Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases
Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases
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DOI：
10.1006/jmbi.1996.0660
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发表时间：
1996-12-06
影响因子：
5.6
通讯作者：
Rosenberg, JM
中科院分区：
文献类型：
--
作者：
Duan, Y;Wilkosz, P;Rosenberg, JM
DNA-EcoRI和DNA-EcoRV复合物的分子动力学模拟表明，这些复合物中的DNA比游离DNA更有序。类似地，蛋白质和DNA在特定（同源）DNA-EcoRV复合物中比它们在非同源DNA-蛋白质复合物中更有序，这与最近提出的蛋白质折叠和序列特异性DNA-蛋白质识别之间的类比一致。轨迹的分析表明，在特异性结合后的净熵增益是相反贡献的结果。溶剂释放，这增加了熵与构型项（如通过原子波动的大小测量的），以及来自蛋白质和DNA运动之间的紧密耦合的集体项。(C)1996年学术出版社
Molecular Dynamics simulations on DNA-EcoRI and DNA-EcoRV complexes suggest that the DNA within these complexes is significantly more ordered than free DNA. Similarly, both the protein and the DNA are more ordered in the specific (cognate) DNA-EcoRV complex than they are in the non-cognate DNA-protein complex, consistent with recently proposed analogies between protein folding and sequence-specific DNA-protein recognition. Analysis of the trajectories shows that the net entropy gain upon specific binding to be the result of opposing contributions. Solvent release, which increases entropy versus configurational terms (as measured by the magnitude of the atomic fluctuations), and collective terms from tight coupling between the motions of the protein and the DNA. (C) 1996 Academic Press Limited