{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,10]],"date-time":"2025-04-10T04:08:18Z","timestamp":1744258098519,"version":"3.40.4"},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2017,12,22]],"date-time":"2017-12-22T00:00:00Z","timestamp":1513900800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2017,12,22]],"date-time":"2017-12-22T00:00:00Z","timestamp":1513900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"University Grants Commission\/Rajiv Gandhi National fellowship","award":["UGC\/RGNF- F1-17.1\/2012-13\/RGNF-2012-13-ST-MAH-34083"],"award-info":[{"award-number":["UGC\/RGNF- F1-17.1\/2012-13\/RGNF-2012-13-ST-MAH-34083"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Virol"],"published-print":{"date-parts":[[2018,4]]},"DOI":"10.1007\/s00705-017-3681-x","type":"journal-article","created":{"date-parts":[[2017,12,22]],"date-time":"2017-12-22T09:16:55Z","timestamp":1513934215000},"page":"1031-1036","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Computational analysis of the effect of polymerase acidic (PA) gene mutation F35L in the 2009 pandemic influenza A (H1N1) virus on binding aspects of mononucleotides in the endonuclease domain"],"prefix":"10.1007","volume":"163","author":[{"given":"Dipali","family":"Bhoye","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah S","family":"Cherian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,12,22]]},"reference":[{"key":"3681_CR1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.gene.2014.12.003","volume":"557","author":"AK Behera","year":"2015","unstructured":"Behera AK, Basu S, Cherian SS (2015) Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: modeling studies of antibody and receptor binding. Gene 557:19\u201327","journal-title":"Gene"},{"key":"3681_CR2","doi-asserted-by":"publisher","first-page":"2054","DOI":"10.1080\/07391102.2015.1106341","volume":"34","author":"AK Behera","year":"2016","unstructured":"Behera AK, Chandra I, Cherian SS (2016) Molecular dynamics simulation of the effects of single (S221P) and double (S221P and K216E) mutations in the hemagglutinin protein of influenza A H5N1 virus: a study on host receptor specificity. J Biomol Struct Dyn 34:2054\u20132067","journal-title":"J Biomol Struct Dyn"},{"key":"3681_CR3","doi-asserted-by":"publisher","first-page":"3684","DOI":"10.1063\/1.448118","volume":"81","author":"HJC Berendsen","year":"1984","unstructured":"Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684\u20133690","journal-title":"J Chem Phys"},{"key":"3681_CR4","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1099\/jgv.0.000500","volume":"97","author":"D Bhoye","year":"2016","unstructured":"Bhoye D, Behera AK, Cherian SS (2016) A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding. J Gen Virol 97:1785\u20131796","journal-title":"J Gen Virol"},{"key":"3681_CR5","doi-asserted-by":"publisher","first-page":"W252","DOI":"10.1093\/nar\/gku340","volume":"42","author":"M Biasini","year":"2014","unstructured":"Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo Cassarino T, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42:W252\u2013258","journal-title":"Nucleic Acids Res"},{"key":"3681_CR6","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.virusres.2008.07.008","volume":"137","author":"M Buragohain","year":"2008","unstructured":"Buragohain M, Cherian SS, Prabhakar G, Chitambar SD (2008) VP6 capsid protein of chicken rotavirus strain CH2: sequence, phylogeny and in silico antigenic analyses. Virus Res 137:173\u2013178","journal-title":"Virus Res"},{"key":"3681_CR7","doi-asserted-by":"publisher","first-page":"7020","DOI":"10.1128\/JVI.00522-11","volume":"85","author":"KA Bussey","year":"2011","unstructured":"Bussey KA, Desmet EA, Mattiacio JL, Hamilton A, Bradel-Tretheway B, Bussey HE, Kim B, Dewhurst S, Takimoto T (2011) PA residues in the 2009 H1N1 pandemic influenza virus enhance avian influenza virus polymerase activity in mammalian cells. J Virol 85:7020\u20137028","journal-title":"J Virol"},{"key":"3681_CR8","doi-asserted-by":"publisher","first-page":"9096","DOI":"10.1128\/JVI.00995-10","volume":"84","author":"T Crepin","year":"2010","unstructured":"Crepin T, Dias A, Palencia A, Swale C, Cusack S, Ruigrok RW (2010) Mutational and metal binding analysis of the endonuclease domain of the influenza virus