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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV</title><author><name sortKey="Wang, Jingqiang" sort="Wang, Jingqiang" uniqKey="Wang J" first="Jingqiang" last="Wang">Jingqiang Wang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Ji, Jia" sort="Ji, Jia" uniqKey="Ji J" first="Jia" last="Ji">Jia Ji</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Ye, Jia" sort="Ye, Jia" uniqKey="Ye J" first="Jia" last="Ye">Jia Ye</name><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zhao, Xiaoqian" sort="Zhao, Xiaoqian" uniqKey="Zhao X" first="Xiaoqian" last="Zhao">Xiaoqian Zhao</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Wen, Jie" sort="Wen, Jie" uniqKey="Wen J" first="Jie" last="Wen">Jie Wen</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Hu, Jianfei" sort="Hu, Jianfei" uniqKey="Hu J" first="Jianfei" last="Hu">Jianfei Hu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0015">College of Life Sciences, Peking University, Beijing 100871, China</nlm:aff></affiliation></author><author><name sortKey="Li, Dawei" sort="Li, Dawei" uniqKey="Li D" first="Dawei" last="Li">Dawei Li</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Sun, Min" sort="Sun, Min" uniqKey="Sun M" first="Min" last="Sun">Min Sun</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zeng, Haipan" sort="Zeng, Haipan" uniqKey="Zeng H" first="Haipan" last="Zeng">Haipan Zeng</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Hu, Yongwu" sort="Hu, Yongwu" uniqKey="Hu Y" first="Yongwu" last="Hu">Yongwu Hu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Tian, Xiangjun" sort="Tian, Xiangjun" uniqKey="Tian X" first="Xiangjun" last="Tian">Xiangjun Tian</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Tan, Xuehai" sort="Tan, Xuehai" uniqKey="Tan X" first="Xuehai" last="Tan">Xuehai Tan</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Ningzhi" sort="Xu, Ningzhi" uniqKey="Xu N" first="Ningzhi" last="Xu">Ningzhi Xu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zeng, Changqing" sort="Zeng, Changqing" uniqKey="Zeng C" first="Changqing" last="Zeng">Changqing Zeng</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Bi, Shengli" sort="Bi, Shengli" uniqKey="Bi S" first="Shengli" last="Bi">Shengli Bi</name><affiliation><nlm:aff id="aff0020">Center of Disease Control and Prevention, Beijing 100050, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">15626344</idno><idno type="pmc">5172421</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5172421</idno><idno type="RBID">PMC:5172421</idno><idno type="doi">10.1016/S1672-0229(03)01018-0</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">001028</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001028</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV</title><author><name sortKey="Wang, Jingqiang" sort="Wang, Jingqiang" uniqKey="Wang J" first="Jingqiang" last="Wang">Jingqiang Wang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Ji, Jia" sort="Ji, Jia" uniqKey="Ji J" first="Jia" last="Ji">Jia Ji</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Ye, Jia" sort="Ye, Jia" uniqKey="Ye J" first="Jia" last="Ye">Jia Ye</name><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zhao, Xiaoqian" sort="Zhao, Xiaoqian" uniqKey="Zhao X" first="Xiaoqian" last="Zhao">Xiaoqian Zhao</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Wen, Jie" sort="Wen, Jie" uniqKey="Wen J" first="Jie" last="Wen">Jie Wen</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Hu, Jianfei" sort="Hu, Jianfei" uniqKey="Hu J" first="Jianfei" last="Hu">Jianfei Hu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0015">College of Life Sciences, Peking University, Beijing 100871, China</nlm:aff></affiliation></author><author><name sortKey="Li, Dawei" sort="Li, Dawei" uniqKey="Li D" first="Dawei" last="Li">Dawei Li</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Sun, Min" sort="Sun, Min" uniqKey="Sun M" first="Min" last="Sun">Min Sun</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zeng, Haipan" sort="Zeng, Haipan" uniqKey="Zeng H" first="Haipan" last="Zeng">Haipan Zeng</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Hu, Yongwu" sort="Hu, Yongwu" uniqKey="Hu Y" first="Yongwu" last="Hu">Yongwu Hu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Tian, Xiangjun" sort="Tian, Xiangjun" uniqKey="Tian X" first="Xiangjun" last="Tian">Xiangjun Tian</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Tan, Xuehai" sort="Tan, Xuehai" uniqKey="Tan X" first="Xuehai" last="Tan">Xuehai Tan</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Xu, Ningzhi" sort="Xu, Ningzhi" uniqKey="Xu N" first="Ningzhi" last="Xu">Ningzhi Xu</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Zeng, Changqing" sort="Zeng, Changqing" uniqKey="Zeng C" first="Changqing" last="Zeng">Changqing Zeng</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation></author><author><name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author><author><name sortKey="Bi, Shengli" sort="Bi, Shengli" uniqKey="Bi S" first="Shengli" last="Bi">Shengli Bi</name><affiliation><nlm:aff id="aff0020">Center of Disease Control and Prevention, Beijing 100050, China</nlm:aff></affiliation></author><author><name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name><affiliation><nlm:aff id="aff0005">Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</nlm:aff></affiliation><affiliation><nlm:aff id="aff0010">James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</nlm:aff></affiliation></author></analytic><series><title level="j">Genomics, Proteomics & Bioinformatics</title><idno type="ISSN">1672-0229</idno><idno type="eISSN">2210-3244</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The <italic>Coronaviridae</italic> family is characterized by a nucleocapsid that is composed of the genome RNA molecule in combination with the nucleoprotein (N protein) within a virion. The most striking physiochemical feature of the N protein of SARS-CoV is that it is a typical basic protein with a high predicted pI and high hydrophilicity, which is consistent with its function of binding to the ribophosphate backbone of the RNA molecule. The predicted high extent of phosphorylation of the N protein on multiple candidate phosphorylation sites demonstrates that it would be related to important functions, such as RNA-binding and localization to the nucleolus of host cells. Subsequent study shows that there is an SR-rich region in the N protein and this region might be involved in the protein-protein interaction. The abundant antigenic sites predicted in the N protein, as well as experimental evidence with synthesized polypeptides, indicate that the N protein is one of the major antigens of the SARS-CoV. Compared with other viral structural proteins, the low variation rate of the N protein with regards to its size suggests its importance to the survival of the virus.