The Evolution of HLA‐B*3501 Binding Affinity to Variable Immunodominant NP418‐426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study
Identifieur interne : 000935 ( Istex/Corpus ); précédent : 000934; suivant : 000936The Evolution of HLA‐B*3501 Binding Affinity to Variable Immunodominant NP418‐426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study
Auteurs : Jingjing Guo ; Xiaoting Wang ; Huijun Sun ; Huanxiang Liu ; Yulin Shen ; Xiaojun YaoSource :
- Chemical Biology & Drug Design [ 1747-0277 ] ; 2012-06.
Abstract
Virus‐specific cytotoxic T lymphocytes contribute to the control of virus infections including those caused by influenza viruses. However, during the evolution of influenza A viruses, variations in cytotoxic T lymphocytes epitopes have been observed and it will affect the recognition by virus‐specific cytotoxic T lymphocytes and the human virus‐specific cytotoxic T lymphocytes response in vitro. Here, to gain further insights into the molecular mechanism of the virus‐specific cytotoxic T lymphocytes immunity, the class I major histocompatibility complex‐encoded HLA‐B*3501 protein with six different NP418‐426 antigenic peptides emerging from 1918 to 2009 pandemic influenza A virus were studied by molecular dynamics simulation. Dynamical and structural properties (such as atomic fluctuations, solvent‐accessible surface areas, binding free energy), based on the solvated protein‐peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC‐I with antigenic non‐apeptides. Furthermore, major interactions with peptides were gained from HLA‐B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP418‐426 mutants effectively bind with the HLA‐B*3501.
A molecular modeling study for six NP418‐426 peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA‐B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus‐specific CTL immunity. Our work will be useful for the design of novel vaccination regimens that provide a measure of protection against unpredicted pandemic and seasonal influenza strains.
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DOI: 10.1111/j.1747-0285.2012.01357.x
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ISTEX:948D1904A72BC5FDF23BE44312584741D83F7B39Le document en format XML
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type="eISSN">1747-0285</idno><imprint><biblScope unit="vol">79</biblScope><biblScope unit="issue">6</biblScope><biblScope unit="page" from="1025">1025</biblScope><biblScope unit="page" to="1032">1032</biblScope><biblScope unit="page-count">8</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2012-06">2012-06</date></imprint><idno type="ISSN">1747-0277</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1747-0277</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Virus‐specific cytotoxic T lymphocytes contribute to the control of virus infections including those caused by influenza viruses. However, during the evolution of influenza A viruses, variations in cytotoxic T lymphocytes epitopes have been observed and it will affect the recognition by virus‐specific cytotoxic T lymphocytes and the human virus‐specific cytotoxic T lymphocytes response in vitro. Here, to gain further insights into the molecular mechanism of the virus‐specific cytotoxic T lymphocytes immunity, the class I major histocompatibility complex‐encoded HLA‐B*3501 protein with six different NP418‐426 antigenic peptides emerging from 1918 to 2009 pandemic influenza A virus were studied by molecular dynamics simulation. Dynamical and structural properties (such as atomic fluctuations, solvent‐accessible surface areas, binding free energy), based on the solvated protein‐peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC‐I with antigenic non‐apeptides. Furthermore, major interactions with peptides were gained from HLA‐B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP418‐426 mutants effectively bind with the HLA‐B*3501.</div><div type="abstract">A molecular modeling study for six NP418‐426 peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA‐B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus‐specific CTL immunity. 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Dynamical and structural properties (such as atomic fluctuations, solvent‐accessible surface areas, binding free energy), based on the solvated protein‐peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC‐I with antigenic non‐apeptides. Furthermore, major interactions with peptides were gained from HLA‐B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP<hi rend="subscript">418‐426</hi> mutants effectively bind with the HLA‐B*3501.</p></abstract><abstract style="graphical"><p>A molecular modeling study for six NP<hi rend="subscript">418‐426</hi> peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA‐B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus‐specific CTL immunity. 