Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential
The membrane protein M of the Porcine Epidemic Diarrhea Virus (PEDV) is the most abundant component of the viral envelope. The M protein plays a central role in the morphogenesis and assembly of the virus through protein interactions of the M-M, M-Spike (S) and M-nucleocapsid (N) type. The M protein...
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| Veröffentlicht in: | PloS one 2022-02, Vol.17 (2), p.e0263582-e0263582 |
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| creator | Rodríguez-Enríquez, Alan Herrera-Camacho, Irma Millán-Pérez-Peña, Lourdes Reyes-Leyva, Julio Santos-López, Gerardo Rivera-Benítez, José Francisco Rosas-Murrieta, Nora Hilda |
| description | The membrane protein M of the Porcine Epidemic Diarrhea Virus (PEDV) is the most abundant component of the viral envelope. The M protein plays a central role in the morphogenesis and assembly of the virus through protein interactions of the M-M, M-Spike (S) and M-nucleocapsid (N) type. The M protein is known to induce protective antibodies in pigs and to participate in the antagonistic response of the cellular antiviral system coordinated by the type I and type III interferon pathways. The 3D structure of the PEDV M protein is still unknown. The present work exposes a predicted 3D model of the M protein generated using the Robetta protocol. The M protein model is organized into a transmembrane and a globular region. The obtained 3D model of the PEDV M protein was compared with 3D models of the SARS-CoV-2 M protein created using neural networks and with initial machine learning-based models created using trRosetta. The 3D model of the present study predicted four linear B-cell epitopes (RSVNASSGTG and KHGDYSAVSNPSALT peptides are noteworthy), six discontinuous B-cell epitopes, forty weak binding and fourteen strong binding T-cell epitopes in the CV777 M protein. A high degree of conservation of the epitopes predicted in the PEDV M protein was observed among different PEDV strains isolated in different countries. The data suggest that the M protein could be a potential candidate for the development of new treatments or strategies that activate protective cellular mechanisms against viral diseases. |
| doi_str_mv | 10.1371/journal.pone.0263582 |
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The M protein plays a central role in the morphogenesis and assembly of the virus through protein interactions of the M-M, M-Spike (S) and M-nucleocapsid (N) type. The M protein is known to induce protective antibodies in pigs and to participate in the antagonistic response of the cellular antiviral system coordinated by the type I and type III interferon pathways. The 3D structure of the PEDV M protein is still unknown. The present work exposes a predicted 3D model of the M protein generated using the Robetta protocol. The M protein model is organized into a transmembrane and a globular region. The obtained 3D model of the PEDV M protein was compared with 3D models of the SARS-CoV-2 M protein created using neural networks and with initial machine learning-based models created using trRosetta. The 3D model of the present study predicted four linear B-cell epitopes (RSVNASSGTG and KHGDYSAVSNPSALT peptides are noteworthy), six discontinuous B-cell epitopes, forty weak binding and fourteen strong binding T-cell epitopes in the CV777 M protein. A high degree of conservation of the epitopes predicted in the PEDV M protein was observed among different PEDV strains isolated in different countries. The data suggest that the M protein could be a potential candidate for the development of new treatments or strategies that activate protective cellular mechanisms against viral diseases.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0263582</identifier><identifier>PMID: 35139120</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino Acid Sequence ; Amino acids ; Analysis ; Animals ; Antibodies ; Binding ; Biochemistry ; Biological response modifiers ; Biology and life sciences ; Care and treatment ; Chemistry ; Cloning ; Conservation ; Coronavirus Infections - immunology ; Coronavirus Infections - veterinary ; Coronavirus Infections - virology ; Coronavirus M Proteins - chemistry ; Coronavirus M Proteins - immunology ; Coronaviruses ; Cytotoxicity ; Diagnosis ; Diarrhea ; Epidemics ; Epitopes ; Epitopes, B-Lymphocyte - chemistry ; Epitopes, B-Lymphocyte - immunology ; Epitopes, T-Lymphocyte - chemistry ; Epitopes, T-Lymphocyte - immunology ; Funding ; Hogs ; Immunogenicity ; Interferon ; Laboratories ; Learning algorithms ; Lymphocytes B ; Lymphocytes T ; M protein ; Machine learning ; Medicine and health sciences ; Membrane proteins ; Modelling ; Models, Molecular ; Molecular biology ; Morphogenesis ; Neural networks ; Nucleocapsids ; Peptides ; Phylogenetics ; Porcine epidemic diarrhea virus - chemistry ; Porcine epidemic diarrhea virus - immunology ; Porcine reproductive and respiratory syndrome ; Protein Conformation ; Protein interaction ; Proteins ; Research and Analysis Methods ; Servers ; Severe acute respiratory syndrome coronavirus 2 ; Swine ; Swine - virology ; Swine Diseases - immunology ; Swine Diseases - virology ; Taxonomy ; Three dimensional models ; Transmissible gastroenteritis ; Viral diseases ; Viral infections ; Virology ; Virulence ; Viruses</subject><ispartof>PloS one, 2022-02, Vol.17 (2), p.e0263582-e0263582</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Rodríguez-Enríquez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Rodríguez-Enríquez et al 2022 Rodríguez-Enríquez et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-4ef1ffec9a4ccfc9b335ed99e6a6b3099b0a0f9d2e0af6a18444cd21c8cfd3c43</citedby><cites>FETCH-LOGICAL-c692t-4ef1ffec9a4ccfc9b335ed99e6a6b3099b0a0f9d2e0af6a18444cd21c8cfd3c43</cites><orcidid>0000-0002-4605-670X ; 0000-0003-0331-6708</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8827446/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8827446/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35139120$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rodríguez-Enríquez, Alan</creatorcontrib><creatorcontrib>Herrera-Camacho, Irma</creatorcontrib><creatorcontrib>Millán-Pérez-Peña, Lourdes</creatorcontrib><creatorcontrib>Reyes-Leyva, Julio</creatorcontrib><creatorcontrib>Santos-López, Gerardo</creatorcontrib><creatorcontrib>Rivera-Benítez, José Francisco</creatorcontrib><creatorcontrib>Rosas-Murrieta, Nora Hilda</creatorcontrib><title>Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The membrane protein M of the Porcine Epidemic Diarrhea Virus (PEDV) is the most abundant component of the viral envelope. The M protein plays a central role in the morphogenesis and assembly of the virus through protein interactions of the M-M, M-Spike (S) and M-nucleocapsid (N) type. The M protein is known to induce protective antibodies in pigs and to participate in the antagonistic response of the cellular antiviral system coordinated by the type I and type III interferon pathways. The 3D structure of the PEDV M protein is still unknown. The present work exposes a predicted 3D model of the M protein generated using the Robetta protocol. The M protein model is organized into a transmembrane and a globular region. The obtained 3D model of the PEDV M protein was compared with 3D models of the SARS-CoV-2 M protein created using neural networks and with initial machine learning-based models created using trRosetta. The 3D model of the present study predicted four linear B-cell epitopes (RSVNASSGTG and KHGDYSAVSNPSALT peptides are noteworthy), six discontinuous B-cell epitopes, forty weak binding and fourteen strong binding T-cell epitopes in the CV777 M protein. A high degree of conservation of the epitopes predicted in the PEDV M protein was observed among different PEDV strains isolated in different countries. The data suggest that the M protein could be a potential candidate for the development of new treatments or strategies that activate protective cellular mechanisms against viral diseases.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Animals</subject><subject>Antibodies</subject><subject>Binding</subject><subject>Biochemistry</subject><subject>Biological response modifiers</subject><subject>Biology and life sciences</subject><subject>Care and treatment</subject><subject>Chemistry</subject><subject>Cloning</subject><subject>Conservation</subject><subject>Coronavirus Infections - immunology</subject><subject>Coronavirus Infections - veterinary</subject><subject>Coronavirus Infections - virology</subject><subject>Coronavirus M Proteins - chemistry</subject><subject>Coronavirus M Proteins - immunology</subject><subject>Coronaviruses</subject><subject>Cytotoxicity</subject><subject>Diagnosis</subject><subject>Diarrhea</subject><subject>Epidemics</subject><subject>Epitopes</subject><subject>Epitopes, B-Lymphocyte - chemistry</subject><subject>Epitopes, B-Lymphocyte - immunology</subject><subject>Epitopes, T-Lymphocyte - chemistry</subject><subject>Epitopes, T-Lymphocyte - immunology</subject><subject>Funding</subject><subject>Hogs</subject><subject>Immunogenicity</subject><subject>Interferon</subject><subject>Laboratories</subject><subject>Learning algorithms</subject><subject>Lymphocytes B</subject><subject>Lymphocytes T</subject><subject>M protein</subject><subject>Machine learning</subject><subject>Medicine and health sciences</subject><subject>Membrane proteins</subject><subject>Modelling</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>Morphogenesis</subject><subject>Neural networks</subject><subject>Nucleocapsids</subject><subject>Peptides</subject><subject>Phylogenetics</subject><subject>Porcine epidemic diarrhea virus - chemistry</subject><subject>Porcine epidemic diarrhea virus - immunology</subject><subject>Porcine reproductive and respiratory syndrome</subject><subject>Protein Conformation</subject><subject>Protein interaction</subject><subject>Proteins</subject><subject>Research and Analysis Methods</subject><subject>Servers</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Swine</subject><subject>Swine - virology</subject><subject>Swine Diseases - immunology</subject><subject>Swine Diseases - virology</subject><subject>Taxonomy</subject><subject>Three dimensional models</subject><subject>Transmissible gastroenteritis</subject><subject>Viral diseases</subject><subject>Viral infections</subject><subject>Virology</subject><subject>Virulence</subject><subject>Viruses</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1trFDEUxwdRbK1-A9EBQfRh19wmM3kRSlt1odLipa8hk8tuykwyJhmx395sd1p2pA8SQsLJ7_xPzklOUbyEYAlxDT9c-zE40S0H7_QSIIqrBj0qDiHDaEERwI_39gfFsxivAahwQ-nT4gBXEDOIwGExXAatrExalfi07L3SXelNmTa6_FoOwSdt3dZw6YO0Tpdng1W6t7I8tSKEjRbllQ1jLIVTeYruJtq45W2Kpe370fm1dhkfspJLVnTPiydGdFG_mNaj4uensx8nXxbnF59XJ8fnC0kZSguiDTRGSyaIlEayFuNKK8Y0FbTFgLEWCGCYQhoIQwVsCCFSISgbaRSWBB8Vr3e6Q-cjn4oVOaKohjDDNBOrHaG8uOZDsL0IN9wLy28NPqy5CMnKTvOaEIO0IBVUiDR11bSSola1sCVNU1Uqa32coo1tr5XMuQbRzUTnJ85u-Nr_5k2D6t1l3k0Cwf8adUy8t1HqrhNO-3F3b1I3Nagz-uYf9OHsJmotcgLWGZ_jyq0oP84VpgwyCjK1fIDK4_aR888yNttnDu9nDplJ-k9aizFGvvr-7f_Zi6s5-3aPzf-qS5vouzFZ7-IcJDtQBh9j0Oa-yBDwbWPcVYNvG4NPjZHdXu0_0L3TXSfgvx5QCV0</recordid><startdate>20220209</startdate><enddate>20220209</enddate><creator>Rodríguez-Enríquez, Alan</creator><creator>Herrera-Camacho, Irma</creator><creator>Millán-Pérez-Peña, Lourdes</creator><creator>Reyes-Leyva, Julio</creator><creator>Santos-López, Gerardo</creator><creator>Rivera-Benítez, José Francisco</creator><creator>Rosas-Murrieta, Nora Hilda</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-4605-670X</orcidid><orcidid>https://orcid.org/0000-0003-0331-6708</orcidid></search><sort><creationdate>20220209</creationdate><title>Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential</title><author>Rodríguez-Enríquez, Alan ; Herrera-Camacho, Irma ; Millán-Pérez-Peña, Lourdes ; Reyes-Leyva, Julio ; Santos-López, Gerardo ; Rivera-Benítez, José Francisco ; Rosas-Murrieta, Nora Hilda</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-4ef1ffec9a4ccfc9b335ed99e6a6b3099b0a0f9d2e0af6a18444cd21c8cfd3c43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Animals</topic><topic>Antibodies</topic><topic>Binding</topic><topic>Biochemistry</topic><topic>Biological response modifiers</topic><topic>Biology and life sciences</topic><topic>Care and treatment</topic><topic>Chemistry</topic><topic>Cloning</topic><topic>Conservation</topic><topic>Coronavirus Infections - immunology</topic><topic>Coronavirus Infections - veterinary</topic><topic>Coronavirus Infections - virology</topic><topic>Coronavirus M Proteins - chemistry</topic><topic>Coronavirus M Proteins - immunology</topic><topic>Coronaviruses</topic><topic>Cytotoxicity</topic><topic>Diagnosis</topic><topic>Diarrhea</topic><topic>Epidemics</topic><topic>Epitopes</topic><topic>Epitopes, B-Lymphocyte - chemistry</topic><topic>Epitopes, B-Lymphocyte - immunology</topic><topic>Epitopes, T-Lymphocyte - chemistry</topic><topic>Epitopes, T-Lymphocyte - immunology</topic><topic>Funding</topic><topic>Hogs</topic><topic>Immunogenicity</topic><topic>Interferon</topic><topic>Laboratories</topic><topic>Learning algorithms</topic><topic>Lymphocytes B</topic><topic>Lymphocytes T</topic><topic>M protein</topic><topic>Machine