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ksiazek, T G" uniqKey="Ksiazek T">T.G. Ksiazek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hiscox, J A" uniqKey="Hiscox J">J.A. Hiscox</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wootton, S K" uniqKey="Wootton S">S.K. Wootton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Laity, J H" uniqKey="Laity J">J.H. Laity</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Molenkamp, R" uniqKey="Molenkamp R">R. Molenkamp</name></author><author><name sortKey="Spaan, W J M" uniqKey="Spaan W">W.J.M. Spaan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ding, P" uniqKey="Ding P">P. Ding</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Narayahan, K" uniqKey="Narayahan K">K. Narayahan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Caceres, J F" uniqKey="Caceres J">J.F. Cáceres</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Furuyama, S" uniqKey="Furuyama S">S. Furuyama</name></author><author><name sortKey="Bruzik, J P" uniqKey="Bruzik J">J.P. Bruzik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wurm, T" uniqKey="Wurm T">T. Wurm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kolaskar, A S" uniqKey="Kolaskar A">A.S. Kolaskar</name></author><author><name sortKey="Tongaonkar, P C" uniqKey="Tongaonkar P">P.C. Tongaonkar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Daginakatte, C G" uniqKey="Daginakatte C">C.G. Daginakatte</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, Q Y" uniqKey="Zhu Q">Q.Y. Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qin, E D" uniqKey="Qin E">E.D. Qin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genomics Proteomics Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Genomics Proteomics Bioinformatics</journal-id><journal-title-group><journal-title>Genomics, Proteomics & Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1672-0229</issn><issn pub-type="epub">2210-3244</issn><publisher><publisher-name>Elsevier</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">15626344</article-id><article-id pub-id-type="pmc">5172421</article-id><article-id pub-id-type="publisher-id">S1672-0229(03)01018-0</article-id><article-id pub-id-type="doi">10.1016/S1672-0229(03)01018-0</article-id><article-categories><subj-group subj-group-type="heading"><subject>Invited Article</subject></subj-group></article-categories><title-group><article-title>The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jingqiang</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="aff0010" ref-type="aff">2</xref><xref rid="fn1" ref-type="fn">*</xref></contrib><contrib contrib-type="author"><name><surname>Ji</surname><given-names>Jia</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="fn1" ref-type="fn">*</xref></contrib><contrib contrib-type="author"><name><surname>Ye</surname><given-names>Jia</given-names></name><xref rid="aff0010" ref-type="aff">2</xref><xref rid="aff0005" ref-type="aff">1</xref><xref rid="fn1" ref-type="fn">*</xref></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Xiaoqian</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="fn1" ref-type="fn">*</xref></contrib><contrib contrib-type="author"><name><surname>Wen</surname><given-names>Jie</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Wei</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Jianfei</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="aff0015" ref-type="aff">3</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Dawei</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Min</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Haipan</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Hu</surname><given-names>Yongwu</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Tian</surname><given-names>Xiangjun</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="aff0010" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Tan</surname><given-names>Xuehai</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Xu</surname><given-names>Ningzhi</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Zeng</surname><given-names>Changqing</given-names></name><xref rid="aff0005" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Jian</given-names></name><xref rid="aff0005" ref-type="aff">1</xref><xref rid="aff0010" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Bi</surname><given-names>Shengli</given-names></name><xref rid="aff0020" ref-type="aff">4</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Huanming</given-names></name><email>yanghm@genomics.org.cn</email><xref rid="aff0005" ref-type="aff">1</xref><xref rid="aff0010" ref-type="aff">2</xref><xref rid="cor1" ref-type="corresp">#</xref></contrib></contrib-group><aff id="aff0005"><label>1</label>Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China</aff><aff id="aff0010"><label>2</label>James D. Watson Institute of Genome Sciences, Zhijiang Campus, Zhejiang University and Hangzhou Genomics Institute, Hangzhou 310008, China</aff><aff id="aff0015"><label>3</label>College of Life Sciences, Peking University, Beijing 100871, China</aff><aff id="aff0020"><label>4</label>Center of Disease Control and Prevention, Beijing 100050, China</aff><author-notes><corresp id="cor1"><label>#</label>Corresponding author. <email>yanghm@genomics.org.cn</email></corresp><fn id="fn1"><label>*</label><p id="ntp0035">These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="pmc-release"><day>28</day><month>11</month><year>2016</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>5</month><year>2003</year></pub-date><pub-date pub-type="epub"><day>28</day><month>11</month><year>2016</year></pub-date><volume>1</volume><issue>2</issue><fpage>145</fpage><lpage>154</lpage><permissions><copyright-statement>.</copyright-statement><copyright-year>2003</copyright-year><copyright-holder>Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China</copyright-holder><license license-type="CC BY-NC-ND" xlink:href="http://creativecommons.org/licenses/by-nc-nd/4.0/"><license-p>This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).</license-p></license></permissions><abstract id="ab0005"><p>The <italic>Coronaviridae</italic> family is characterized by a nucleocapsid that is composed of the genome RNA molecule in combination with the nucleoprotein (N protein) within a virion. The most striking physiochemical feature of the N protein of SARS-CoV is that it is a typical basic protein with a high predicted pI and high hydrophilicity, which is consistent with its function of binding to the ribophosphate backbone of the RNA molecule. The predicted high extent of phosphorylation of the N protein on multiple candidate phosphorylation sites demonstrates that it would be related to important functions, such as RNA-binding and localization to the nucleolus of host cells. Subsequent study shows that there is an SR-rich region in the N protein and this region might be involved in the protein-protein interaction. The abundant antigenic sites predicted in the N protein, as well as experimental evidence with synthesized polypeptides, indicate that the N protein is one of the major antigens of the SARS-CoV. Compared with other viral structural proteins, the low variation rate of the N protein with regards to its size suggests its importance to the survival of the virus.</p></abstract><kwd-group id="keys0005"><title>Key words</title><kwd>SARS-CoV</kwd><kwd>nucleoprotein</kwd><kwd>phosphorylation</kwd><kwd>SR-rich region</kwd><kwd>antigenic sites</kwd></kwd-group></article-meta></front><body><sec id="s0005"><title>Introduction</title><p>It has been established that a variant of coronaviruses, SARS-CoV, is the pathogen of SARS <xref rid="bib1" ref-type="bibr">(<italic>1</italic>)</xref>. The N protein (nucleoprotein) is one of the major structural proteins in a viral particle, playing a critical role in the transcription regulation of the genomic RNA and other viral proteins <xref rid="bib2" ref-type="bibr">(<italic>2</italic>)</xref>. It might also be involved in the virulence and virus-specific post-translational modifications <xref rid="bib3" ref-type="bibr">(<italic>3</italic>)</xref>.