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Chem Phys Lett. 2017 Sep 1;683:276-280. doi: 10.1016/j.cplett.2017.02.049. Epub 2017 Feb 16.

Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field.

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1
Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States.

Abstract

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.

KEYWORDS:

Force Field; Molecular Dynamics; Nucleoside; Nucleotide

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