learning</topic><topic>Medicine and health sciences</topic><topic>Membrane proteins</topic><topic>Modelling</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Morphogenesis</topic><topic>Neural networks</topic><topic>Nucleocapsids</topic><topic>Peptides</topic><topic>Phylogenetics</topic><topic>Porcine epidemic diarrhea virus - 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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>Rodríguez-Enríquez, Alan</au><au>Herrera-Camacho, Irma</au><au>Millán-Pérez-Peña, Lourdes</au><au>Reyes-Leyva, Julio</au><au>Santos-López, Gerardo</au><au>Rivera-Benítez, José Francisco</au><au>Rosas-Murrieta, Nora Hilda</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2022-02-09</date><risdate>2022</risdate><volume>17</volume><issue>2</issue><spage>e0263582</spage><epage>e0263582</epage><pages>e0263582-e0263582</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The membrane protein M of the Porcine Epidemic Diarrhea Virus (PEDV) is the most abundant component of the viral envelope. The M protein plays a central role in the morphogenesis and assembly of the virus through protein interactions of the M-M, M-Spike (S) and M-nucleocapsid (N) type. The M protein is known to induce protective antibodies in pigs and to participate in the antagonistic response of the cellular antiviral system coordinated by the type I and type III interferon pathways. The 3D structure of the PEDV M protein is still unknown. The present work exposes a predicted 3D model of the M protein generated using the Robetta protocol. The M protein model is organized into a transmembrane and a globular region. The obtained 3D model of the PEDV M protein was compared with 3D models of the SARS-CoV-2 M protein created using neural networks and with initial machine learning-based models created using trRosetta. The 3D model of the present study predicted four linear B-cell epitopes (RSVNASSGTG and KHGDYSAVSNPSALT peptides are noteworthy), six discontinuous B-cell epitopes, forty weak binding and fourteen strong binding T-cell epitopes in the CV777 M protein. A high degree of conservation of the epitopes predicted in the PEDV M protein was observed among different PEDV strains isolated in different countries. The data suggest that the M protein could be a potential candidate for the development of new treatments or strategies that activate protective cellular mechanisms against viral diseases.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35139120</pmid><doi>10.1371/journal.pone.0263582</doi><tpages>e0263582</tpages><orcidid>https://orcid.org/0000-0002-4605-670X</orcidid><orcidid>https://orcid.org/0000-0003-0331-6708</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2022-02, Vol.17 (2), p.e0263582-e0263582 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2627114446 |
| source | PubMed (Medline); MEDLINE; Public Library of Science; DOAJ Directory of Open Access Journals; Free Full-Text Journals in Chemistry; EZB Electronic Journals Library |
| subjects | Amino Acid Sequence Amino acids Analysis Animals Antibodies Binding Biochemistry Biological response modifiers Biology and life sciences Care and treatment Chemistry Cloning Conservation Coronavirus Infections - immunology Coronavirus Infections - veterinary Coronavirus Infections - virology Coronavirus M Proteins - chemistry Coronavirus M Proteins - immunology Coronaviruses Cytotoxicity Diagnosis Diarrhea Epidemics Epitopes Epitopes, B-Lymphocyte - chemistry Epitopes, B-Lymphocyte - immunology Epitopes, T-Lymphocyte - chemistry Epitopes, T-Lymphocyte - immunology Funding Hogs Immunogenicity Interferon Laboratories Learning algorithms Lymphocytes B Lymphocytes T M protein Machine learning Medicine and health sciences Membrane proteins Modelling Models, Molecular Molecular biology Morphogenesis Neural networks Nucleocapsids Peptides Phylogenetics Porcine epidemic diarrhea virus - chemistry Porcine epidemic diarrhea virus - immunology Porcine reproductive and respiratory syndrome Protein Conformation Protein interaction Proteins Research and Analysis Methods Servers Severe acute respiratory syndrome coronavirus 2 Swine Swine - virology Swine Diseases - immunology Swine Diseases - virology Taxonomy Three dimensional models Transmissible gastroenteritis Viral diseases Viral infections Virology Virulence Viruses |
| title | Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential |
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