</p><p>In this paper, we report the predicted structure, possible functions, evolution, and the immunoassay of the N protein of SARS-CoV to confirm that the N protein is one of the major antigens with synthesized polypeptides.</p></sec><sec id="s0010"><title>Results and Discussion</title><sec id="s0015"><title>The ORF of the N protein</title><p>The ORF (open-reading frame) for the N protein is located at the 3′ end (nucleotide position 28,101-29,369) of the SARS-CoV genome. The ORF is 1,269 nucleotide (nt) long, accounting for 4.27% of the total genome. It has a GC content of 48.38% (A: U: C: G = 31.60: 20.02: 26.32: 22.06), which is significantly higher than the average of the complete SARS-CoV genome (40.76%). And the GC content in the left half near the 5′ end (51.63%) is obviously higher than that in the right half near the 3′ end (44.68%) (<xref rid="f0005" ref-type="fig">Figure 1</xref>).</p></sec><sec id="s0020"><title>General physiochemical features of the N protein</title><p>The N protein is composed of 422 amino acids (a.a.) with an estimated molecular weight of 46.03 KD, the second largest of the structural viral protein. It has a low percentage (< 1.7%) of methionine, tryptophan and histidine residues, but does not contain any cysteine (<xref rid="t0005" ref-type="table">Table 1</xref>).</p><p>Absence of the cysteine is one of the common features in coronavirus N proteins. Cysteine is an important amino acid in zinc knuckle structure that may be involved in packaging signal recognition <xref rid="bib4" ref-type="bibr">(<italic>4</italic>)</xref>. It has been reported that the N protein of MHV (murine hepatitis virus) has no any known RNA-binding motif, such as arginine-rich motif or zinc finger <xref rid="bib5" ref-type="bibr">(<italic>5</italic>)</xref>. The lack of cysteine in the N protein of SARS-CoV indicates that the interaction of the N protein and signal packaging may occur in the absence of zinc knuckle structure.</p><p>The complete N protein is a highly basic protein. It has positively net charges, and has the highest pI (pI 10.11) among all known structural proteins in the virus, making it easier to interact with acidic genomic RNA. The charge distribution shows five positive peaks with relatively even distance (<xref rid="f0005" ref-type="fig">Figure 1</xref>). Positively charged amino acids, histidine, lysine and arginine, account for a big portion in each peak. In addition to high pI and positive charges, the N protein has a high hydrophilicity (54%). The middle of the N protein is relatively hydrophobic, but the two termini are hydrophilic (<xref rid="f0005" ref-type="fig">Figure 1</xref>). The N-terminus is basic with positive charge, while the C-terminus is acidic with negative charge. In a model for demonstrating the interaction of multiple N proteins, the two termini are supposed to be linked end to end <xref rid="bib6" ref-type="bibr">(<italic>6</italic>)</xref>.</p></sec><sec id="s0025"><title>Phosphorylation of the N protein</title><p>Phosphorylation of the N protein is related to RNA-binding, oligomerization and localization to nucleoli <xref rid="bib3" ref-type="bibr">(<italic>3</italic>)</xref>. We identified 33 potential phosphorylation sites in the N protein, including 22 serines, 8 threonines and 3 tyrosines. The average score of serines is the highest among the three amino acids. This demonstrates that serines are the predominant phosphorylated residues in the N protein, consistent with the previous reports <xref rid="bib5" ref-type="bibr">(<italic>5</italic>)</xref>. The phosphorylation sites concentrate in the middle of the N protein (<xref rid="f0010" ref-type="fig">Figure 2</xref>). However, the exact number and location of phosphoserines have not been identified by experiments yet.</p></sec><sec id="s0030"><title>Structure of the N protein</title><p>Through multi-alignment of total nineteen sequences of the coronavirus N proteins, we found two conserved structural regions at Codons 81-140 and 270-320 (a.a. positions are all referred to the N protein of SARS-CoV, Isolate BJ01), with the former more conserved (<xref rid="f0015" ref-type="fig">Figure 3</xref>). This result is consistent with the conserved domains that we have predicted by using CDS (Conserved Domain Search). A highly conserved domain (FYYLGTGP at Codons 111-118) was identified within the first conserved region in all coronaviruses. These conserved regions and domains could serve as potential drug targets because of their great possibility of performing critical functions. In contrast, the two termini of the N protein are more variable, particularly the C-terminus.</p><p>We also predicted the secondary structure of the N protein by using PSIPRED. According to the result, the N protein is composed of coils, strands, and helices. There are totally eight helices and seven of them are distributed in the 3′ end of the N protein.</p></sec><sec id="s0035"><title>SR-rich region of the N protein</title><p>An SR-rich region (a region rich of serine and arginine) was identified in the coronavirus N protein, which has a core motif of SR{X<sub>2</sub>}SR{X<sub>2</sub>}SR (X indicates any amino acid, and subscript number indicates the number of amino acids between two SRs.). In the N protein of SARS-CoV, its SR-rich region presents a symmetric structure: SR{X<sub>6</sub>}SR{X<sub>2</sub>}SRSR{X<sub>2</sub>}SR{X<sub>6</sub>}SR (Codons 177-204).</p><p>The SR-rich region has been found in all coronavirus N proteins. However, it is not within conserved regions that we have detected this region from similarity analysis. Further study showed that this region is relatively variable. For example, in the N protein of SARS-CoV, there is a substitution in SR-rich region. Therefore, we used SR as a marker to identify this region, though amino acid change may occur in SR and cause marker to disappear. We classified all SR-rich regions of coronavirus N proteins into a few types (<xref rid="t0010" ref-type="table">Table 2</xref>), and discovered that the classification of those coronaviruses by their core motifs of the SR-rich region was consistent with the phylogenic tree that we had constructed. It seems that the SR-rich region is typically common and representative, though it is outside the conserved regions and has easily-varied sequence.</p><p>Previous study reported that the N protein of MHV could interact with the M (membrane) protein to help the envelopment of MHV nucleocapsid <xref rid="bib7" ref-type="bibr">(<italic>7</italic>)</xref>. By targeting RNA recombination, Ding, <italic>et al</italic>. found that the SR-rich region could not be transferred from MHV to BCoV (bovine coronavirus), which means that this region was unable to be substituted between various species <xref rid="bib6" ref-type="bibr">(<italic>6</italic>)</xref>. It is believed that the SR-rich region is possibly derived from the SR (or RS) domain of many RNA-binding proteins, such as SR proteins <xref rid="bib6" ref-type="bibr">(<italic>6</italic>)</xref>. The SR proteins are essential for constitutive mRNA splicing and the regulation of alternative splice site selection <xref rid="bib8" ref-type="bibr">(<italic>8</italic>)</xref>. The C-terminal SR domain of SR proteins is involved in mediating protein-protein interaction as well as nuclear localization <xref rid="bib8" ref-type="bibr">8.