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Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines
I DEB, R PAL,
Published in John Wiley and Sons Inc.
2016
Volume: 37
   
Issue: 17
Pages: 1576 - 1588
Abstract
The currently available force field parameters for modified RNA residues in AMBER show significant deviations in conformational properties from experimental observations. The examination of the transferability of the recently revised torsion parameters revealed that there was an overall improvement in the conformational properties for some of the modifications but the improvements were still insufficient in describing the sugar pucker preferences (J. Chem. Inf. Model. 2014, 54, 1129-1142). Here, we report an approach for the development and fine tuning of the AMBER force field parameters for 2-thiouridine, 4-thiouridine, and pseudouridine with diverse conformational preferences. The χ torsion parameters were reparameterized at the individual nucleoside level. The effect of combining the revised γ torsion parameter and modifying the Lennard-Jones σ parameters were also tested by directly comparing the conformational preferences obtained from our extensive molecular dynamics simulations with those from experimental observations. © 2016 Wiley Periodicals, Inc.
About the journal
JournalData powered by TypesetJournal of Computational Chemistry
PublisherData powered by TypesetJohn Wiley and Sons Inc.
ISSN0192-8651
Open AccessNo