BANÁŠ, Pavel, Arnošt MLÁDEK, Michal OTYEPKA, Marie ZGARBOVA, Petr JURECKA, Daniel SVOZIL, Filip LANKAŠ a Jiří ŠPONER. Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2012, roč. 8, č. 7, s. 2448-2460. ISSN 1549-9618. doi:10.1021/ct3001238.
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Základní údaje
Originální název Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics
Autoři BANÁŠ, Pavel (203 Česká republika), Arnošt MLÁDEK (203 Česká republika), Michal OTYEPKA (203 Česká republika), Marie ZGARBOVA (203 Česká republika), Petr JURECKA (203 Česká republika), Daniel SVOZIL (203 Česká republika), Filip LANKAŠ (203 Česká republika) a Jiří ŠPONER (203 Česká republika, garant, domácí).
Vydání Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2012, 1549-9618.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10610 Biophysics
Stát vydavatele Spojené státy
Utajení není předmětem státního či obchodního tajemství
WWW URL
Impakt faktor Impact factor: 5.389
Kód RIV RIV/00216224:14740/12:00057521
Organizační jednotka Středoevropský technologický institut
Doi http://dx.doi.org/10.1021/ct3001238
UT WoS 000306245900030
Klíčová slova anglicky PLESSET PERTURBATION-THEORY; AMBER FORCE-FIELD; LIMIT INTERACTION ENERGIES; EMPIRICAL DISPERSION TERM; UNIQUE DINUCLEOTIDE STEPS; SEPARATE TOTAL ENERGIES; NUCLEIC-ACID STRUCTURES; BASIS-SET CONVERGENCE; BASE-PAIR STEPS; DYNAMICS SIMULATIONS
Štítky ok, rivok
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: Olga Křížová, učo 56639. Změněno: 6. 4. 2013 21:49.
Anotace
Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA. A-tracts, i.e., stretches of several consecutive adenines in one strand that are in phase with the DNA helical repeat, mediate significant DNA bending. During the past few decades, there have been intense efforts to understand the sequence dependence of helical parameters in DNA. Molecular dynamics (MD) simulations can provide valuable insights into the molecular mechanism behind the relationship between sequence and structure. However, although recent improvements in empirical force fields have helped to capture many sequence-dependent B-DNA properties, several problems remain, such as underestimation of the helical twist and suspected underestimation of the propeller twist in A-tracts. Here, we employ reference quantum mechanical (QM) calculations, explicit solvent MD, and bioinformatics to analyze the underestimation of propeller twisting of A-tracts in simulations. Although we did not identify a straightforward explanation, we discovered two imbalances in the empirical force fields. The first was overestimation of stacking interactions accompanied by underestimation of base-pairing energy, which we attribute to anisotropic polarizabilities that are not reflected by the isotropic force fields. This may lead to overstacking with potentially important consequences for MD simulations of nucleic acids. The second observed imbalance was steric clash between A(N1) and T(N3) nitrogens of AT base pairs in force-field descriptions, resulting in overestimation of the AT pair stretch in MD simulations. We also substantially extend the available set of benchmark estimated CCSD(T)/CBS data for B-DNA base stacking and provide a code that allows the generation of diverse base-stacking geometries suitable for QM computations with predefined intra- and interbase pair parameters.
Návaznosti
ED1.1.00/02.0068, projekt VaVNázev: CEITEC - central european institute of technology
GBP305/12/G034, projekt VaVNázev: Centrum biologie RNA
GD203/09/H046, projekt VaVNázev: Biochemie na rozcestí mezi in silico a in vitro
Investor: Grantová agentura ČR, Biochemie na rozcestí mezi in silico a in vitro
VytisknoutZobrazeno: 27. 11. 2022 09:48