How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

0476273 - BFÚ 2018 RIV GB eng J - Článek v odborném periodiku
Šponer, Jiří - Krepl, Miroslav - Banáš, P. - Kührová, P. - Zgarbová, M. - Jurečka, P. - Havrila, Marek - Otyepka, M.
How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?
Wiley Interdisciplinary Reviews-RNA. Roč. 8, č. 3 (2017), č. článku e1405. ISSN 1757-7004. E-ISSN 1757-7012
Grant CEP: GA ČR(CZ) GBP305/12/G034
Grant ostatní: GA MŠk(CZ) LO1305
Institucionální podpora: RVO:68081707
Klíčová slova: hepatitis-delta-virus * amber force-field * free-energy landscape * hdv ribozyme
Obor OECD: Physical chemistry
Impakt faktor: 5.844, rok: 2017

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the .
Trvalý link: http://hdl.handle.net/11104/0272813