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

ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO and P. JUREČKA. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2015, vol. 11, No 12, p. 5723-5736. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/acs.jctc.5b00716.

Basic information

• Original name: Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
• Authors: ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO and P. JUREČKA.
• Edition: Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2015, 1549-9618.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10403 Physical chemistry
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 5.301
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1021/acs.jctc.5b00716
• UT WoS: 000366223400016
• Keywords in English: MOLECULAR-DYNAMICS SIMULATIONS; NUCLEIC-ACID STRUCTURES; QUANTUM-CHEMICAL COMPUTATIONS; DENSITY-FUNCTIONAL THEORY; BASIS-SET CONVERGENCE; QUADRUPLEX DNA; SEQUENCE PREFERENCES; CRYSTAL-STRUCTURES; ORBITAL METHODS; RNA DUPLEXES
• Tags: neMU
• Tags: International impact, Reviewed

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.