Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Journal: JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11, 5723-5736
Authors: Zgarbova, M., Sponer, J., Otyepka, M., Cheatham, TE., Galindo-Murillo, R., Jurecka, P.
Year: 2015

Abstract

Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the epsilon/zeta and glycosidic torsions. None of these force fields described the epsilon/zeta and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar phosphate backbone torsion angle beta. We suggest a refinement of this potential, beta(OLI), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BIT backbone substates, providing a better agreement with experiment. We recommend using beta(OLI) in combination with our previously introduced corrections, epsilon zeta(OLI) and chi(OLA), (the combination being named OL15) as a possible alternative to the current beta torsion potential for more accurate modeling of nucleic acids.