Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein
Abstract The hexon protein of human adenovirus (HAdV) processes type-specific B-cell neutralizing epitopes. We developed a new effective, reliable approach to map these epitopes on hexon protein of HAdVs. A three-dimensional (3D) model of the HAdV3 hexon was obtained by homology modeling and refined...
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| Veröffentlicht in: | Vaccine 2009-08, Vol.27 (37), p.5103-5110 |
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| creator | Yuan, Xiaohui Qu, Zhangyi Wu, Xiaomin Wang, Yingchen Liu, Lei Wei, Fengxiang Gao, Hong Shang, Lei Zhang, Hongyan Cui, Hongbo Zhao, Yuehui Wu, Na Tang, Yanhong Qin, Le |
| description | Abstract The hexon protein of human adenovirus (HAdV) processes type-specific B-cell neutralizing epitopes. We developed a new effective, reliable approach to map these epitopes on hexon protein of HAdVs. A three-dimensional (3D) model of the HAdV3 hexon was obtained by homology modeling and refined by molecular mechanics and molecular dynamics simulations. A modified evolutionary trace (ET) analysis called reverse ET (RET) was used to predict the type-specific B-cell neutralizing epitopes. An epitope-screening algorithm based on analyzing the solvent accessibility surface (SAS) area from the 3D model and calculation of sites homology using RET was designed and implemented in the BioPerl script language. Five epitope polypeptide segments were predicted and mapped onto the 3D model. Finally five polypeptides were synthesized and the predicted epitopes were identified by enzyme-linked immunosorbent assay (ELISA) and Neutralization Test (NT). It was found that the type-specific neutralizing epitopes of HAdV3 are located at the top surface of hexon tower regions (residue numbers: 135–146, 169–178, 237–251, 262–272, 420–434). This work is of great significance to the molecular design of a multivalent HAdVs vaccine. |
| doi_str_mv | 10.1016/j.vaccine.2009.06.041 |
| format | Article |
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We developed a new effective, reliable approach to map these epitopes on hexon protein of HAdVs. A three-dimensional (3D) model of the HAdV3 hexon was obtained by homology modeling and refined by molecular mechanics and molecular dynamics simulations. A modified evolutionary trace (ET) analysis called reverse ET (RET) was used to predict the type-specific B-cell neutralizing epitopes. An epitope-screening algorithm based on analyzing the solvent accessibility surface (SAS) area from the 3D model and calculation of sites homology using RET was designed and implemented in the BioPerl script language. Five epitope polypeptide segments were predicted and mapped onto the 3D model. Finally five polypeptides were synthesized and the predicted epitopes were identified by enzyme-linked immunosorbent assay (ELISA) and Neutralization Test (NT). It was found that the type-specific neutralizing epitopes of HAdV3 are located at the top surface of hexon tower regions (residue numbers: 135–146, 169–178, 237–251, 262–272, 420–434). This work is of great significance to the molecular design of a multivalent HAdVs vaccine.</description><identifier>ISSN: 0264-410X</identifier><identifier>EISSN: 1873-2518</identifier><identifier>DOI: 10.1016/j.vaccine.2009.06.041</identifier><identifier>PMID: 19573641</identifier><identifier>CODEN: VACCDE</identifier><language>eng</language><publisher>Kidlington: Elsevier Ltd</publisher><subject>Adenoviruses, Human - chemistry ; Adenoviruses, Human - immunology ; Allergy and Immunology ; Amino Acid Sequence ; Antigens, Viral - chemistry ; Antigens, Viral - immunology ; Applied microbiology ; Atoms & subatomic particles ; Bioinformatics ; Biological and medical sciences ; Capsid Proteins - chemistry ; Capsid Proteins - immunology ; Enzyme-Linked Immunosorbent Assay ; Epitope Mapping ; Epitopes - chemistry ; Epitopes - immunology ; Experiments ; Fundamental and applied biological sciences. Psychology ; HAdV ; Hexon protein ; Human adenovirus ; Humans ; Infections ; Laboratories ; Microbiology ; Miscellaneous ; Models, Molecular ; Molecular Sequence Data ; Neutralization ; Neutralization Tests ; Polypeptides ; Protein Structure, Secondary ; Proteins ; Sequence Homology, Amino Acid ; Studies ; Vaccines ; Vaccines, antisera, therapeutical immunoglobulins and monoclonal antibodies (general aspects) ; Viral infections ; Virology</subject><ispartof>Vaccine, 2009-08, Vol.27 (37), p.5103-5110</ispartof><rights>Elsevier Ltd</rights><rights>2009 Elsevier Ltd</rights><rights>2009 INIST-CNRS</rights><rights>Copyright Elsevier Limited Aug 13, 2009</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c507t-e6a311dbf2a7e3ba800f9727c5df639df17f5038bae4fd6332a4d0d7d05713</citedby><cites>FETCH-LOGICAL-c507t-e6a311dbf2a7e3ba800f9727c5df639df17f5038bae4fd6332a4d0d7d05713</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0264410X09008901$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21792480$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19573641$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yuan, Xiaohui</creatorcontrib><creatorcontrib>Qu, Zhangyi</creatorcontrib><creatorcontrib>Wu, Xiaomin</creatorcontrib><creatorcontrib>Wang, Yingchen</creatorcontrib><creatorcontrib>Liu, Lei</creatorcontrib><creatorcontrib>Wei, Fengxiang</creatorcontrib><creatorcontrib>Gao, Hong</creatorcontrib><creatorcontrib>Shang, Lei</creatorcontrib><creatorcontrib>Zhang, Hongyan</creatorcontrib><creatorcontrib>Cui, Hongbo</creatorcontrib><creatorcontrib>Zhao, Yuehui</creatorcontrib><creatorcontrib>Wu, Na</creatorcontrib><creatorcontrib>Tang, Yanhong</creatorcontrib><creatorcontrib>Qin, Le</creatorcontrib><title>Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein</title><title>Vaccine</title><addtitle>Vaccine</addtitle><description>Abstract The hexon protein of human adenovirus (HAdV) processes type-specific B-cell neutralizing epitopes. We developed a new effective, reliable approach to map these epitopes on hexon protein of HAdVs. A three-dimensional (3D) model of the HAdV3 hexon was obtained by homology modeling and refined by molecular mechanics and molecular dynamics simulations. A modified evolutionary trace (ET) analysis called reverse ET (RET) was used to predict the type-specific B-cell neutralizing epitopes. An epitope-screening algorithm based on analyzing the solvent accessibility surface (SAS) area from the 3D model and calculation of sites homology using RET was designed and implemented in the BioPerl script language. Five epitope polypeptide segments were predicted and mapped onto the 3D model. Finally five polypeptides were synthesized and the predicted epitopes were identified by enzyme-linked immunosorbent assay (ELISA) and Neutralization Test (NT). It was found that the type-specific neutralizing epitopes of HAdV3 are located at the top surface of hexon tower regions (residue numbers: 135–146, 169–178, 237–251, 262–272, 420–434). This work is of great significance to the molecular design of a multivalent HAdVs vaccine.</description><subject>Adenoviruses, Human - chemistry</subject><subject>Adenoviruses, Human - immunology</subject><subject>Allergy and Immunology</subject><subject>Amino Acid Sequence</subject><subject>Antigens, Viral - chemistry</subject><subject>Antigens, Viral - immunology</subject><subject>Applied microbiology</subject><subject>Atoms & subatomic particles</subject><subject>Bioinformatics</subject><subject>Biological and medical sciences</subject><subject>Capsid Proteins - chemistry</subject><subject>Capsid Proteins - immunology</subject><subject>Enzyme-Linked Immunosorbent Assay</subject><subject>Epitope Mapping</subject><subject>Epitopes - chemistry</subject><subject>Epitopes - immunology</subject><subject>Experiments</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>HAdV</subject><subject>Hexon protein</subject><subject>Human adenovirus</subject><subject>Humans</subject><subject>Infections</subject><subject>Laboratories</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Neutralization</subject><subject>Neutralization Tests</subject><subject>Polypeptides</subject><subject>Protein Structure, Secondary</subject><subject>Proteins</subject><subject>Sequence