polymerase PA subunit. J Virol 84:9096\u20139104","journal-title":"J Virol"},{"key":"3681_CR9","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1038\/nature07745","volume":"458","author":"A Dias","year":"2009","unstructured":"Dias A, Bouvier D, Crepin T, McCarthy AA, Hart DJ, Baudin F, Cusack S, Ruigrok RW (2009) The cap-snatching endonuclease of influenza virus polymerase resides in the PA subunit. Nature 458:914\u2013918","journal-title":"Nature"},{"key":"3681_CR10","doi-asserted-by":"publisher","first-page":"5612","DOI":"10.1021\/bi9828932","volume":"38","author":"LHB Doan","year":"1999","unstructured":"Doan LHB, Roberts NA, Klumpp K (1999) Metal ion catalysis of RNA cleavage by the influenza virus endonuclease. Biochemistry 38:5612\u20135619","journal-title":"Biochemistry"},{"key":"3681_CR11","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/nsmb.1421","volume":"15","author":"D Guilligay","year":"2008","unstructured":"Guilligay D, Tarendeau F, Resa-Infante P, Coloma R, Crepin T, Sehr P, Lewis J, Ruigrok RW, Ortin J, Hart DJ, Cusack S (2008) The structural basis for cap binding by influenza virus polymerase subunit PB2. Nat Struct Mol Biol 15:500\u2013506","journal-title":"Nat Struct Mol Biol"},{"issue":"Suppl 3","key":"3681_CR12","doi-asserted-by":"publisher","first-page":"S24","DOI":"10.1186\/1471-2164-10-S3-S24","volume":"10","author":"N Jongkon","year":"2009","unstructured":"Jongkon N, Mokmak W, Chuakheaw D, Shaw PJ, Tongsima S, Sangma C (2009) Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. BMC Genomics 10(Suppl 3):S24","journal-title":"BMC Genomics"},{"key":"3681_CR13","doi-asserted-by":"publisher","first-page":"e1002831","DOI":"10.1371\/journal.ppat.1002831","volume":"8","author":"E Kowalinski","year":"2012","unstructured":"Kowalinski E, Zubieta C, Wolkerstorfer A, Szolar OH, Ruigrok RW, Cusack S (2012) Structural analysis of specific metal chelating inhibitor binding to the endonuclease domain of influenza pH1N1 (2009) polymerase. PLoS Pathog 8:e1002831","journal-title":"PLoS Pathog"},{"key":"3681_CR14","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1002\/prot.20251","volume":"57","author":"E Krieger","year":"2004","unstructured":"Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (2004) Making optimal use of empirical energy functions: force-field parameterization in crystal space. Proteins 57:678\u2013683","journal-title":"Proteins"},{"key":"3681_CR15","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1016\/j.jmb.2007.05.022","volume":"372","author":"E Krissinel","year":"2007","unstructured":"Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774\u2013797","journal-title":"J Mol Biol"},{"key":"3681_CR16","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1107\/S0907444911007232","volume":"67","author":"E Krissinel","year":"2011","unstructured":"Krissinel E (2011) Macromolecular complexes in crystals and solutions. Acta Crystallogr D Biol Crystallogr 67:376\u2013385","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"3681_CR17","doi-asserted-by":"publisher","first-page":"17430","DOI":"10.1021\/ja904052q","volume":"131","author":"EI Newhouse","year":"2009","unstructured":"Newhouse EI, Xu D, Markwick PRL, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon JA, WW L (2009) Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc 131:17430\u201317442","journal-title":"J Am Chem Soc"},{"key":"3681_CR18","doi-asserted-by":"publisher","first-page":"4355","DOI":"10.1007\/s00894-012-1423-2","volume":"18","author":"D Pan","year":"2012","unstructured":"Pan D, Xue W, Wang X, Guo J, Liu H, Yao X (2012) Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. J Mol Model 18:4355\u20134366","journal-title":"J Mol Model"},{"key":"3681_CR19","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/0092-8674(81)90449-9","volume":"23","author":"SJ Plotch","year":"1981","unstructured":"Plotch SJ, Bouloy M, Ulmanen I, Krug RM (1981) A unique cap (m7G pppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 23:847\u2013858","journal-title":"Cell"},{"key":"3681_CR20","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1080\/07391102.2011.10507379","volume":"29","author":"R Purohit","year":"2011","unstructured":"Purohit R, Rajendran V, Sethumadhavan R (2011) Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants. J