{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T10:41:16Z","timestamp":1649155276314},"reference-count":30,"publisher":"World Scientific Pub Co Pte Ltd","issue":"02","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,4]]},"abstract":"<jats:p>Using the combination of molecular dynamics (MD) simulations and geometric clustering we analyzed the role of arginine at 209 position in the transition of protein kinase A I\u03b1 (PKA I\u03b1) regulatory subunit A-domain from H- to B-conformation and stabilization of the latter. The mechanism underlying the role of the residue at position 209 in the realization of B-conformation includes: (1) possibility to bind the ligand tightly (if transition happens in the presence of cAMP), (2) capability to hold \u03b22\u03b23-loop in the correct conformation, (3) tendency of residue at 209 position to stabilize B-conformation in the absence and in presence of the ligand. In terms of the effect produced on transition of A-domain from H- to B-conformation in the presence of cAMP, mutational substitutions for R209 can be arranged in the following order: Glu(Gly)&gt;Lys&gt;Ile. In the absence of cAMP the order is different Lys&gt;Gly&gt;Glu&gt;Ile. Thus, our results allow us to presume that the role of arginine at 209 position can be important though not crucial.<\/jats:p>","DOI":"10.1142\/s0219720014410054","type":"journal-article","created":{"date-parts":[[2014,1,23]],"date-time":"2014-01-23T07:24:54Z","timestamp":1390461894000},"page":"1441005","source":"Crossref","is-referenced-by-count":1,"title":["Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RI\u03b1 A-domain"],"prefix":"10.1142","volume":"12","author":[{"given":"Olga N.","family":"Rogacheva","sequence":"first","affiliation":[{"name":"St. Petersburg State University, Universitetskaya nab. 7\/9, 199034 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasiliy E.","family":"Stefanov","sequence":"additional","affiliation":[{"name":"St. Petersburg State University, Universitetskaya nab. 7\/9, 199034 St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boris F.","family":"Shchegolev","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, nab. Makarova 6 199034, St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena A.","family":"Vershinina","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, nab. Makarova 6 199034, St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena V.","family":"Savvateeva-Popova","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, nab. Makarova 6 199034, St. Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2014,4,9]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.2741\/A195"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1021\/cr000226k"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbapap.2007.10.002"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M110.004390"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1126\/science.7638597"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.07.018"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1002\/pro.400"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M109.059493"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21446"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M900388-MCP200"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.272.26.16343"},{"key":"rf12","doi-asserted-by":"crossref","first-page":"9668","DOI":"10.1016\/S0021-9258(19)81569-7","volume":"263","author":"Bubis J.","journal-title":"J. Biol. Chem."},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.271.44.27630"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1134\/S0006297912050057"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-12-r264"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2010.12.005"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1006\/jcph.1999.6201"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1021\/jp973084f"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(96)00018-5"},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1063\/1.3301140"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1063\/1.2714539"},{"key":"rf24","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-158"},{"key":"rf25","doi-asserted-by":"publisher","DOI":"10.1021\/bi0302503"},{"key":"rf27","first-page":"7","volume":"49","author":"Loohach R.","journal-title":"Int. J. Comp. Appl."},{"key":"rf28","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.4655"},{"key":"rf30","doi-asserted-by":"publisher","DOI":"10.1038\/nsb878"},{"key":"rf31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M707849200"},{"key":"rf32","doi-asserted-by":"publisher","DOI":"10.1134\/S0006297912050069"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720014410054","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,24]],"date-time":"2022-03-24T09:23:41Z","timestamp":1648113821000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720014410054"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,4]]},"references-count":30,"journal-issue":{"issue":"02","published-online":{"date-parts":[[2014,4,9]]},"published-print":{"date-parts":[[2014,4]]}},"alternative-id":["10.1142\/S0219720014410054"],"URL":"https:\/\/doi.org\/10.1142\/s0219720014410054","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4]]}}}