</xref>, <xref rid="bib9" ref-type="bibr">9.</xref>. The SR-rich region might be necessary for the interaction of the N and M proteins. It also possibly contributes to the interaction of the N protein with other viral proteins, including the N protein itself.</p><p>Localization to the nucleolus is a common feature of coronavirus N proteins. This feature helps with disrupting host cell division to promote virus assembly and sequestering ribosomes for translation of viral proteins <xref rid="bib10" ref-type="bibr">(<italic>10</italic>)</xref>. It has been reported that the SR domain in SR proteins is a nuclear localization signal but not a subnuclear speckle one <xref rid="bib8" ref-type="bibr">(<italic>8</italic>)</xref>. Consequently, the SR-rich region may function only as a nuclear localization signal. Subnuclear localization of the N protein might need several additive and redundant signals. InterproScan has revealed that there is a bipartite nuclear localization signal domain (NLS-BP, IPR001472) in the N protein, which has a sequence of KKKKTDEAQPLPQRQKKQ at Codons 373-390. NLS-BP is a domain for the protein translocation from cytoplasm to nucleus.</p><p>Phosphorylation and dephosphorylation of the SR domain in SR proteins are necessary for its function. We also detected that in the N protein, the SR-rich region has eleven possible phosphoserines, which account for 50% of the total. This indicates that the SR-rich region is an important region involved in phosphorylation and this post-transcription modification is greatly required for RNA-binding, oligomerization, and localization to nucleoli of the N protein.</p></sec><sec id="s0040"><title>Prediction and immunoassay confirmation of antigenic sites of the N protein</title><p>Previous experiments showed that hydrophobic residues, such as cysteine, leucine and valine, on the surface of the protein are most likely to be part of antigenic determinants. Based on a semi-empirical method through making a statistics of appearance frequency of each amino acid in known segmental epitopes <xref rid="bib11" ref-type="bibr">(<italic>11</italic>)</xref>, we have predicted 16 antigenic sites of the N protein and found they are clustering in the middle and the C-terminus (<xref rid="f0020" ref-type="fig">Figure 4</xref> and <xref rid="t0015" ref-type="table">Table 3</xref>). There is a strong antigenic site (TALALLLLDR) located around Codons 218-227. In addition, another three strong antigenic sites were detected around Codons 156-166 (AATVLQLPQGT), Codons 347-363 (FKDNVILLNKHIDAYKT) and Codons 389-398 (KQPTVTLLPA) (<xref rid="t0015" ref-type="table">Table 3</xref>).</p><p>To confirm the antigenicity of the N protein, we synthesized peptides of 20-25 amino acids covering the complete N protein. We designed fourteen peptides that are in the region of low conservativeness, excluding those of high conservativeness (<xref rid="t0020" ref-type="table">Table 4</xref>). By using sera samples of nine SARS patients with ELISA (enzyme-linked immunosorbent assay), We found that two out of fourteen peptides showed strong immunogenicity and seven peptides showed medium-strong immunogenicity (<xref rid="t0020" ref-type="table">Table 4</xref>).</p><p>Compared with the experimental outcome on immunogenicity of synthesized peptides, the predicted result about the antigenicity of the N protein is fairly reliable. Synthesized peptides containing the corresponding predicted antigenic sites showed strong or medium-strong immunogenicity, except for peptides N99 (Codons 99-120). This might because that its position is within the conserved region, which decreases the specificity of reaction. The different immunogenicity of peptides in different regions on the N protein is also consistent with the predicted antigenicity map.</p><p>It was reported that in the coronavirus-infected cells, the N protein was a more abundant antigen than the S (spike) protein <xref rid="bib12" ref-type="bibr">(<italic>12</italic>)</xref>. We also performed the same experiments on the S protein of SARS-CoV (see the article about the S protein in this issue). The comparison of both results demonstrates that the percentage of strongly positive results in the N protein (64%) is significantly higher than that in the S protein (28%). One of the explanations might be that the N protein is the most abundant protein produced throughout infection, because its template mRNA is the smallest and it has the most abundant sgRNA (subgenome RNA) during transcription <xref rid="bib2" ref-type="bibr">(<italic>2</italic>)</xref>. When the infected cells broke up and released the inside content, the N protein showed the strongest antigenicity. Combined with our prediction and experimental results, we believe that the N protein is a predominant antigen of SARS-CoV.</p></sec><sec id="s0045"><title>Evolution and substitution of the N protein</title><p>Based on the nineteen coronavirus N proteins, we constructed an evolutionary tree (<xref rid="f0025" ref-type="fig">Figure 5</xref>). It reveals that SARS-CoV is closer to Group 2 than to Groups 1 and 3. We also performed a global pair-wise alignment of these nineteen sequences (<xref rid="s0080" ref-type="sec">Table S1</xref>). The N protein of SARS-CoV is highly similar to that of Equine coronavirus (49.8% similarity, 34.3% identity), with the lowest similarity to that of human coronavirus 229E strain (32.1% similarity, 21.2% identity).</p><p>To date there are seventeen isolates of SARS-CoV that have complete sequences. Only four substitutions have been identified in the N protein (<xref rid="t0025" ref-type="table">Table 5</xref>). The substitution rate of the N protein is 0.32%, lower than the average of SARS-CoV genome (0.46%). We suggest that the N protein is much more conserved than other structural proteins for its substitution rate is the lowest among all known proteins. These four substitutions resulted in the change of three codons. There are two substitutions juxtaposed within the same codon of leucine. One is at the second nucleotide of Codon 140 (nt position 28,519), leading to amino acid change from leucine to tryptophan, and the other is at the third nucleotide of Codon 140 (nt position 28,520) as a synonymous substitution.</p></sec></sec><sec id="s0050"><title>Methods and Materials</title><sec id="s0055"><title>Samples and sequences</title><p>The SARS patients, from whom the genome sequences of Isolates BJ01-BJ04 were extracted, were diagnosed according to WHO guidelines (<ext-link ext-link-type="uri" xlink:href="http://www.who.int/csr/sars/guidelines/en/" id="ir0010">http://www.who.int/csr/sars/guidelines/en/</ext-link>) in February and March 2003 in Beijing, China. The processing of tissue samples and viral RNA, RT-PCR, cloning, and sequencing were performed according to standard protocols at Beijing Genomics Institute (BGI) and Center of Disease Control and Prevention of China <xref rid="bib13" ref-type="bibr">(<italic>13</italic>)</xref>.