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

J 2013

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

ZGARBOVA, Marie, Javier F. LUQUE, Jiří ŠPONER, Thomas E III CHEATHAM, Michal OTYEPKA et. al.

Basic information

Original name

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

Authors

ZGARBOVA, Marie (203 Czech Republic), Javier F. LUQUE (724 Spain), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution), Thomas E III CHEATHAM (840 United States of America), Michal OTYEPKA (203 Czech Republic) and Petr JUREČKA (203 Czech Republic)

Edition

Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2013, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.310

RIV identification code

RIV/00216224:14740/13:00069532

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ct400154j

UT WoS

000319184800020

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; PHOSPHORUS CHEMICAL-SHIFTS; SUGAR-PHOSPHATE BACKBONE; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; B-II TRANSITIONS; CRYSTAL-STRUCTURES; A-TRACT; CONFORMATIONAL PROPERTIES; RELATIVE FLEXIBILITY

Abstract

V originále

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.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

ZGARBOVA, Marie, Javier F. LUQUE, Jiří ŠPONER, Thomas E III CHEATHAM, Michal OTYEPKA and Petr JUREČKA. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, vol. 9, No 5, p. 2339-2354. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct400154j.

@article{1124235,
   author = {Zgarbova, Marie and Luque, Javier F. and Šponer, Jiří and Cheatham, Thomas E III and Otyepka, Michal and Jurečka, Petr},
   article_location = {WASHINGTON},
   article_number = {5},
   doi = {http://dx.doi.org/10.1021/ct400154j},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; PHOSPHORUS CHEMICAL-SHIFTS; SUGAR-PHOSPHATE BACKBONE; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; B-II TRANSITIONS; CRYSTAL-STRUCTURES; A-TRACT; CONFORMATIONAL PROPERTIES; RELATIVE FLEXIBILITY},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters},
   url = {http://pubs.acs.org/doi/abs/10.1021/ct400154j},
   volume = {9},
   year = {2013}
}

TY  - JOUR
ID  - 1124235
AU  - Zgarbova, Marie - Luque, Javier F. - Šponer, Jiří - Cheatham, Thomas E III - Otyepka, Michal - Jurečka, Petr
PY  - 2013
TI  - Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
JF  - Journal of Chemical Theory and Computation
VL  - 9
IS  - 5
SP  - 2339-2354
EP  - 2339-2354
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - PHOSPHORUS CHEMICAL-SHIFTS
KW  - SUGAR-PHOSPHATE BACKBONE
KW  - NUCLEIC-ACID STRUCTURES
KW  - BASIS-SET CONVERGENCE
KW  - B-II TRANSITIONS
KW  - CRYSTAL-STRUCTURES
KW  - A-TRACT
KW  - CONFORMATIONAL PROPERTIES
KW  - RELATIVE FLEXIBILITY
UR  - http://pubs.acs.org/doi/abs/10.1021/ct400154j
L2  - http://pubs.acs.org/doi/abs/10.1021/ct400154j
N2  - 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.
ER  -

ZGARBOVA, Marie, Javier F. LUQUE, Jiří ŠPONER, Thomas E III CHEATHAM, Michal OTYEPKA and Petr JUREČKA. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, vol.~9, No~5, p.~2339-2354. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct400154j.

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