Briki F, Genest D
Centre de Biophysique Moléculaire, CNRS, Orleans, France.
J Biomol Struct Dyn. 1995 Apr;12(5):1063-82. doi: 10.1080/07391102.1995.10508798.
A 200 ps molecular dynamics simulation of the B-form double stranded self-complementary octanucleotide d(CTGATCAG) is analyzed in terms of correlated motions using the canonical analysis approach. Each nucleotide is decomposed in three sub-units corresponding to the base, the sugar ring and the backbone respectively. The correlation between the full dynamics of two sub-units was found to decrease as their mutual distance increases. The interpretation of the full dynamics of sub-units as the superimposition of rigid-body motions (translation and orientation) and deformation shows that the main source of correlation is rigid-body motions. Correlation between sub-units deformation is weak and practically vanishes for sub-units belonging to non-adjacent nucleotides. It is also shown that the correlation is much more important for sub-units of the same strand than of opposite strands. We conclude that the internal dynamics of the octanucleotide may be well described by rigid-body motions, the sub-units deformation having only local influence whereas sub-units translation and rotation have repercussion to long distances. The results presented in this study suggest how the number of degrees of freedom may be reduced for simulating long-time dynamics of oligonucleotides.
使用正则分析方法，从相关运动的角度对B型双链自互补八聚体核苷酸d(CTGATCAG)进行了200皮秒的分子动力学模拟。每个核苷酸分别分解为对应于碱基、糖环和主链的三个亚基。发现两个亚基的完整动力学之间的相关性随着它们相互距离的增加而降低。将亚基的完整动力学解释为刚体运动（平移和取向）和变形的叠加表明，相关性的主要来源是刚体运动。亚基变形之间的相关性较弱，对于属于非相邻核苷酸的亚基，这种相关性实际上消失了。还表明，对于同一条链的亚基，相关性比对链的亚基重要得多。我们得出结论，八聚体核苷酸的内部动力学可以通过刚体运动很好地描述，亚基变形仅具有局部影响，而亚基平移和旋转具有长距离影响。本研究中给出的结果表明了在模拟寡核苷酸的长时间动力学时如何减少自由度的数量。