</p><p>The updated complete genome sequences of the BJ Group (BJ01–BJ04) have been deposited by BGI in GenBank (accession numbers: AY278488, AY278487, AY278490, and AY279354) (<ext-link ext-link-type="uri" xlink:href="http://www.genomics.org.cn/bgi/news/zhongxin/news030416-2_fasta.htm" id="ir0015">http://www.genomics.org.cn/bgi/news/zhongxin/news030416-2_fasta.htm</ext-link>). All the sequences and experimental materials are available freely.</p><p>Thirteen other full-length sequences of SARS-CoV strains, which have been published by BGI or other laboratories since March 2003, have been used in this study (accession numbers: AY278554, AY297028, AY274119, AY291451, AY283798, AY283797, AY283796, AY283795, AY283794, AY282752, AY278741, AY278491, and AY278489). Nineteen coronavirus N protein sequences were downloaded from GenBank (accession numbers: AAP30037, NP_045302, CAD67607, AAF97743, AAG39339, NP_150083, AAL80036, P33469, AAD33104, AAF23872, NP_040838, P33463, NP_058428, Q04700, BAC65328, BAC01157, BAC01161, NP_073556, and NP_598314). The nucleotide positions of SARS-CoV are all referred to the complete genome sequence of Isolate BJ01 <xref rid="bib14" ref-type="bibr">(<italic>14</italic>)</xref>.</p></sec><sec id="s0060"><title>Structure and function analysis</title><p>ORF Finder (<ext-link ext-link-type="uri" xlink:href="http://ww.ncbi.nlm.nih.gov/gorf/gorf.html" id="ir0020">http://ww.ncbi.nlm.nih.gov/gorf/gorf.html</ext-link>) was used to determine ORFs, EMBOSS package (<ext-link ext-link-type="uri" xlink:href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/" id="ir0025">http://www.hgmp.mrc.ac.uk/Software/EMBOSS/</ext-link>) to characterize proteins, NetPhos (<ext-link ext-link-type="uri" xlink:href="http://www.cbs.dtu.dk/services/NetPhos/" id="ir0030">http://www.cbs.dtu.dk/services/NetPhos/</ext-link>) and PhosphoBase (<ext-link ext-link-type="uri" xlink:href="http://www.cbs.dtu.dk/databases/PhosphoBase/" id="ir0035">http://www.cbs.dtu.dk/databases/PhosphoBase/</ext-link>) to predict phosphorylation sites, TopPred2 (<ext-link ext-link-type="uri" xlink:href="http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html" id="ir0040">http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html</ext-link>) and ProtScale (<ext-link ext-link-type="uri" xlink:href="http://us.expasy.org/cgi-bin/protscale.pl" id="ir0045">http://us.expasy.org/cgi-bin/protscale.pl</ext-link>) to identify the hydrophobic region, ClustalW (<ext-link ext-link-type="uri" xlink:href="http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/" id="ir0050">http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/</ext-link>) to perform multiple-alignment and phylogenetic analysis, PSIPRED (<ext-link ext-link-type="uri" xlink:href="http://bioinf.cs.ucl.ac.uk/psiform.html" id="ir0055">http://bioinf.cs.ucl.ac.uk/psiform.html</ext-link>) to analyze secondary structures, InterproScan (<ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/interpro/" id="ir0060">http://www.ebi.ac.uk/interpro/</ext-link>) and CDS (Conserved Domain Search, <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi" id="ir0065">http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi</ext-link>) to predict conserved protein domains. All the analyses were accomplished on supercomputers DOWNING 2000/3000 (DOWNING Computers Inc., Beijing, China), SUN E10K (SUN Microsystems Inc., California, USA), SGI Origin 3800 (Silicon Graphics, Inc., California, USA), and IBM P690 (IBM Corp., New York, USA).</p></sec><sec id="s0065"><title>Design and synthesis of peptides</title><p>The peptides were designed on the basis of the combined analyses of the proteins. The peptides were synthesized by Hangzhou Zhongtai Inc.(Hangzhou, China).</p></sec><sec id="s0070"><title>ELISA test</title><p>Blood samples of two normal controls and nine SARS patients were provided by Beijing Plastic Surgery Hospital, Beijing Peoples’ Hospital, and Beijing Tiantan Hospital. Peroxidase-conjugated mouse anti-human IgG and peroxidase-HRP (P6782) were purchased from Sigma (New Jersey, USA). Peptides (1 <italic>μ</italic>g/mL, in 0.5 M carbonate buffer, pH 9.6) were dispensed into a 96-well microplate (100 <italic>μ</italic>L/well) and then incubated at 4°C overnight. After being washed with PBS containing 0.5 M Tween-20 (PBS-T), BSA (2 mg/mL) was added up and the plates were incubated at 37°C for 1 h for blocking. The patient serum sample (10 <italic>μ</italic>L), diluted with 100 <italic>μ</italic>L of sample buffer, was added into each well and incubated at 37°C for 30 min. After being further washed with PBS-T, 100 <italic>μ</italic>L mouse anti-human IgG was added and incubated at 37°C for 20 min. Finally, the wells were washed with PBS-T. The reaction was observed by adding the TMB solution as substrate, after inculation at 37°C for 10 min. The reaction was stopped by adding 50 <italic>μ</italic>L 4 M sulphuric acid, and optical density at 450 nm (ref. 630 nm) was measured with an automatic ELISA reader (Multiskan Ascent, Finland).</p></sec></sec></body><back><ref-list id="bibliog0005"><title>References</title><ref id="bib1"><label>1.</label><element-citation publication-type="journal" id="sbref1"><person-group person-group-type="author"><name><surname>Ksiazek</surname><given-names>T.G.</given-names></name></person-group><article-title>A Novel Coronavirus Associated with Severe Acute Respiratory Syndrome</article-title><source>N. Engl. J. Med.</source><volume>348</volume><year>2003</year><fpage>1953</fpage><lpage>1966</lpage><pub-id pub-id-type="pmid">12690092</pub-id></element-citation></ref><ref id="bib2"><label>2.</label><element-citation publication-type="journal" id="sbref2"><person-group person-group-type="author"><name><surname>Hiscox</surname><given-names>J.A.</given-names></name></person-group><article-title>The coronavirus infectious bronchitis virus nucleoprotein localizes to the nucleolus</article-title><source>J. Virol.</source><volume>75</volume><year>2001</year><fpage>10506</fpage><lpage>10512</lpage></element-citation></ref><ref id="bib3"><label>3.</label><element-citation publication-type="journal" id="sbref3"><person-group person-group-type="author"><name><surname>Wootton</surname><given-names>S.K.</given-names></name></person-group><article-title>Phosphorylation of the porcine reproductive and respiratory syndrome virus nucleocapsid protein</article-title><source>J. Virol.</source><volume>76</volume><year>2002</year><fpage>10569</fpage><lpage>10576</lpage><pub-id pub-id-type="pmid">12239338</pub-id></element-citation></ref><ref id="bib4"><label>4.</label><element-citation publication-type="journal" id="sbref4"><person-group person-group-type="author"><name><surname>Laity</surname><given-names>J.H.</given-names></name></person-group><article-title>Zinc finger proteins: new insights into structural and functional diversity</article-title><source>Curr Opin Struct Biol.</source><volume>11</volume><year>2001</year><fpage>39</fpage><lpage>46</lpage><pub-id pub-id-type="pmid">11179890</pub-id></element-citation></ref><ref id="bib5"><label>5.</label><element-citation publication-type="journal" id="sbref5"><person-group person-group-type="author"><name><surname>Molenkamp</surname><given-names>R.</given-names></name><name><surname>Spaan</surname><given-names>W.J.M.