Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins

0353763 - BFÚ 2011 RIV US eng J - Journal Article
Banáš, P. - Hollas, D. - Zgarbová, M. - Jurečka, P. - Orozco, M. - Cheatham III, T.E. - Šponer, Jiří - Otyepka, M.
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins.
Journal of Chemical Theory and Computation. Roč. 6, č. 12 (2010), s. 3836-3849. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA MŠMT(CZ) LC06030; GA ČR(CZ) GA203/09/1476; GA ČR(CZ) GD203/09/H046; GA AV ČR(CZ) IAA400040802
Grant - others:GA MŠk(CZ) LC512
Program: LC
Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702
Keywords : molecular dynamics * force fields * RNA * tetraloops
Subject RIV: BO - Biophysics
Impact factor: 5.138, year: 2010

The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, outcome of simulations is often compromised by imperfections in parameterization of simplified pair-wise additive empirical potentials referred also as force fields. We have pointed out in several recent studies that force field description of single stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields.
Permanent Link: http://hdl.handle.net/11104/0192916