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 : 000B05 ( Main/Exploration ); précédent : 000B04; suivant : 000B06The 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 [République populaire de Chine] ; Xiaoting Wang [République populaire de Chine] ; Huijun Sun [République populaire de Chine] ; Huanxiang Liu [République populaire de Chine] ; Yulin Shen [République populaire de Chine] ; Xiaojun Yao [République populaire de Chine]Source :
- 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
Affiliations:
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type="main">Chemical Biology & Drug Design</title><title level="j" type="alt">CHEMICAL BIOLOGY DRUG DESIGN</title><idno type="ISSN">1747-0277</idno><idno 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. 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.</div></front></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Guo, Jingjing" sort="Guo, Jingjing" uniqKey="Guo J" first="Jingjing" last="Guo">Jingjing Guo</name></noRegion><name sortKey="Liu, Huanxiang" sort="Liu, Huanxiang" uniqKey="Liu H" first="Huanxiang" last="Liu">Huanxiang Liu</name><name sortKey="Shen, Yulin" sort="Shen, Yulin" uniqKey="Shen Y" first="Yulin" last="Shen">Yulin Shen</name><name sortKey="Sun, Huijun" sort="Sun, Huijun" uniqKey="Sun H" first="Huijun" last="Sun">Huijun Sun</name><name sortKey="Wang, Xiaoting" sort="Wang, Xiaoting" uniqKey="Wang X" first="Xiaoting" last="Wang">Xiaoting Wang</name><name sortKey="Yao, Xiaojun" sort="Yao, Xiaojun" uniqKey="Yao X" first="Xiaojun" last="Yao">Xiaojun Yao</name><name sortKey="Yao, Xiaojun" sort="Yao, Xiaojun" uniqKey="Yao X" first="Xiaojun" last="Yao">Xiaojun Yao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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