{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:04:38Z","timestamp":1791219878542,"version":"4.1.0"},"reference-count":53,"publisher":"American Chemical Society (ACS)","issue":"25","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Phys. Chem. B"],"published-print":{"date-parts":[[2011,6,30]]},"DOI":"10.1021\/jp203202e","type":"journal-article","created":{"date-parts":[[2011,6,7]],"date-time":"2011-06-07T08:30:19Z","timestamp":1307435419000},"page":"8346-8357","source":"Crossref","is-referenced-by-count":36,"title":["Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation"],"prefix":"10.1021","volume":"115","author":[{"given":"Narayanan","family":"Veeraraghavan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abir","family":"Ganguly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara L.","family":"Golden","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip C.","family":"Bevilacqua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon","family":"Hammes-Schiffer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2011,6,7]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/S0959-440X(03)00077-0","volume":"13","author":"DeRose V. J.","year":"2003","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref2\/cit2","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1371\/journal.pbio.0030277","volume":"3","author":"Hougland J. L.","year":"2005","journal-title":"PLoS Biol."},{"key":"ref3\/cit3","author":"Ferre-D\u2019Amare A. R.","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref4\/cit4","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.cbpa.2006.08.014","volume":"10","author":"Bevilacqua P. C.","year":"2006","journal-title":"Curr. Opin. Chem. Biol."},{"key":"ref5\/cit5","first-page":"11","volume-title":"Ribozymes and RNA Catalysis","author":"Bevilacqua P. C.","year":"2008"},{"key":"ref6\/cit6","doi-asserted-by":"crossref","first-page":"12022","DOI":"10.1021\/bi011253n","volume":"40","author":"Nakano S.","year":"2001","journal-title":"Biochemistry"},{"key":"ref7\/cit7","doi-asserted-by":"crossref","first-page":"11357","DOI":"10.1021\/bi061215+","volume":"45","author":"Perrotta A. T.","year":"2006","journal-title":"Biochemistry"},{"key":"ref8\/cit8","doi-asserted-by":"crossref","first-page":"6508","DOI":"10.1021\/bi100670p","volume":"49","author":"Chen J. H.","year":"2010","journal-title":"Biochemistry"},{"key":"ref9\/cit9","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1126\/science.1129308","volume":"313","author":"Salehi-Ashtiani K.","year":"2006","journal-title":"Science"},{"key":"ref10\/cit10","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1126\/science.1178084","volume":"326","author":"Webb C.-H. T.","year":"2009","journal-title":"Science"},{"key":"ref11\/cit11","doi-asserted-by":"crossref","first-page":"2982","DOI":"10.1021\/bi026815x","volume":"42","author":"Nakano S.","year":"2003","journal-title":"Biochemistry"},{"key":"ref12\/cit12","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/26912","volume":"395","author":"Ferre-D\u2019Amare A. R.","year":"1998","journal-title":"Nature"},{"key":"ref13\/cit13","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1126\/science.287.5457.1493","volume":"287","author":"Nakano S.","year":"2000","journal-title":"Science"},{"key":"ref14\/cit14","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nchembio703","volume":"1","author":"Das S. R.","year":"2005","journal-title":"Nat. Chem. Biol."},{"key":"ref15\/cit15","doi-asserted-by":"crossref","first-page":"14504","DOI":"10.1021\/ja801816k","volume":"130","author":"Cerrone-Szakal A. L.","year":"2008","journal-title":"J. Am. Chem. Soc."},{"key":"ref16\/cit16","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1021\/bi2000164","volume":"50","author":"Veeraraghavan N.","year":"2011","journal-title":"Biochemistry"},{"key":"ref17\/cit17","doi-asserted-by":"crossref","first-page":"3001","DOI":"10.1021\/bi061732s","volume":"46","author":"Nakano S.","year":"2007","journal-title":"Biochemistry"},{"key":"ref18\/cit18","doi-asserted-by":"crossref","first-page":"13335","DOI":"10.1021\/ja0743893","volume":"129","author":"Gong B.","year":"2007","journal-title":"J. Am. Chem. Soc."},{"key":"ref19\/cit19","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1006\/jmbi.1999.3398","volume":"295","author":"Ferre-D\u2019Amare A. R.","year":"2000","journal-title":"J. Mol. Biol."},{"key":"ref20\/cit20","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature02522","volume":"429","author":"Ke A.","year":"2004","journal-title":"Nature"},{"key":"ref21\/cit21","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.str.2007.01.017","volume":"15","author":"Ke A.","year":"2007","journal-title":"Structure"},{"key":"ref22\/cit22","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4612-5190-3","volume-title":"Principles of Nucleic Acid Structure","author":"Saenger W.","year":"1984"},{"key":"ref23\/cit23","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1021\/bi061375l","volume":"46","author":"Siegfried N. A.","year":"2007","journal-title":"Biochemistry"},{"key":"ref24\/cit24","unstructured":"Sokoloski, J. E.; Godfrey, S. A.; Dombrowski, S. E.; Bevilacqua, P. C. (2011, submitted for publication."