</given-names></name></person-group><article-title>Identification of a specific interaction between the coronavirus mouse hepatitis virus A59 nucleocapsid protein and packaging signal</article-title><source>Virology</source><volume>239</volume><year>1997</year><fpage>78</fpage><lpage>86</lpage><pub-id pub-id-type="pmid">9426448</pub-id></element-citation></ref><ref id="bib6"><label>6.</label><element-citation publication-type="journal" id="sbref6"><person-group person-group-type="author"><name><surname>Ding</surname><given-names>P.</given-names></name></person-group><article-title>Construction of murine coronavirus mutants containing interspecies chimeric nucleocapsid proteins</article-title><source>J. Virol.</source><volume>69</volume><year>1995</year><fpage>5475</fpage><lpage>5484</lpage><pub-id pub-id-type="pmid">7636993</pub-id></element-citation></ref><ref id="bib7"><label>7.</label><element-citation publication-type="journal" id="sbref7"><person-group person-group-type="author"><name><surname>Narayahan</surname><given-names>K.</given-names></name></person-group><article-title>Characterization of the coronavirus M protein and nucleocapsid interaction in infected cells</article-title><source>J. Virol.</source><volume>74</volume><year>2000</year><fpage>8127</fpage><lpage>8134</lpage><pub-id pub-id-type="pmid">10933723</pub-id></element-citation></ref><ref id="bib8"><label>8.</label><element-citation publication-type="journal" id="sbref8"><person-group person-group-type="author"><name><surname>Cáceres</surname><given-names>J.F.</given-names></name></person-group><article-title>Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity</article-title><source>J. Cell Biol.</source><volume>138</volume><year>1997</year><fpage>225</fpage><lpage>238</lpage><pub-id pub-id-type="pmid">9230067</pub-id></element-citation></ref><ref id="bib9"><label>9.</label><element-citation publication-type="journal" id="sbref9"><person-group person-group-type="author"><name><surname>Furuyama</surname><given-names>S.</given-names></name><name><surname>Bruzik</surname><given-names>J.P.</given-names></name></person-group><article-title>Multiple roles for SR proteins in <italic>trans</italic> splicing</article-title><source>Mol. Cell. Biol.</source><volume>22</volume><year>2002</year><fpage>5337</fpage><lpage>5346</lpage><pub-id pub-id-type="pmid">12101229</pub-id></element-citation></ref><ref id="bib10"><label>10.</label><element-citation publication-type="journal" id="sbref10"><person-group person-group-type="author"><name><surname>Wurm</surname><given-names>T.</given-names></name></person-group><article-title>Localization to the nucleolus is a common feature of coronavirus nucleoproteins, and the protein may disrupt host cell division</article-title><source>J. Virol.</source><volume>75</volume><year>2001</year><fpage>9345</fpage><lpage>9356</lpage><pub-id pub-id-type="pmid">11533198</pub-id></element-citation></ref><ref id="bib11"><label>11.</label><element-citation publication-type="journal" id="sbref11"><person-group person-group-type="author"><name><surname>Kolaskar</surname><given-names>A.S.</given-names></name><name><surname>Tongaonkar</surname><given-names>P.C.</given-names></name></person-group><article-title>A semi-empirical method for prediction of antigenic determinants on protein antigens</article-title><source>FEBS Lett.</source><volume>276</volume><year>1990</year><fpage>172</fpage><lpage>174</lpage><pub-id pub-id-type="pmid">1702393</pub-id></element-citation></ref><ref id="bib12"><label>12.</label><element-citation publication-type="journal" id="sbref12"><person-group person-group-type="author"><name><surname>Daginakatte</surname><given-names>C.G.</given-names></name></person-group><article-title>Production, characterization, and uses of monoclonal antibodies against recombinant nucleoprotein of Elk Coronavirus</article-title><source>Clin. Diagn. Lab. Immunol.</source><volume>6</volume><year>1999</year><fpage>341</fpage><lpage>344</lpage><pub-id pub-id-type="pmid">10225833</pub-id></element-citation></ref><ref id="bib13"><label>13.</label><element-citation publication-type="journal" id="sbref13"><person-group person-group-type="author"><name><surname>Zhu</surname><given-names>Q.Y.</given-names></name></person-group><article-title>Isolation and Identification of a Novel Coronavirus from Patients with SARS</article-title><source>Chin. J. Biotechnol.</source><year>2003</year><fpage>4</fpage></element-citation></ref><ref id="bib14"><label>14.</label><element-citation publication-type="journal" id="sbref14"><person-group person-group-type="author"><name><surname>Qin</surname><given-names>E.D.</given-names></name></person-group><article-title>A complete sequence and comparative analysis of SARS-associated virus (Isolate BJ01)</article-title><source>Chin. Sci. Bull.</source><volume>48</volume><year>2003</year><fpage>941</fpage><lpage>948</lpage></element-citation></ref></ref-list><sec id="s0080" sec-type="supplementary-material"><title>Supporting Online Material</title><p><ext-link ext-link-type="uri" xlink:href="http://www.gpbjournal.org/journal/pdf/GPBl(2)-07.htm" id="ir0070">http://www.gpbjournal.org/journal/pdf/GPBl(2)-07.htm</ext-link></p><p><supplementary-material content-type="local-data" id="ec0005"><caption><p>Table S1</p></caption><media xlink:href="mmc1.doc"></media></supplementary-material></p></sec><ack id="s0075"><title>Acknowledgements</title><p>The authors thank the Ministry of Science and Technology of China, Chinese Academy of Sciences, and National Natural Science Foundation of China for financial support. We are indebted to collaborators and clinicians from National Center of Disease Control of China, Beijing Plastic Surgery Hospital, Beijing Peoples’ Hospital, Beijing Tiantan Hospital, the Provincial Government of Zhejiang, the Provincial Government of Inner Mongolia, the Municipal Governments of Beijing and Hangzhou, and the Library of Chinese Academy of Science. Special gratitude is expressed here to the patients and their families for their devotion and cooperation. We appreciate the comments of Dr. Gwendolyn Zahner, visiting professor at BGI, Dr. Qimin You, Dr. Lin Hu and other colleagues on drafts of this manuscript.</p></ack></back><floats-group><fig id="f0005"><label>Fig. 1</label><caption><p>The predicted distributions of GC content (A), electric charge (B), hydrophobicity (C) and secondary structure (D) in the N protein of SARS-CoV.</p></caption><alt-text id="at0005">Fig. 1</alt-text><graphic xlink:href="gr1"></graphic></fig><fig id="f0010"><label>Fig. 2</label><caption><p>The predicted phosphorylation sites on the N protein. We identified 33 potential phosphorylation sites in the N protein, including 22 serines, 8 threonines and 3 tyrosines. The average score of serines are significantly higher than that of the other two. The phosphorylation sites concentrate in the middle of the N protein.</p></caption><alt-text id="at0010">Fig. 2</alt-text><graphic xlink:href="gr2"></graphic></fig><fig id="f0015"><label>Fig. 3</label><caption><p>The similarity chart of the N protein. Based on multi-alignment of totally nineteen coronavirus N proteins, two conserved regions were found around a.a. 81-140 and a.a. 270-320 (amino acid positions are all referred to the N protein of SARS-CoV, Isolate BJ01). The arrow indicates the most conserved domain, and its sequence and amino acid position are given. In contrast, the two termini of the N protein are more variable, particularly the C- terminal. The figure was generated by Plotcon in the EMBOSS package (<ext-link ext-link-type="uri" xlink:href="http://www.hgmp.mrc.ac.uk/Software/EMBOSS/" id="ir0005">http://www.hgmp.mrc.ac.uk/Software/EMBOSS/</ext-link>).