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

J 2015

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 et. al.

Základní údaje

Originální název

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

Autoři

ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO a P. JUREČKA

Vydání

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2015, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.301

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/acs.jctc.5b00716

UT WoS

000366223400016

Klíčová slova anglicky

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

Štítky

neMU

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 2. 2016 08:01, Martina Prášilová

Anotace

V originále

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.

Citovat

ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO a 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, roč. 11, č. 12, s. 5723-5736. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b00716.

@article{1335877,
   author = {Zgarbová, M. and Šponer, Jiří and Otyepka, Michal and Cheatham, T.E. and GalindoandMurillo, R. and Jurečka, P.},
   article_location = {Washington DC},
   article_number = {12},
   doi = {http://dx.doi.org/10.1021/acs.jctc.5b00716},
   keywords = {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},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA},
   url = {http://pubs.acs.org/doi/ipdf/10.1021/acs.jctc.5b00716},
   volume = {11},
   year = {2015}
}

TY  - JOUR
ID  - 1335877
AU  - Zgarbová, M. - Šponer, Jiří - Otyepka, Michal - Cheatham, T.E. - Galindo-Murillo, R. - Jurečka, P.
PY  - 2015
TI  - Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA
JF  - Journal of Chemical Theory and Computation
VL  - 11
IS  - 12
SP  - 5723-5736
EP  - 5723-5736
PB  - American Chemical Society
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - NUCLEIC-ACID STRUCTURES
KW  - QUANTUM-CHEMICAL COMPUTATIONS
KW  - DENSITY-FUNCTIONAL THEORY
KW  - BASIS-SET CONVERGENCE
KW  - QUADRUPLEX DNA
KW  - SEQUENCE PREFERENCES
KW  - CRYSTAL-STRUCTURES
KW  - ORBITAL METHODS
KW  - RNA DUPLEXES
UR  - http://pubs.acs.org/doi/ipdf/10.1021/acs.jctc.5b00716
L2  - http://pubs.acs.org/doi/ipdf/10.1021/acs.jctc.5b00716
N2  - 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.
ER  -

ZGARBOVÁ, M., Jiří ŠPONER, Michal OTYEPKA, T.E. CHEATHAM, R. GALINDO-MURILLO a P. JUREČKA. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2015, roč.~11, č.~12, s.~5723-5736. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/acs.jctc.5b00716.

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