Pérez Alberto, Lankas Filip, Luque F Javier, Orozco Modesto
Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
Nucleic Acids Res. 2008 Apr;36(7):2379-94. doi: 10.1093/nar/gkn082. Epub 2008 Feb 24.
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.
我们使用核酸力场的两个最新版本（CHARMM27和parmbsc0），通过长时间尺度的分子动力学模拟，对水溶液中的B-DNA柔韧性进行了系统研究。模拟采用了四条长双链，每条双链设计为包含每个单碱基对步的多个拷贝。我们的研究突出了parmbsc0和CHARMM27模拟家族之间的一些差异，但在DNA柔韧性的表现方面也有广泛的一致性。我们还使用了经过非规范主链翻转校正的较旧的AMBER力场parm94和parm99进行了额外的模拟。综合这些结果，我们首次绘制出了B-DNA柔韧性的一致分子动力学图景。