</p></caption><alt-text id="at0015">Fig. 3</alt-text><graphic xlink:href="gr3"></graphic></fig><fig id="f0020"><label>Fig. 4</label><caption><p>The possible antigenic sites of the N protein. We have predicted sixteen antigenic sites of the N protein, and found they are clustering in the middle and the C-terminal. There is a strong antigenic site (TALALLLLDR) located around Codons 218-227. In addition, another three strong antigenic sites are detected around Codons 156-166 (AATVLQLPQGT), Codons 347-363 (FKDNVILLNKHIDAYKT) and Codons 389-398 (KQPTVTLLPA).</p></caption><alt-text id="at0020">Fig. 4</alt-text><graphic xlink:href="gr4"></graphic></fig><fig id="f0025"><label>Fig. 5</label><caption><p>The phylogenetic tree based on nineteen coronavirus N proteins. It reveals that SARS-CoV is closer to Group 2 than to Groups 1 and 3. Abbreviations: AIBV: avian infectious bronchitis virus; BCoV: bovine coronavirus; CCoV: canine coronavirus; CECoV: canine enteric coronavirus; ECoV: equine coronavirus; FCoV: feline coronavirus; FIPV: feline infectious peritonitis virus; HCoV-OC43: human coronavirus strain OC43; HCoV-229E: human coronavirus strain 229E; MHV: murine hepatitis virus; PEDV: porcine epidemic diarrhea virus; PHEV: porcine hemagglutmating encephalomyelitis virus; PRCoV: porcine respiratory coronavirus; PTGV: transmissible gastroenteritis virus; PV: puffinosis virus; RCoV: rat coronavirus; RSCoV: Rat sialodacryoadenitis coronavirus; SARS-CoV: human severe acute respiratory syndrome-associated coronavirus isolate BJ01; TCoV: turkey coronavirus.</p></caption><alt-text id="at0025">Fig. 5</alt-text><graphic xlink:href="gr5"></graphic></fig><table-wrap id="t0005" position="float"><label>Table 1</label><caption><p>The Amino Acid Composition of the SARS-CoV N Protein</p></caption><alt-text id="at0030">Table 1</alt-text><table frame="hsides" rules="groups"><thead><tr><th></th><th align="right">Number</th><th align="right">Percentage (%)</th></tr></thead><tbody><tr><td align="center"><bold>Non-polar, Neutral</bold></td><td></td><td></td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center">Ala, A</td><td align="right">34</td><td align="char">8.06</td></tr><tr><td align="center">Phe, F</td><td align="right">13</td><td align="char">3.08</td></tr><tr><td align="center">Gly, G</td><td align="right">45</td><td align="char">10.66</td></tr><tr><td align="center">Ile, I</td><td align="right">11</td><td align="char">2.61</td></tr><tr><td align="center">Leu, L</td><td align="right">26</td><td align="char">6.16</td></tr><tr><td align="center">Met, M</td><td align="right">7</td><td align="char">1.66</td></tr><tr><td align="center">Pro, P</td><td align="right">31</td><td align="char">7.35</td></tr><tr><td align="center">Val, V</td><td align="right">11</td><td align="char">2.61</td></tr><tr><td align="center">Trp, W</td><td align="right">5</td><td align="char">1.18</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Total</bold></td><td align="right">183</td><td align="char">43.36</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Polar, Neutral</bold></td><td></td><td></td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center">Cys, C</td><td align="right">0</td><td align="char">0.00</td></tr><tr><td align="center">Asn. N</td><td align="right">25</td><td align="char">5.92</td></tr><tr><td align="center">Gln, Q</td><td align="right">34</td><td align="char">8.06</td></tr><tr><td align="center">Ser, S</td><td align="right">35</td><td align="char">8.29</td></tr><tr><td align="center">Thr, T</td><td align="right">33</td><td align="char">7.82</td></tr><tr><td align="center">Tyr, Y</td><td align="right">11</td><td align="char">2.61</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Total</bold></td><td align="right">138</td><td align="char">32.70</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Polar, Positive</bold></td><td></td><td></td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center">His, H</td><td align="right">5</td><td align="char">1.18</td></tr><tr><td align="center">Lys, K</td><td align="right">29</td><td align="char">6.87</td></tr><tr><td align="center">Arg, R</td><td align="right">31</td><td align="char">7.35</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Total</bold></td><td align="right">65</td><td align="char">15.40</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Polar, Negative</bold></td><td></td><td></td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center">Asp, D</td><td align="right">22</td><td align="char">5.21</td></tr><tr><td align="center">Glu, E</td><td align="right">14</td><td align="char">3.32</td></tr><tr><td colspan="3"><hr></hr></td></tr><tr><td align="center"><bold>Total</bold></td><td align="right">36</td><td align="char">8.53</td></tr></tbody></table></table-wrap><table-wrap id="t0010" position="float"><label>Table 2</label><caption><p>The Core Motif of SR-rich Region in the Coronavirus N Protein</p></caption><alt-text id="at0035">Table 2</alt-text><table frame="hsides" rules="groups"><thead><tr><th>Coronavirus</th><th>Core motif of SR-rich region in the N protein</th></tr></thead><tbody><tr><td>SARS Coronavirus BJ01</td><td><bold>SR</bold>GGSQAS<bold>SR</bold>SS<bold>SRSR</bold>GN<bold>SR</bold>NSTPGS <bold>SR</bold><xref rid="tbl2fnStar" ref-type="table-fn">*</xref></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Murine Hepatitis Virus</td><td></td></tr><tr><td>Puffinosis Virus</td><td></td></tr><tr><td>Rat Sialodacryoadenitis Coronavirus</td><td><bold>SR</bold>SG<bold>SR</bold>SQ<bold>SR</bold></td></tr><tr><td>Rat Coronavirus</td><td></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Equine Coronavirus</td><td></td></tr><tr><td>Bovine Coronavirus</td><td></td></tr><tr><td>Porcine Hemagglutinating Encephalomyelitis Virus</td><td><bold>SR</bold>ST<bold>SR</bold>[A/T]<xref rid="tbl2fn1" ref-type="table-fn">#</xref>[S/P][<bold>S/N</bold>]<bold>R</bold>A[S/P]SAG<bold>SR</bold>(<bold>SR</bold>)<xref rid="tbl2fn2" ref-type="table-fn">†</xref></td></tr><tr><td>HCoV-OC43</td><td></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Turkey Coronavirus</td><td></td></tr><tr><td>Avian Infectious Bronchitis Virus</td><td><bold>S</bold>(T)<bold>R</bold>AP<bold>SR</bold>EG <bold>SR</bold>{Xn}<xref rid="tbl2fn3" ref-type="table-fn">‡</xref><bold>SR</bold></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Porcine Respiratory Coronavirus</td><td></td></tr><tr><td>Transmissible Gastroenteritis Virus</td><td></td></tr><tr><td>Canine Enteric Coronavirus</td><td><bold>SR</bold>DN<bold>SRS</bold>[<bold>R/P</bold>] SQ<bold>SRS</bold>[<bold>R/Q</bold>]<bold>SR</bold>NRSQ<bold>SR</bold>{Xn}<bold>SR</bold></td></tr><tr><td>Canine Coronavirus</td><td></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Feline Infectious Peritonitis Virus</td><td><bold>SR</bold>NN <bold>SR</bold>SGSQ<bold>SR</bold>SV<bold>SR</bold> NRSQ{Xn}<bold>SR</bold>{Xn}<bold>SR</bold></td></tr><tr><td>Feline Coronavirus</td><td></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Human Coronavirus 229E</td><td><bold>SR</bold>AP<bold>SR</bold>SQ<bold>SR</bold>SQ <bold>SR</bold>{Xn}<bold>SR</bold>{Xn}<bold>SR</bold></td></tr><tr><td colspan="2"><hr></hr></td></tr><tr><td>Porcine Epidemic Diarrhea Virus</td><td><bold>SR</bold>AN<bold>SRSRSR</bold>{Xn} <bold>SR</bold>{Xn}<bold>SR</bold>{Xn}<bold>SR</bold>{Xn}<bold>SR</bold></td></tr></tbody></table><table-wrap-foot><fn id="tbl2fnStar"><label>*</label><p id="ntp0005">Bold letter indicates the marker SR. Normal letter indicates the amino acid between two SRs.