Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one
Understanding the basis of the binding of a T cell receptor (TR) to the peptide-MHC (pMHC) complex is essential due to the vital role it plays in adaptive immune response. We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential...
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| Veröffentlicht in: | PloS one 2011-02, Vol.6 (2), p.e17194-e17194 |
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| creator | Khan, Javed Mohammed Ranganathan, Shoba |
| description | Understanding the basis of the binding of a T cell receptor (TR) to the peptide-MHC (pMHC) complex is essential due to the vital role it plays in adaptive immune response. We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. In doing so, we have successfully demonstrated a novel/rational approach for θ calculation, obtained a linear correlation between BE and θ without any "codon" or amino acid preference, provided an explanation for TR ability to scan many pMHC ligands yet specifically bind one, proposed a mechanism for pMHC recognition by TR leading to T cell activation and illustrated the importance of the peptide in determining TR specificity, challenging the "germline bias" theory. |
| doi_str_mv | 10.1371/journal.pone.0017194 |
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We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. In doing so, we have successfully demonstrated a novel/rational approach for θ calculation, obtained a linear correlation between BE and θ without any "codon" or amino acid preference, provided an explanation for TR ability to scan many pMHC ligands yet specifically bind one, proposed a mechanism for pMHC recognition by TR leading to T cell activation and illustrated the importance of the peptide in determining TR specificity, challenging the "germline bias" theory.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0017194</identifier><identifier>PMID: 21364947</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adaptive immunity ; Amino acids ; Animals ; Antigenic determinants ; Antigens ; B cells ; Bias ; Binding ; Binding sites ; Bioinformatics ; Biology ; Cell activation ; Codons ; Comprehension - physiology ; Crystal structure ; Crystallography ; Datasets ; Docking ; Electrostatic properties ; Energy Metabolism - physiology ; Epitopes ; Histocompatibility Antigens Class I - chemistry ; Histocompatibility Antigens Class I - immunology ; Histocompatibility Antigens Class I - metabolism ; Humans ; Immune response ; Immune system ; Lymphocyte Activation - immunology ; Lymphocytes ; Major histocompatibility complex ; Mathematical analysis ; Medicine ; Mice ; Models, Biological ; Models, Molecular ; Multiprotein Complexes - chemistry ; Multiprotein Complexes - immunology ; Multiprotein Complexes - metabolism ; Peptides ; Physics ; Protein Binding - physiology ; Protein folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Receptors, Antigen, T-Cell - agonists ; Receptors, Antigen, T-Cell - chemistry ; Receptors, Antigen, T-Cell - immunology ; Receptors, Antigen, T-Cell - metabolism ; Substrate Specificity - immunology ; T cell receptors ; T cells ; T-Cell Antigen Receptor Specificity - immunology ; T-Cell Antigen Receptor Specificity - physiology ; T-cell receptor</subject><ispartof>PloS one, 2011-02, Vol.6 (2), p.e17194-e17194</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Khan, Ranganathan. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. 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agonists</topic><topic>Receptors, Antigen, T-Cell - chemistry</topic><topic>Receptors, Antigen, T-Cell - immunology</topic><topic>Receptors, Antigen, T-Cell - metabolism</topic><topic>Substrate Specificity - immunology</topic><topic>T cell receptors</topic><topic>T cells</topic><topic>T-Cell Antigen Receptor Specificity - immunology</topic><topic>T-Cell Antigen Receptor Specificity - physiology</topic><topic>T-cell receptor</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Khan, Javed Mohammed</creatorcontrib><creatorcontrib>Ranganathan, Shoba</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Khan, Javed Mohammed</au><au>Ranganathan, Shoba</au><au>Brusic, Vladimir</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-02-22</date><risdate>2011</risdate><volume>6</volume><issue>2</issue><spage>e17194</spage><epage>e17194</epage><pages>e17194-e17194</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Understanding the basis of the binding of a T cell receptor (TR) to the peptide-MHC (pMHC) complex is essential due to the vital role it plays in adaptive immune response. We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. In doing so, we have successfully demonstrated a novel/rational approach for θ calculation, obtained a linear correlation between BE and θ without any "codon" or amino acid preference, provided an explanation for TR ability to scan many pMHC ligands yet specifically bind one, proposed a mechanism for pMHC recognition by TR leading to T cell activation and illustrated the importance of the peptide in determining TR specificity, challenging the "germline bias" theory.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21364947</pmid><doi>10.1371/journal.pone.0017194</doi><tpages>e17194</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adaptive immunity Amino acids Animals Antigenic determinants Antigens B cells Bias Binding Binding sites Bioinformatics Biology Cell activation Codons Comprehension - physiology Crystal structure Crystallography Datasets Docking Electrostatic properties Energy Metabolism - physiology Epitopes Histocompatibility Antigens Class I - chemistry Histocompatibility Antigens Class I - immunology Histocompatibility Antigens Class I - metabolism Humans Immune response Immune system Lymphocyte Activation - immunology Lymphocytes Major histocompatibility complex Mathematical analysis Medicine Mice Models, Biological Models, Molecular Multiprotein Complexes - chemistry Multiprotein Complexes - immunology Multiprotein Complexes - metabolism Peptides Physics Protein Binding - physiology Protein folding Protein Structure, Quaternary Protein Structure, Secondary Receptors, Antigen, T-Cell - agonists Receptors, Antigen, T-Cell - chemistry Receptors, Antigen, T-Cell - immunology Receptors, Antigen, T-Cell - metabolism Substrate Specificity - immunology T cell receptors T cells T-Cell Antigen Receptor Specificity - immunology T-Cell Antigen Receptor Specificity - physiology T-cell receptor |
| title | Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one |
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