Towards a molecular dynamics consensus view of B-DNA flexibility

被引：135

作者：

Perez, Alberto ^{[1
,2
,3
]}

Lankas, Filip ^{[4
,5
]}

Luque, F. Javier ^{[3
]}

Orozco, Modesto ^{[1
,2
,6
,7
]}

机构：

[1] Joint IRB BSC Program Computat Biol, Inst Res Biomed, Barcelona 08028, Spain

[2] Barcelona Supercomp Ctr, Barcelona 08034, Spain

[3] Univ Barcelona, Fac Farm, Dept Fisicoquim, E-08028 Barcelona, Spain

[4] Swiss Fed Inst Technol, Lab Computat & Visualizat Math & Mech, CH-1015 Lausanne, Switzerland

[5] Acad Sci Czech Republ, Inst Organ Chem & Biochem, Ctr Complex Mol Syst & Biomol, CR-16610 Prague, Czech Republic

[6] Natl Inst Bioinformat, Barcelona 08028, Spain

[7] Univ Barcelona, Fac Biol, Dept Bioquim, E-08028 Barcelona, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷 / 07期

关键词：

D O I：

10.1093/nar/gkn082

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.

引用

页码：2379 / 2394

页数：16

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