The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops
Of the complementarity‐determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the resid...
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| Veröffentlicht in: | Protein science 2016-04, Vol.25 (4), p.815-825 |
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| creator | Tsuchiya, Yuko Mizuguchi, Kenji |
| description | Of the complementarity‐determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops. |
| doi_str_mv | 10.1002/pro.2874 |
| format | Article |
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The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops.</description><identifier>ISSN: 0961-8368</identifier><identifier>EISSN: 1469-896X</identifier><identifier>DOI: 10.1002/pro.2874</identifier><identifier>PMID: 26749247</identifier><identifier>CODEN: PRCIEI</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Algorithms ; Amino Acid Sequence ; Amino acids ; Antibodies ; Antibodies - chemistry ; Antibodies - metabolism ; antigen recognition by antibodies ; Antigens ; Antigens - metabolism ; antigen‐binding tendency ; Binding ; Complementarity ; Complementarity Determining Regions - chemistry ; Complementarity Determining Regions - metabolism ; Crystallography, X-Ray ; diverse conformations of long H3 loops ; diversity of CDR‐H3 ; hydrogen bond networks ; Models, Molecular ; Pattern recognition ; Protein Conformation ; Residues</subject><ispartof>Protein science, 2016-04, Vol.25 (4), p.815-825</ispartof><rights>2016 The Protein Society</rights><rights>2016 The Protein Society.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941225/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941225/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,1411,1427,27903,27904,45553,45554,46387,46811,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26749247$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tsuchiya, Yuko</creatorcontrib><creatorcontrib>Mizuguchi, Kenji</creatorcontrib><title>The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops</title><title>Protein science</title><addtitle>Protein Sci</addtitle><description>Of the complementarity‐determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops.</description><subject>Algorithms</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Antibodies</subject><subject>Antibodies - chemistry</subject><subject>Antibodies - metabolism</subject><subject>antigen recognition by antibodies</subject><subject>Antigens</subject><subject>Antigens - metabolism</subject><subject>antigen‐binding tendency</subject><subject>Binding</subject><subject>Complementarity</subject><subject>Complementarity Determining Regions - chemistry</subject><subject>Complementarity Determining Regions - metabolism</subject><subject>Crystallography, X-Ray</subject><subject>diverse conformations of long H3 loops</subject><subject>diversity of CDR‐H3</subject><subject>hydrogen bond networks</subject><subject>Models, Molecular</subject><subject>Pattern recognition</subject><subject>Protein Conformation</subject><subject>Residues</subject><issn>0961-8368</issn><issn>1469-896X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kU1qHDEQhYVJsCdOwCcwDdlk007pp9XSxmAm_gkYHIwDgSyEplU91tAjjVs9NrPzEXJGnyRqxjFxFlmIQryvHlX1CDmgcEQB2OdVH4-YqsUOmVAhdam0_PGGTEBLWiou1R55l9ICAARlfJfsMVkLzUQ9IT9vbrFw_h775IdNEdvighddjKtUOBywX_qAqRgyZMPg5xieHn_NfHA-zIsBg8PQ-AzkvlGfRbcppl-utw7vydvWdgk_PNd98v3s9GZ6UV5enX-dnlyWCyFBlByqGWcgmkpA3TDNUFJopKiVkxZow6mrUeWH2Fo77mSdE6pqbds6azXfJ8db39V6tkTXYBh625lV75e235hovXmtBH9r5vHeCJ3vwaps8OnZoI93a0yDWfrUYNfZgHGdDK1rCZoB5Rn9-A-6iOs-5PUMo1yDoopW_6OyV1UprajI1OHfc78M_CedDJRb4MF3uHnRKZgx9fyPZkzdfLu-Giv_DXAfn-E</recordid><startdate>201604</startdate><enddate>201604</enddate><creator>Tsuchiya, Yuko</creator><creator>Mizuguchi, Kenji</creator><general>Wiley Subscription Services, Inc</general><general>John Wiley and Sons Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QO</scope><scope>7T5</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201604</creationdate><title>The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops</title><author>Tsuchiya, Yuko ; 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The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>26749247</pmid><doi>10.1002/pro.2874</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Wiley Free Content; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Algorithms Amino Acid Sequence Amino acids Antibodies Antibodies - chemistry Antibodies - metabolism antigen recognition by antibodies Antigens Antigens - metabolism antigen‐binding tendency Binding Complementarity Complementarity Determining Regions - chemistry Complementarity Determining Regions - metabolism Crystallography, X-Ray diverse conformations of long H3 loops diversity of CDR‐H3 hydrogen bond networks Models, Molecular Pattern recognition Protein Conformation Residues |
| title | The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops |
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