},{"key":"ref25\/cit25","doi-asserted-by":"crossref","first-page":"2189","DOI":"10.1261\/rna.778107","volume":"13","author":"Chadalavada D. M.","year":"2007","journal-title":"RNA"},{"key":"ref26\/cit26","doi-asserted-by":"crossref","first-page":"1746","DOI":"10.1261\/rna.1140308","volume":"14","author":"Cerrone-Szakal A. L.","year":"2008","journal-title":"RNA"},{"key":"ref27\/cit27","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/S0960-9822(00)00109-3","volume":"4","author":"Tanner N. K.","year":"1994","journal-title":"Curr. Biol."},{"key":"ref28\/cit28","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1016\/j.jmb.2010.07.025","volume":"402","author":"Veeraraghavan N.","year":"2010","journal-title":"J. Mol. Biol."},{"key":"ref29\/cit29","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"Jorgensen W. L.","year":"1983","journal-title":"J. Chem. Phys."},{"key":"ref30\/cit30","unstructured":"Maestro; version 9.0;Schr\u00f6dinger L.L.C.:New York, 2010."},{"key":"ref31\/cit31","unstructured":"Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I. K.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E.Proceedings of the ACM\/IEEE Conference on Supercomputing (SC06), 2006."},{"key":"ref32\/cit32","unstructured":"Desmond Molecular Dynamics System;D. E. Shaw Research:New York, 2008."},{"key":"ref33\/cit33","doi-asserted-by":"crossref","first-page":"5179","DOI":"10.1021\/ja00124a002","volume":"117","author":"Cornell W. D.","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref34\/cit34","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1002\/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F","volume":"21","author":"Wang J. M.","year":"2000","journal-title":"J. Comput. Chem."},{"key":"ref35\/cit35","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"Darden T.","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref36\/cit36","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","volume":"23","author":"Ryckaert J. P.","year":"1977","journal-title":"J. Comput. Phys"},{"key":"ref37\/cit37","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1080\/00268978400101201","volume":"52","author":"Nos\u00e9 S.","year":"1984","journal-title":"Mol. Phys."},{"key":"ref38\/cit38","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","volume":"31","author":"Hoover W. G.","year":"1985","journal-title":"Phys. Rev. A"},{"key":"ref39\/cit39","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/jcc.540090407","volume":"9","author":"Gilson M. K.","year":"1987","journal-title":"J. Comput. Chem."},{"key":"ref40\/cit40","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1002\/prot.340040104","volume":"4","author":"Gilson M. K.","year":"1988","journal-title":"Proteins"},{"key":"ref41\/cit41","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"Humphrey W.","year":"1996","journal-title":"J. Mol. Graphics"},{"key":"ref42\/cit42","volume-title":"The PyMOL Molecular Graphics System","author":"DeLano W. L.","year":"2002"},{"key":"ref43\/cit43","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"Lindahl E.","year":"2001","journal-title":"J. Mol. Model."},{"key":"ref44\/cit44","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1261\/rna.5205404","volume":"10","author":"Draper D. E.","year":"2004","journal-title":"RNA"},{"key":"ref45\/cit45","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1038\/14940","volume":"6","author":"Chin K.","year":"1999","journal-title":"Nat. Struct. Biol."},{"key":"ref46\/cit46","doi-asserted-by":"crossref","first-page":"12051","DOI":"10.1021\/bi026101m","volume":"41","author":"Harris D. A.","year":"2002","journal-title":"Biochemistry"},{"key":"ref47\/cit47","doi-asserted-by":"crossref","first-page":"8447","DOI":"10.1021\/ja016091x","volume":"123","author":"Luptak A.","year":"2001","journal-title":"J. Am. Chem. Soc."},{"key":"ref48\/cit48","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1093\/nar\/25.15.3124","volume":"25","author":"Fauzi H.","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref49\/cit49","doi-asserted-by":"crossref","first-page":"11333","DOI":"10.1021\/ja0166850","volume":"123","author":"Nakano S.","year":"2001","journal-title":"J. Am. Chem. Soc."},{"key":"ref50\/cit50","doi-asserted-by":"crossref","first-page":"1498","DOI":"10.1021\/bi8020108","volume":"48","author":"Chen J. H.","year":"2009","journal-title":"Biochemistry"},{"key":"ref51\/cit51","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1002\/(SICI)1097-0134(199706)28:2<144::AID-PROT2>3.0.CO;2-F","volume":"28","author":"Amzel L. M.","year":"1997","journal-title":"Proteins"},{"key":"ref52\/cit52","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1126\/science.1085515","volume":"301","author":"Benkovic S. J.","year":"2003","journal-title":"Science"},{"key":"ref53\/cit53","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1016\/j.cbpa.2010.07.020","volume":"14","author":"Nashine V. C.","year":"2010","journal-title":"Curr. Opin. Chem. Biol."}],"container-title":["The Journal of Physical Chemistry B"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jp203202e","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,23]],"date-time":"2023-04-23T21:27:26Z","timestamp":1682285246000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/jp203202e"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,7]]},"references-count":53,"journal-issue":{"issue":"25","published-print":{"date-parts":[[2011,6,30]]}},"alternative-id":["10.1021\/jp203202e"],"URL":"https:\/\/doi.org\/10.1021\/jp203202e","relation":{},"ISSN":["1520-6106","1520-5207"],"issn-type":[{"value":"1520-6106","type":"print"},{"value":"1520-5207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,6,7]]}}}