Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

0345016 - BFÚ 2011 RIV US eng J - Journal Article
Mlýnský, V. - Banáš, P. - Hollas, D. - Réblová, Kamila - Walter, N.G. - Šponer, Jiří - Otyepka, M.
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.
Journal of Physical Chemistry B. Roč. 114, č. 19 (2010), s. 6642-6652. ISSN 1520-6106. E-ISSN 1520-5207
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GA203/09/1476; GA MŠMT(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) KJB400040901; GA AV ČR(CZ) 1QS500040581
Grant - others:GA MŠk(CZ) LC512
Program: LC
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics simulations * hairpin ribozyme
Subject RIV: BO - Biophysics
Impact factor: 3.603, year: 2010

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.
Permanent Link: http://hdl.handle.net/11104/0005937