pi systems, emphasizing structures of relevance to biological receptors and prototypical heterocycles of the type often of importance in medicinal chemistry. Trends in the data can be rationalized using a relatively simple model that emphasizes the electrostatic component of the cation-pi interaction. In particular, plots of the electrostatic potential surfaces of the relevant aromatics provide useful guidelines for predicting cation-pi interactions in new systems.
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Affiliation(s)
- S Mecozzi
- Arnold and Mabel Beckman Laboratories of Chemical Synthesis, California Institute of Technology, Pasadena 91125, USA
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95
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West AP, Willison KR. Brefeldin A and mannose 6-phosphate regulation of acrosomic related vesicular trafficking. Eur J Cell Biol 1996; 70:315-21. [PMID: 8864659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Acrosomal biogenesis represents a unique system for the molecular analysis of the various processes involved in vesicular membrane transport. To assess the basic membrane trafficking mechanisms used in spermatids, we have used two fluorescent lipid compounds that label: a) the Golgi and Golgi-derived vesicles (C5-DMB-Cer), and b) endocytic vesicles (FM4-64). Incubation of mouse testicular germ cells at 33 degrees C for 1.5 h with C5-DMB-Cer revealed that C5-DMB-Cer labeling is localized in the Golgi and acrosome of early-maid round spermatid stages, with no labeling of the acrosome in late round spermatid stages. Culturing germ cells with FM4-64 for 1.5 h at 33 degrees C, showed that FM4-64 labeling in spermatids was localized in endocytic vesicles and Golgi of early-mid round spermatid stages, whereas in a small population of late round spermatid stages, FM4-64 was also localized in the apex region of the acrosome. Incubation with brefeldin A (BFA) (5 micrograms/ml) inhibited the distribution of C5-DMB-Cer and FM4-64 to the acrosome, however, it did not affect the localization of acrosin-an acrosome-specific protein-indicating that there was no apparent acrosome disassembly in the presence of BFA. Localization of FM4-64 in late round spermatids in the presence of 2.5 mM mannose 6-phosphate was found in endocytic vesicles and the Golgi, but not the acrosome. These results show that there are at least two sources of vesicular transport to the acrosome derived from the Golgi and plasma membrane.
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Affiliation(s)
- A P West
- CRC Centre for Cell and Molecular Biology, Chester Beatty Laboratories, London, United Kingdom
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Affiliation(s)
- Sandro Mecozzi
- Contribution No. 9162 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Anthony P. West
- Contribution No. 9162 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Dennis A. Dougherty
- Contribution No. 9162 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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West AP, Silverman SK, Dougherty DA. Do High-Spin Topology Rules Apply to Charged Polyradicals? Theoretical and Experimental Evaluation of Pyridiniums as Magnetic Coupling Units. J Am Chem Soc 1996. [DOI: 10.1021/ja9527941] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony P. West
- Contribution No. 9118 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Scott K. Silverman
- Contribution No. 9118 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Dennis A. Dougherty
- Contribution No. 9118 from the Arnold and Mabel Beckman Laboratories of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
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Abstract
Sixty two patients (mean age 45.6 years) were assessed for oral hygiene and periodontal disease by dental examination before endoscopy. Information about oral care, smoking, and dentures was obtained and samples of dental plaque collected. The presence of Helicobacter pylori in plaque as sought by culture and polymerase chain reaction (PCR), and gastric antral biopsy specimens were taken for histological examination. Although H pylori was detected in the antral specimens of 34 patients (54%) all of the cultures of dental plaque were negative, and PCR was only positive from the dentures of one patient. Smokers had poor oral hygiene, visited their dentist less often, and brushed their teeth less frequently. There was no correlation of H pylori gastritis with either dental hygiene or periodontal disease. These results suggest that dental plaque or dentures are not an important reservoir for H pylori and are probably not a significant factor in transmission of the organism. The conflicting results in published works may be caused by differences in sample collection, culture techniques, or oral contamination from gastric juice as a result of gastro-oesophageal reflux at the time of endoscopy.
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Affiliation(s)
- P G Hardo
- Department of Gastroenterology, Centre for Digestive Diseases, General Infirmary, Leeds
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Abstract
Campylobacter jejuni is the commonest cause of acute bacterial enteritis in the UK. However, in this case a 74-year-old lady underwent gastroscopy for an upper gastrointestinal haemorrhage and was noted to have a gastric ulcer. Gastric biopsy revealed spiral gram-negative bacteria and culture yielded a moderate growth of C. jejuni. Identification was confirmed by growth characteristics, biochemical tests and PCR amplification of the species-specific flagellin gene--fla A. To prevent misidentification, it is important that laboratories routinely culturing gastric biopsies for Helicobacter pylori should perform a rapid urease test and not rely solely on microscopic morphology.
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Affiliation(s)
- P Sahay
- Scunthorpe General Hospital, South Humberside
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