Structure, Stiffness and Substates of the Dickerson-Drew
Dodecamer

J 2013

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER et. al.

Základní údaje

Originální název

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

Autoři

DRŠATA, Tomáš (203 Česká republika), Alberto PEREZ (840 Spojené státy), Modesto OROZCO (724 Španělsko), Alexandre V MOROZOV (840 Spojené státy), Jiří ŠPONER (203 Česká republika, garant, domácí) a Filip LANKAŠ (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10610 Biophysics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.310

Kód RIV

RIV/00216224:14740/13:00067939

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1021/ct300671y

UT WoS

000313378700071

Klíčová slova anglicky

MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 20. 3. 2013 14:06, Olga Křížová

Anotace

V originále

The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER a Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, roč. 9, č. 1, s. 707-721. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct300671y.

@article{1092256,
   author = {Dršata, Tomáš and Perez, Alberto and Orozco, Modesto and Morozov, Alexandre V and Šponer, Jiří and Lankaš, Filip},
   article_location = {WASHINGTON},
   article_number = {1},
   doi = {http://dx.doi.org/10.1021/ct300671y},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; NUCLEIC-ACID STRUCTURES; B-DNA DODECAMER; BASE-PAIR LEVEL; X-RAY; COUPLING-CONSTANTS; MONOVALENT CATIONS; CRYSTAL-STRUCTURES; ATOMIC-RESOLUTION},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer},
   url = {http://pubs.acs.org/toc/jctcce/9/1},
   volume = {9},
   year = {2013}
}

TY  - JOUR
ID  - 1092256
AU  - Dršata, Tomáš - Perez, Alberto - Orozco, Modesto - Morozov, Alexandre V - Šponer, Jiří - Lankaš, Filip
PY  - 2013
TI  - Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
JF  - Journal of Chemical Theory and Computation
VL  - 9
IS  - 1
SP  - 707-721
EP  - 707-721
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - UNIQUE TETRANUCLEOTIDE SEQUENCES
KW  - NUCLEIC-ACID STRUCTURES
KW  - B-DNA DODECAMER
KW  - BASE-PAIR LEVEL
KW  - X-RAY
KW  - COUPLING-CONSTANTS
KW  - MONOVALENT CATIONS
KW  - CRYSTAL-STRUCTURES
KW  - ATOMIC-RESOLUTION
UR  - http://pubs.acs.org/toc/jctcce/9/1
L2  - http://pubs.acs.org/toc/jctcce/9/1
N2  - The Dickerson-Drew dodecamer (DD) d[CGCGAATTCGCG](2) is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-mu s-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
ER  -

DRŠATA, Tomáš, Alberto PEREZ, Modesto OROZCO, Alexandre V MOROZOV, Jiří ŠPONER a Filip LANKAŠ. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, roč.~9, č.~1, s.~707-721. ISSN~1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct300671y.

Podrobný výpis o publikaci