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Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme
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SYSNO ASEP 0345016 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme Author(s) Mlýnský, V. (CZ)
Banáš, P. (CZ)
Hollas, D. (CZ)
Réblová, Kamila (BFU-R)
Walter, N.G. (US)
Šponer, Jiří (BFU-R) RID, ORCID
Otyepka, M. (CZ)Number of authors 7 Source Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 114, č. 19 (2010), s. 6642-6652Number of pages 11 s. Language eng - English Country US - United States Keywords molecular dynamics simulations ; hairpin ribozyme Subject RIV BO - Biophysics R&D Projects LC06030 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) GA203/09/1476 GA ČR - Czech Science Foundation (CSF) GD203/09/H046 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) KJB400040901 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) 1QS500040581 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR) CEZ AV0Z50040507 - BFU-R (2005-2011) AV0Z50040702 - BFU-R (2007-2013) UT WOS 000277499700047 DOI Annotation The hairpin ribozyme is a prominent member of the group of small catalytic RNAs because it does not require metal ions to achieve catalysis. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit solvent molecular dynamics (MD) simulations on time scales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A-1(2'-methosy) substitution employed in crystallography. Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2011
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