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Dependence of A-RNA simulations on the choice of the force field and salt strength

SYSNO ASEP	0333332
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	Dependence of A-RNA simulations on the choice of the force field and salt strength
Title	Závislost simulací A-RNA na volbě silového pole a velikosti iontové síly
Author(s)	Beššeová, Ivana (BFU-R) Otyepka, Michal (BFU-R)_{RID, ORCID} Réblová, Kamila (BFU-R) Šponer, Jiří (BFU-R)_{RID, ORCID}
Number of authors	4
Source Title	Physical Chemistry Chemical Physics. - : Royal Society of Chemistry - ISSN 1463-9076 Roč. 11, č. 45 (2009), s. 10701-10711
Number of pages	11 s.
Language	eng - English
Country	GB - United Kingdom
Keywords	force fileds ; RNA ; A-form
Subject RIV	BO - Biophysics
R&D Projects	LC06030 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
	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)
	IAA400040802 GA AV ČR - Academy of Sciences of the Czech Republic (AV ČR)
	GD203/09/H046 GA ČR - Czech Science Foundation (CSF)
CEZ	AV0Z50040507 - BFU-R (2005-2011)
	AV0Z50040702 - BFU-R (2007-2013)
UT WOS	000271907200016
DOI	10.1039/b911169g
Annotation	We carried out an extensive molecular dynamics study on three A-RNA duplexes. Dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in comparison to the Parm99 by preventing temporary alpha/gamma t/t flips common in Parm99 simulations. The stabilization of the A-RNA helices caused by the Parmbsc0 force field includes visible reduction of the major groove width, increase of the base pair roll, larger helical inclination and small increases of twist. Therefore, the Parmbsc0 shifts the simulated duplexes more deeply into the A-form.
Workplace	Institute of Biophysics
Contact	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Year of Publishing	2010

Number of the records: 1