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xml:id="pub2tei">formatting</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-Q3QN13Q5-P/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1747-0285</doi><issn type="print">1747-0277</issn><issn type="electronic">1747-0285</issn><idGroup><id type="product" value="CBDD"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="CHEMICAL BIOLOGY DRUG DESIGN">Chemical Biology & Drug Design</title></titleGroup></publicationMeta><publicationMeta level="part" position="06106"><doi origin="wiley">10.1111/jpp.2012.79.issue-6</doi><numberingGroup><numbering type="journalVolume" number="79">79</numbering><numbering type="journalIssue" number="6">6</numbering></numberingGroup><coverDate startDate="2012-06">June 2012</coverDate></publicationMeta><publicationMeta level="unit" type="letter" position="18" status="forIssue"><doi origin="wiley">10.1111/j.1747-0285.2012.01357.x</doi><idGroup><id type="unit" value="CBDD1357"></id></idGroup><countGroup><count type="pageTotal" number="8"></count></countGroup><titleGroup><title type="tocHeading1">Research Letters</title><title type="articleCategory">Research Letter</title></titleGroup><copyright>© 2012 John Wiley & Sons A/S</copyright><eventGroup><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:3.1.3 standalone mode:FullText" date="2012-05-01"></event><event type="publishedOnlineAccepted" date="2012-02-09"></event><event type="publishedOnlineEarlyUnpaginated" date="2012-03-19"></event><event type="firstOnline" date="2012-03-19"></event><event type="publishedOnlineFinalForm" date="2012-05-01"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-08"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.3.4 mode:FullText" date="2015-02-25"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="1025">1025</numbering><numbering type="pageLast" number="1032">1032</numbering></numberingGroup><correspondenceTo><i>Corresponding author: Xiaojun Yao, </i><email>xjyao@lzu.edu.cn</email></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:CBDD.CBDD1357.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 13 April 2011, revised 12 December 2011 and accepted for publication 31 January 2012</unparsedEditorialHistory><countGroup><count type="figureTotal" number="8"></count><count type="tableTotal" number="3"></count></countGroup><titleGroup><title type="main">The Evolution of HLA‐B*3501 Binding Affinity to Variable Immunodominant NP<sub>418‐426</sub> Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study</title><title type="shortAuthors"><b>Guo et al.</b></title><title type="short"><b>Binding Affinity between NP<sub>418‐426</sub> and HLA‐B*3501</b></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1"><personName><givenNames>Jingjing</givenNames><familyName>Guo</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>Xiaoting</givenNames><familyName>Wang</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1"><personName><givenNames>Huijun</givenNames><familyName>Sun</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a2"><personName><givenNames>Huanxiang</givenNames><familyName>Liu</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a3"><personName><givenNames>Yulin</givenNames><familyName>Shen</familyName></personName></creator><creator creatorRole="author" xml:id="cr6" affiliationRef="#a1" corresponding="yes"><personName><givenNames>Xiaojun</givenNames><familyName>Yao</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="CN"><unparsedAffiliation>State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China</unparsedAffiliation></affiliation><affiliation xml:id="a2" countryCode="CN"><unparsedAffiliation>School of Pharmacy, Lanzhou University, Lanzhou 730000, China</unparsedAffiliation></affiliation><affiliation xml:id="a3" countryCode="CN"><unparsedAffiliation>Gansu Computing Center, Lanzhou 730030, China</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">2009 influenza A virus</keyword><keyword xml:id="k2">HLA‐B*3501</keyword><keyword xml:id="k3">molecular dynamics simulation</keyword><keyword xml:id="k4">NP<sub>418‐426</sub></keyword><keyword xml:id="k5">pMHC‐I</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><p>Virus‐specific cytotoxic T lymphocytes contribute to the control of virus infections including those caused by influenza viruses. However, during the evolution of influenza A viruses, variations in cytotoxic T lymphocytes epitopes have been observed and it will affect the recognition by virus‐specific cytotoxic T lymphocytes and the human virus‐specific cytotoxic T lymphocytes response <i>in vitro</i>. Here, to gain further insights into the molecular mechanism of the virus‐specific cytotoxic T lymphocytes immunity, the class I major histocompatibility complex‐encoded HLA‐B*3501 protein with six different NP<sub>418‐426</sub> antigenic peptides emerging from 1918 to 2009 pandemic influenza A virus were studied by molecular dynamics simulation. Dynamical and structural properties (such as atomic fluctuations, solvent‐accessible surface areas, binding free energy), based on the solvated protein‐peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC‐I with antigenic non‐apeptides. Furthermore, major interactions with peptides were gained from HLA‐B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP<sub>418‐426</sub> mutants effectively bind with the HLA‐B*3501.</p></abstract><abstract type="graphical"><p>A molecular modeling study for six NP<sub>418‐426</sub> peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA‐B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus‐specific CTL immunity. Our work will be useful for the design of novel vaccination regimens that provide a measure of protection against unpredicted pandemic and seasonal influenza strains.