Homology, Amino Acid</subject><subject>Studies</subject><subject>Vaccines</subject><subject>Vaccines, antisera, therapeutical immunoglobulins and monoclonal antibodies (general aspects)</subject><subject>Viral infections</subject><subject>Virology</subject><issn>0264-410X</issn><issn>1873-2518</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNqFkl-L1DAUxYMo7jj6EZSC6FvHm6RN2hdFFv_BiqI--BYyya2bsU1q0g7Otzdligv7sk-By--em3vOJeQphR0FKl4ddkdtjPO4YwDtDsQOKnqPbGgjeclq2twnG2CiKisKPy_Io5QOAFBz2j4kF7StJRcV3ZCvn0OPZu51LIZgsXf-V6G9LXB0UxgxFYMex6UYuuJ6HrQvtEUfji7OqZhOIxa8uMa_wRdjDBM6_5g86HSf8Mn6bsm39-9-XH4sr758-HT59qo0NcipRKE5pXbfMS2R73UD0LWSSVPbTvDWdlR2NfBmr7HqrOCc6cqClRZqSfmWvDyL5qF_ZkyTGlwy2PfaY5iTErJmLav5nSADCbTJtmzJ81vgIczR5w0UFbRpgUHFMlWfKRNDShE7NUY36HhSFNQSizqoNRa1xKJAqBxL7nu2qs_7Ae1N15pDBl6sgE5G913U3rj0n2NUtqxqIHNvzhxma48Oo0rGoTdoXUQzKRvcnV95fUvB5NBdHvobT5hutlaJKVDflxtaTghagGwD5f8AA8vCIQ</recordid><startdate>20090813</startdate><enddate>20090813</enddate><creator>Yuan, Xiaohui</creator><creator>Qu, Zhangyi</creator><creator>Wu, Xiaomin</creator><creator>Wang, Yingchen</creator><creator>Liu, Lei</creator><creator>Wei, Fengxiang</creator><creator>Gao, Hong</creator><creator>Shang, Lei</creator><creator>Zhang, Hongyan</creator><creator>Cui, Hongbo</creator><creator>Zhao, Yuehui</creator><creator>Wu, Na</creator><creator>Tang, Yanhong</creator><creator>Qin, Le</creator><general>Elsevier Ltd</general><general>Elsevier</general><general>Elsevier Limited</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7RV</scope><scope>7T2</scope><scope>7T5</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88C</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9-</scope><scope>K9.</scope><scope>KB0</scope><scope>LK8</scope><scope>M0R</scope><scope>M0S</scope><scope>M0T</scope><scope>M1P</scope><scope>M2O</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>NAPCQ</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope></search><sort><creationdate>20090813</creationdate><title>Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein</title><author>Yuan, Xiaohui ; Qu, Zhangyi ; Wu, Xiaomin ; Wang, Yingchen ; Liu, Lei ; Wei, Fengxiang ; Gao, Hong ; Shang, Lei ; Zhang, Hongyan ; Cui, Hongbo ; Zhao, Yuehui ; Wu, Na ; Tang, Yanhong ; Qin, Le</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c507t-e6a311dbf2a7e3ba800f9727c5df639df17f5038bae4fd6332a4d0d7d05713</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Adenoviruses, Human - chemistry</topic><topic>Adenoviruses, Human - immunology</topic><topic>Allergy and Immunology</topic><topic>Amino Acid Sequence</topic><topic>Antigens, Viral - chemistry</topic><topic>Antigens, Viral - immunology</topic><topic>Applied microbiology</topic><topic>Atoms & subatomic particles</topic><topic>Bioinformatics</topic><topic>Biological and medical sciences</topic><topic>Capsid Proteins - chemistry</topic><topic>Capsid Proteins - immunology</topic><topic>Enzyme-Linked Immunosorbent Assay</topic><topic>Epitope Mapping</topic><topic>Epitopes - chemistry</topic><topic>Epitopes - immunology</topic><topic>Experiments</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>HAdV</topic><topic>Hexon protein</topic><topic>Human adenovirus</topic><topic>Humans</topic><topic>Infections</topic><topic>Laboratories</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Neutralization</topic><topic>Neutralization Tests</topic><topic>Polypeptides</topic><topic>Protein Structure, Secondary</topic><topic>Proteins</topic><topic>Sequence Homology, Amino Acid</topic><topic>Studies</topic><topic>Vaccines</topic><topic>Vaccines, antisera, therapeutical immunoglobulins and monoclonal antibodies (general aspects)</topic><topic>Viral infections</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yuan, Xiaohui</creatorcontrib><creatorcontrib>Qu, Zhangyi</creatorcontrib><creatorcontrib>Wu, Xiaomin</creatorcontrib><creatorcontrib>Wang, Yingchen</creatorcontrib><creatorcontrib>Liu, Lei</creatorcontrib><creatorcontrib>Wei, Fengxiang</creatorcontrib><creatorcontrib>Gao, Hong</creatorcontrib><creatorcontrib>Shang, Lei</creatorcontrib><creatorcontrib>Zhang, Hongyan</creatorcontrib><creatorcontrib>Cui, Hongbo</creatorcontrib><creatorcontrib>Zhao, Yuehui</creatorcontrib><creatorcontrib>Wu, Na</creatorcontrib><creatorcontrib>Tang, Yanhong</creatorcontrib><creatorcontrib>Qin, Le</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Nursing & Allied Health Database</collection><collection>Health and Safety Science Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Healthcare Administration Database (Alumni)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>ProQuest SciTech 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>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>Consumer Health Database (Alumni Edition)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>ProQuest Biological Science Collection</collection><collection>Consumer Health Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Healthcare Administration Database</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Nursing & Allied Health Premium</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Vaccine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yuan, Xiaohui</au><au>Qu, Zhangyi</au><au>Wu, Xiaomin</au><au>Wang, Yingchen</au><au>Liu, Lei</au><au>Wei, Fengxiang</au><au>Gao, Hong</au><au>Shang, Lei</au><au>Zhang, Hongyan</au><au>Cui, Hongbo</au><au>Zhao, Yuehui</au><au>Wu, Na</au><au>Tang, Yanhong</au><au>Qin, Le</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein</atitle><jtitle>Vaccine</jtitle><addtitle>Vaccine</addtitle><date>2009-08-13</date><risdate>2009</risdate><volume>27</volume><issue>37</issue><spage>5103</spage><epage>5110</epage><pages>5103-5110</pages><issn>0264-410X</issn><eissn>1873-2518</eissn><coden>VACCDE</coden><abstract>Abstract The hexon protein of human adenovirus (HAdV) processes type-specific B-cell neutralizing epitopes. We developed a new effective, reliable approach to map these epitopes on hexon protein of HAdVs. A three-dimensional (3D) model of the HAdV3 hexon was obtained by homology modeling and refined by molecular mechanics and molecular dynamics simulations. A modified evolutionary trace (ET) analysis called reverse ET (RET) was used to predict the type-specific B-cell neutralizing epitopes. An epitope-screening algorithm based on analyzing the solvent accessibility surface (SAS) area from the 3D model and calculation of sites homology using RET was designed and implemented in the BioPerl script language. Five epitope polypeptide segments were predicted and mapped onto the 3D model. Finally five polypeptides were synthesized and the predicted epitopes were identified by enzyme-linked immunosorbent assay (ELISA) and Neutralization Test (NT). It was found that the type-specific neutralizing epitopes of HAdV3 are located at the top surface of hexon tower regions (residue numbers: 135–146, 169–178, 237–251, 262–272, 420–434). This work is of great significance to the molecular design of a multivalent HAdVs vaccine.</abstract><cop>Kidlington</cop><pub>Elsevier Ltd</pub><pmid>19573641</pmid><doi>10.1016/j.vaccine.2009.06.041</doi><tpages>8</tpages></addata></record> |
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| subjects | Adenoviruses, Human - chemistry Adenoviruses, Human - immunology Allergy and Immunology Amino Acid Sequence Antigens, Viral - chemistry Antigens, Viral - immunology Applied microbiology Atoms & subatomic particles Bioinformatics Biological and medical sciences Capsid Proteins - chemistry Capsid Proteins - immunology Enzyme-Linked Immunosorbent Assay Epitope Mapping Epitopes - chemistry Epitopes - immunology Experiments Fundamental and applied biological sciences. Psychology HAdV Hexon protein Human adenovirus Humans Infections Laboratories Microbiology Miscellaneous Models, Molecular Molecular Sequence Data Neutralization Neutralization Tests Polypeptides Protein Structure, Secondary Proteins Sequence Homology, Amino Acid Studies Vaccines Vaccines, antisera, therapeutical immunoglobulins and monoclonal antibodies (general aspects) Viral infections Virology |
| title | Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein |
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