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Conformational preferences of modified uridines: Comparison of AMBER derived force fields
I DEB, L NILSSON,
Published in American Chemical Society
2014
PMID: 24697757
Volume: 54
   
Issue: 4
Pages: 1129 - 1142
Abstract
The widespread occurrence of modified residues in RNA sequences necessitates development of accurate parameters for these modifications for reliable modeling of RNA structure and dynamics. A comprehensive set of parameters for the 107 naturally occurring RNA modifications was proposed by Aduri et al. (J. Chem. Theory Comput. 2007, 3, 1464-1475) for the AMBER FF99 force field. In this work, we tested these parameters on a set of modified uridine residues, namely, dihydrouridine, 2-thiouridine, 4-thiouridine, pseudouridine, and uridine-5-oxyacetic acid, by performing molecular dynamics and replica exchange molecular dynamics simulations of these nucleosides. Although our simulations using the FF99 force field did not, in general, reproduce the experimentally observed conformational characteristics well, combination of the parameter set with recent revisions of the FF99 force field for RNA showed noticeable improvement for some of the nucleosides. © 2014 American Chemical Society.
About the journal
JournalData powered by TypesetJournal of Chemical Information and Modeling
PublisherData powered by TypesetAmerican Chemical Society
ISSN1549-9596
Open AccessNo