<blockFixed type="graphic" xml:id="f1ga"><mediaResourceGroup><mediaResource alt="image" href="urn:x-wiley:17470277:media:CBDD1357:CBDD_1357_f1ga"></mediaResource></mediaResourceGroup></blockFixed></p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>The Evolution of HLA‐B*3501 Binding Affinity to Variable Immunodominant NP418‐426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Binding Affinity between NP418‐426 and HLA‐B*3501</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>The Evolution of HLA‐B*3501 Binding Affinity to Variable Immunodominant NP418‐426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study</title></titleInfo><name type="personal"><namePart type="given">Jingjing</namePart><namePart type="family">Guo</namePart><affiliation>State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Xiaoting</namePart><namePart type="family">Wang</namePart><affiliation>State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Huijun</namePart><namePart type="family">Sun</namePart><affiliation>State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Huanxiang</namePart><namePart type="family">Liu</namePart><affiliation>School of Pharmacy, Lanzhou University, Lanzhou 730000, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Yulin</namePart><namePart type="family">Shen</namePart><affiliation>Gansu Computing Center, Lanzhou 730030, China</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Xiaojun</namePart><namePart type="family">Yao</namePart><affiliation>State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China</affiliation><affiliation>E-mail: xjyao@lzu.edu.cn</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="review-article" displayLabel="letter" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-L5L7X3NF-P">review-article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2012-06</dateIssued><edition>Received 13 April 2011, revised 12 December 2011 and accepted for publication 31 January 2012</edition><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">8</extent><extent unit="tables">3</extent></physicalDescription><abstract lang="en">Virus‐specific cytotoxic T lymphocytes contribute to the control of virus infections including those caused by influenza viruses. However, during the evolution of influenza A viruses, variations in cytotoxic T lymphocytes epitopes have been observed and it will affect the recognition by virus‐specific cytotoxic T lymphocytes and the human virus‐specific cytotoxic T lymphocytes response in vitro. Here, to gain further insights into the molecular mechanism of the virus‐specific cytotoxic T lymphocytes immunity, the class I major histocompatibility complex‐encoded HLA‐B*3501 protein with six different NP418‐426 antigenic peptides emerging from 1918 to 2009 pandemic influenza A virus were studied by molecular dynamics simulation. Dynamical and structural properties (such as atomic fluctuations, solvent‐accessible surface areas, binding free energy), based on the solvated protein‐peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC‐I with antigenic non‐apeptides. Furthermore, major interactions with peptides were gained from HLA‐B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP418‐426 mutants effectively bind with the HLA‐B*3501.</abstract><abstract type="graphical">A molecular modeling study for six NP418‐426 peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA‐B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus‐specific CTL immunity. Our work will be useful for the design of novel vaccination regimens that provide a measure of protection against unpredicted pandemic and seasonal influenza strains.</abstract><subject lang="en"><genre>keywords</genre><topic>2009 influenza A virus</topic><topic>HLA‐B*3501</topic><topic>molecular dynamics simulation</topic><topic>NP418‐426</topic><topic>pMHC‐I</topic></subject><relatedItem type="host"><titleInfo><title>Chemical Biology & Drug Design</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><subject><genre>article-category</genre><topic>Research Letters</topic><topic>Research Letter</topic></subject><identifier type="ISSN">1747-0277</identifier><identifier type="eISSN">1747-0285</identifier><identifier type="DOI">10.1111/(ISSN)1747-0285</identifier><identifier type="PublisherID">CBDD</identifier><part><date>2012</date><detail type="volume"><caption>vol.</caption><number>79</number></detail><detail type="issue"><caption>no.</caption><number>6</number></detail><extent unit="pages"><start>1025</start><end>1032</end><total>8</total></extent></part></relatedItem><relatedItem type="references" displayLabel="cit1"><titleInfo><title>Evolution of human receptor binding affinity of H1N1 hemagglutinins from 1918 to 2009 pandemic influenza A virus</title></titleInfo><name type="personal"><namePart type="given">N.</namePart><namePart type="family">Nunthaboot</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">T.</namePart><namePart type="family">Rungrotmongkol</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="family">Malaisree</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">N.</namePart><namePart type="family">Kaiyawet</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P.</namePart><namePart type="family">Decha</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">P.</namePart><namePart type="family">Sompornpisut</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Y.</namePart><namePart type="family">Poovorawan</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">S.</namePart><namePart type="family">Hannongbua</namePart><role><roleTerm type="text">author</roleTerm></role></name><genre>journal-article</genre><note type="citation/reference">Nunthaboot N., Rungrotmongkol T., Malaisree M., Kaiyawet N., Decha P., Sompornpisut P., Poovorawan Y., Hannongbua S. 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