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl2fn1"><label>#</label><p id="ntp0010">Square brackets indicate this position may be occupied by one of the amino acids in them.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl2fn2"><label>†</label><p id="ntp0015">Round brackets indicate the amino acids in them may occur in some viruses while may not in other viruses.</p></fn></table-wrap-foot><table-wrap-foot><fn id="tbl2fn3"><label>‡</label><p id="ntp0020">Curly brackets indicate amino acids between SRs, X indicates any amino acid, and subscript letter n indicates the number of amino acids between SRs.</p></fn></table-wrap-foot></table-wrap><table-wrap id="t0015" position="float"><label>Table 3</label><caption><p>The Predicted Antigenic Sites on the SARS-CoV N Protein</p></caption><alt-text id="at0040">Table 3</alt-text><table frame="hsides" rules="groups"><thead><tr><th align="center">No.</th><th align="center">Start Position<xref rid="tbl3fnStar" ref-type="table-fn">*</xref></th><th align="center">Sequence</th><th align="center">End Position</th></tr></thead><tbody><tr><td align="center">1</td><td align="center">52</td><td align="center">SWFTALTQ</td><td align="center">59</td></tr><tr><td align="center">2</td><td align="center">69</td><td align="center">RGQGVPI</td><td align="center">75</td></tr><tr><td align="center">3</td><td align="center">83</td><td align="center">DQIGYYR</td><td align="center">89</td></tr><tr><td align="center">4</td><td align="center">106</td><td align="center">SPRWYFYYLG</td><td align="center">115</td></tr><tr><td align="center">5</td><td align="center">118</td><td align="center">PEASLPY</td><td align="center">124</td></tr><tr><td align="center">6</td><td align="center">130</td><td align="center">GIVWVAT</td><td align="center">136</td></tr><tr><td align="center">7</td><td align="center">156</td><td align="center">AATVLQLPQGT</td><td align="center">166</td></tr><tr><td align="center">8</td><td align="center">218</td><td align="center">TALALLLLDR</td><td align="center">227</td></tr><tr><td align="center">9</td><td align="center">229</td><td align="center">NQLESKVSG</td><td align="center">237</td></tr><tr><td align="center">10</td><td align="center">243</td><td align="center">QGQTVTK</td><td align="center">249</td></tr><tr><td align="center">11</td><td align="center">267</td><td align="center">KQYNVTQ</td><td align="center">273</td></tr><tr><td align="center">12</td><td align="center">299</td><td align="center">YKHWPQIAQFAPSASAF</td><td align="center">315</td></tr><tr><td align="center">13</td><td align="center">323</td><td align="center">MEVTPSGTWLTYHGAIK</td><td align="center">339</td></tr><tr><td align="center">14</td><td align="center">347</td><td align="center">FKDNVILLNKHIDAYKT</td><td align="center">363</td></tr><tr><td align="center">15</td><td align="center">379</td><td align="center">EAQPLPQ</td><td align="center">385</td></tr><tr><td align="center">16</td><td align="center">389</td><td align="center">KQPTVTLLPA</td><td align="center">398</td></tr></tbody></table><table-wrap-foot><fn id="tbl3fnStar"><label>*</label><p id="ntp0025">amino acid position in the SARS-CoV N protein (BJ01)</p></fn></table-wrap-foot></table-wrap><table-wrap id="t0020" position="float"><label>Table 4</label><caption><p>The Synthesized Peptides Representing the N Protein of SARS-CoV and Their ELISA Result</p></caption><alt-text id="at0045">Table 4</alt-text><table frame="hsides" rules="groups"><thead><tr><th align="center">Peptides Number</th><th align="center">Start Position<xref rid="tbl4fnStar" ref-type="table-fn">*</xref></th><th align="center">Sequence</th><th align="center">End Position</th><th align="center">ELISA Result</th></tr></thead><tbody><tr><td align="center">N1</td><td align="center">1</td><td>MSDNGPQSNQRSAPRITFGGPTD</td><td align="center">23</td><td align="center">++</td></tr><tr><td align="center">N21</td><td align="center">21</td><td>PTDSTDNNQNGGRNGARPKQRR</td><td align="center">42</td><td align="center">++</td></tr><tr><td align="center">N35</td><td align="center">35</td><td>GARPKQRRPQGLPNNTASWFTA</td><td align="center">56</td><td align="center">+</td></tr><tr><td align="center">N99</td><td align="center">99</td><td>DGKMKELSPRWYFYYLGTGPEA</td><td align="center">120</td><td align="center">-</td></tr><tr><td align="center">N161</td><td align="center">161</td><td>QLPQGTTLPKGFYAEGSRGGSQ</td><td align="center">182</td><td align="center">+++</td></tr><tr><td align="center">N177</td><td align="center">177</td><td>SRGGSQASSRSSSRSRGNSRNS</td><td align="center">198</td><td align="center">++</td></tr><tr><td align="center">N196</td><td align="center">196</td><td>RNSTPGSSRGNSPARMASGGGE</td><td align="center">217</td><td align="center">-</td></tr><tr><td align="center">N215</td><td align="center">215</td><td>GGETALALLLLDRLNQLESKVSGKG</td><td align="center">239</td><td align="center">++</td></tr><tr><td align="center">N245</td><td align="center">245</td><td>QTVTKKSAAEASKKPRQKRTATKQ</td><td align="center">268</td><td align="center">++</td></tr><tr><td align="center">N258</td><td align="center">258</td><td>KPRQKRTATKQYNVTQAFGRRG</td><td align="center">279</td><td align="center">+</td></tr><tr><td align="center">N355</td><td align="center">355</td><td>NKHIDAYKTFPPTEPKKDKKKK</td><td align="center">376</td><td align="center">++</td></tr><tr><td align="center">N371</td><td align="center">371</td><td>KDKKKKTDEAQPLPQRQKKQ</td><td align="center">390</td><td align="center">+++</td></tr><tr><td align="center">N385</td><td align="center">385</td><td>QRQKKQPTVTLLPAADMDDFSRQ</td><td align="center">407</td><td align="center">++</td></tr><tr><td align="center">N401</td><td align="center">401</td><td>MDDFSRQLQNSMSGASADSTQA</td><td align="center">422</td><td align="center">-</td></tr></tbody></table><table-wrap-foot><fn id="tbl4fnStar"><label>*</label><p id="ntp0030">amino acid position in the SARS-CoV N protein (BJ01)</p></fn></table-wrap-foot></table-wrap><table-wrap id="t0025" position="float"><label>Table 5</label><caption><p>The Four Substitutions in the N Protein of SARS-CoV</p></caption><alt-text id="at0050">Table 5</alt-text><table frame="hsides" rules="groups"><thead><tr><th align="center">Nt Position in BJ01</th><th align="center">a.a. Position in the ORF</th><th align="center">a.a. (Ratio)</th><th align="center">Synonymous Substitution</th></tr></thead><tbody><tr><td align="center">28,519</td><td align="center">140</td><td align="center">L(16)/W(1)</td><td align="center">No</td></tr><tr><td align="center">28,520</td><td align="center">140</td><td align="center">L(17)</td><td align="center">Yes</td></tr><tr><td align="center">28,560</td><td align="center">154</td><td align="center">N(16)/Y(1)</td><td align="center">No</td></tr><tr><td align="center">28,677</td><td align="center">193</td><td align="center">G(16)/C(1)</td><td align="center">No</td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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