Biomol Struct Dyn 29:137\u2013152","journal-title":"J Biomol Struct Dyn"},{"key":"3681_CR21","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.virusres.2011.03.022","volume":"158","author":"S Sakabe","year":"2011","unstructured":"Sakabe S, Ozawa M, Takano R, Iwastuki-Horimoto K, Kawaoka Y (2011) Mutations in PA, NP, and HA of a pandemic (H1N1) 2009 influenza virus contribute to its adaptation to mice. Virus Res 158:124\u2013129","journal-title":"Virus Res"},{"key":"3681_CR22","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1093\/infdis\/jir716","volume":"205","author":"R Seyer","year":"2012","unstructured":"Seyer R, Hrincius ER, Ritzel D, Abt M, Mellmann A, Marjuki H, Kuhn J, Wolff T, Ludwig S, Ehrhardt C (2012) Synergistic adaptive mutations in the hemagglutinin and polymerase acidic protein lead to increased virulence of pandemic 2009 H1N1 influenza A virus in mice. J Infect Dis 205:262\u2013271","journal-title":"J Infect Dis"},{"key":"3681_CR23","doi-asserted-by":"publisher","first-page":"3669","DOI":"10.1073\/pnas.1519772113","volume":"113","author":"MS Song","year":"2016","unstructured":"Song MS, Kumar G, Shadrick WR, Zhou W, Jeevan T, Li Z, Slavish PJ, Fabrizio TP, Yoon SW, Webb TR, Webby RJ, White SW (2016) Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor. Proc Natl Acad Sci USA 113:3669\u20133674","journal-title":"Proc Natl Acad Sci USA"},{"key":"3681_CR24","doi-asserted-by":"publisher","first-page":"4600","DOI":"10.1128\/JVI.03158-13","volume":"88","author":"Y Sun","year":"2014","unstructured":"Sun Y, Xu Q, Shen Y, Liu L, Wei K, Sun H, Pu J, Chang KC, Liu J (2014) Naturally occurring mutations in the PA gene are key contributors to increased virulence of pandemic H1N1\/09 influenza virus in mice. J Virol 88:4600\u20134604","journal-title":"J Virol"},{"key":"3681_CR25","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731\u20132739","journal-title":"Mol Biol Evol"},{"key":"3681_CR26","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/nature07720","volume":"458","author":"P Yuan","year":"2009","unstructured":"Yuan P, Bartlam M, Lou Z, Chen S, Zhou J, He X, Lv Z, Ge R, Li X, Deng T, Fodor E, Rao Z, Liu Y (2009) Crystal structure of an avian influenza polymerase PA(N) reveals an endonuclease active site. Nature 458:909\u2013913","journal-title":"Nature"},{"key":"3681_CR27","doi-asserted-by":"publisher","first-page":"9024","DOI":"10.1128\/JVI.00911-09","volume":"83","author":"C Zhao","year":"2009","unstructured":"Zhao C, Lou Z, Guo Y, Ma M, Chen Y, Liang S, Zhang L, Chen S, Li X, Liu Y, Bartlam M, Rao Z (2009) Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center. J Virol 83:9024\u20139030","journal-title":"J Virol"},{"key":"3681_CR28","doi-asserted-by":"publisher","first-page":"e33383","DOI":"10.1371\/journal.pone.0033383","volume":"7","author":"W Zhu","year":"2012","unstructured":"Zhu W, Zhu Y, Qin K, Yu Z, Gao R, Yu H, Zhou J, Shu Y (2012) Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. PLoS One 7:e33383","journal-title":"PLoS One"}],"container-title":["Archives of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00705-017-3681-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00705-017-3681-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00705-017-3681-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T04:48:43Z","timestamp":1744174123000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00705-017-3681-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12,22]]},"references-count":28,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2018,4]]}},"alternative-id":["3681"],"URL":"https:\/\/doi.org\/10.1007\/s00705-017-3681-x","relation":{},"ISSN":["0304-8608","1432-8798"],"issn-type":[{"type":"print","value":"0304-8608"},{"type":"electronic","value":"1432-8798"}],"subject":[],"published":{"date-parts":[[2017,12,22]]},"assertion":[{"value":"25 September 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 December 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 December 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors declare that they have no conflict of interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"This article does not contain any studies with human participants or animals performed by any of the authors.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}