Number of the records: 1

An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods

SYSNO ASEP	0340907
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods
Author(s)	Réblová, Kamila (BFU-R) Střelcová, Z. (CZ) Kulhánek, P. (CZ) Beššeová, Ivana (BFU-R) Mathews, D.H. (US) Van Nostrand, K. (US) Yildirim, I. (US) Turner, D.H. (US) Šponer, Jiří (BFU-R)_{RID, ORCID}
Number of authors	9
Source Title	Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618 Roč. 6, č. 3 (2010), s. 910-929
Number of pages	20 s.
Language	eng - English
Country	US - United States
Keywords	RNA ; internal loop ; molecular dynamics
Subject RIV	AQ - Safety, Health Protection, Human - Machine
R&D Projects	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)
	KJB400040901 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	000275189400029
DOI	10.1021/ct900440t
Annotation	Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. We performed 3.1 us of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na+ versus excess salt KCl ion environments.
Workplace	Institute of Biophysics
Contact	Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244
Year of Publishing	2010

Number of the records: 1