Translational-entropy gain of solvent upon protein folding
Translational-entropy gain of solvent upon protein folding
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DOI：
10.1529/biophysj.104.057604
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发表时间：
2005-10-01
影响因子：
3.4
通讯作者：
Kinoshita, M
中科院分区：
文献类型：
--
作者：
Harano, Y;Kinoshita, M
我们发现，即使在蛋白质-水溶液体系中原子之间完全没有势能的情况下，也存在有利于蛋白质折叠状态的物理因素。它是水分子平移运动产生的水的平动熵(TE)的增益。一个复杂的统计力学理论被用来分析水的TE，其中具有规定构象的蛋白质或肽被浸泡在水中。结果表明，如果残基数目足够大，TE增益足够强大，足以与折叠时的构象熵损失竞争。对于蛋白质G，我们已经测试了100多个紧凑的构象，这些构象是通过计算机模拟全原子势和自然结构产生的。一个重要的发现是，在自然结构中获得了最大的TE。水分子的平移运动非常有效地实现了天然蛋白质内部的紧密堆积。只有当溶剂是分子尺寸在自然界中普通液体中最小的水时，这些结果才是正确的。
We show that even in the complete absence of potential energies among the atoms in a protein- aqueous solution system, there is a physical factor that favors the folded state of the protein. It is a gain in the translational entropy ( TE) of water originating from the translational movement of water molecules. An elaborate statistical- mechanical theory is employed to analyze the TE of water in which a protein or peptide with a prescribed conformation is immersed. It is shown that if the number of residues is sufficiently large, the TE gain is powerful enough to compete with the conformational- entropy loss upon folding. For protein G we have tested over 100 compact conformations generated by a computer simulation with the all- atom potentials as well as the native structure. A significant finding is that the largest TE is attained in the native structure. The translational movement of water molecules is quite effective in achieving the tight packing in the interior of a natural protein. These results are true only when the solvent is water whose molecular size is the smallest among the ordinary liquids in nature.