Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

被引:238
作者
Zgarbova, Marie [1 ]
Javier Luque, F. [2 ,3 ]
Sponer, Jiri [4 ,5 ]
Cheatham, Thomas E., III [6 ]
Otyepka, Michal [1 ]
Jurecka, Petr [1 ]
机构
[1] Palacky Univ, Fac Sci, Dept Phys Chem, Reg Ctr Adv Technol & Mat, Olomouc 77146, Czech Republic
[2] Univ Barcelona, Fac Farm, Dept Fisicoquim, Santa Coloma de Gramenet 080921, Spain
[3] Univ Barcelona, Fac Farm, Inst Biomed IBUB, Santa Coloma de Gramenet 080921, Spain
[4] Acad Sci Czech Republ, Inst Biophys, CS-61265 Brno, Czech Republic
[5] CEITEC Cent European Inst Technol, Brno 62500, Czech Republic
[6] Univ Utah, Dept Med Chem, Salt Lake City, UT 84112 USA
关键词
MOLECULAR-DYNAMICS SIMULATIONS; PHOSPHORUS CHEMICAL-SHIFTS; SUGAR-PHOSPHATE BACKBONE; BASIS-SET CONVERGENCE; B-II TRANSITIONS; NUCLEIC-ACIDS; CONFORMATIONAL PROPERTIES; RELATIVE FLEXIBILITY; CRYSTAL-STRUCTURES; RNA DUPLEXES;
D O I
10.1021/ct400154j
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We present a refinement of the backbone torsion parameters epsilon and zeta of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as epsilon zeta(OL1), were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7 (9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the epsilon zeta(OL1) refinement improves the backbone description of B-DNA double helices and the G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted toward the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA), the epsilon zeta(OL1) modification improved the description of noncanonical alpha/gamma backbone substates, which were shown to be coupled to the epsilon/zeta torsion potential. Thus, the refinement is suggested as a possible alternative to the current epsilon/zeta torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.
引用
收藏
页码:2339 / 2354
页数:16
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