Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines

Indrajit Deb (Lead / Corresponding author), Rupak Pal, Joanna Sarzynska, Ansuman Lahiri (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1576-1588
Number of pages13
JournalJournal of Computational Chemistry
Volume37
Issue number17
Early online date30 Mar 2016
DOIs
Publication statusPublished - 30 Jun 2016

Keywords

  • force field
  • glycosidic torsion parameter
  • Lennard-Jones parameter
  • modified RNA
  • replica exchange molecular dynamics

ASJC Scopus subject areas

  • General Chemistry
  • Computational Mathematics

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