Briki F, Genest D
Centre de Biophysique Moléculaire, CNRS, Orleans, France.
Biophys Chem. 1994 Sep;52(1):35-43. doi: 10.1016/0301-4622(94)00063-8.
We report a method for analyzing atomic correlated motions in biopolymers from trajectories obtained by molecular dynamics simulation. A correlation coefficient based on the canonical analysis of data is defined which is independent on the relative orientation of atomic displacement. To illustrate the method we studied correlation between positional fluctuations of protons in the double-stranded self complementary oligonucleotide d(CTGAT-CAG), deduced from a 200 ps molecular dynamics simulation in the presence of explicit water molecules and counterions. It is found that on this time scale the motions of protons belonging to different residues are poorly coupled while the motion of a base proton is correlated to the motion of the sugar ring protons of the same nucleotide. Such a method may be generalized to study correlated motions of two distinct domains of a macro-molecule.
我们报告了一种从分子动力学模拟获得的轨迹分析生物聚合物中原子相关运动的方法。定义了基于数据规范分析的相关系数，该系数与原子位移的相对取向无关。为了说明该方法，我们研究了在存在明确水分子和抗衡离子的情况下，通过200皮秒分子动力学模拟推导得到的双链自互补寡核苷酸d(CTGAT-CAG)中质子位置波动之间的相关性。发现在这个时间尺度上，属于不同残基的质子运动耦合性很差，而碱基质子的运动与同一核苷酸的糖环质子运动相关。这种方法可以推广到研究大分子两个不同结构域的相关运动。
