Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.
Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.
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DOI：
10.1093/protein/gzp028
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发表时间：
2009-09
期刊：
影响因子：
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通讯作者：
Emil Sobolewski;M. Makowski;S. Ołdziej;C. Czaplewski;A. Liwo;H. Scheraga
中科院分区：
文献类型：
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作者：
Emil Sobolewski;M. Makowski;S. Ołdziej;C. Czaplewski;A. Liwo;H. Scheraga
通过对TIP3P周期性水箱中甲烷分子对在6个温度下的NVT方案和在T = 283~373 K的3个温度下的NPT方案的分子动力学模拟，确定了甲烷分子对在水中相互作用的平均力势（PMF）随甲烷分子间距离的变化.在所有温度下，仅当r> 11 A时，PMF收敛到单个基线。在不同温度下用NVT方案得到的无量纲PMF曲线在接触最小值区域几乎完全重叠，在去溶剂化最大值和溶剂分离最小值区域仍然很好地重叠，这表明在联合残基力场中恒定体积下的温度依赖性疏水相互作用势可以通过用RT标度相应的无量纲势来获得，R是通用气体常数。对于无量纲潜力的平均力与NPT计划，接触的最小值的深度增加，而去溶剂化的最大值的高度和溶剂分离的最小值的深度随温度的降低，在协议与文献中报道的结果。
By means of molecular dynamics simulations of a pair of methane molecules in a TIP3P periodic water box with the NVT scheme at six temperatures and, additionally, the NPT scheme at three temperatures ranging from T = 283 to 373 K, we determined the potential of mean force (PMF) of pairs of interacting methane molecules in water as functions of distance between the methane molecules. The PMFs converge to a single baseline only for r> 11 A at all temperatures. The curves of the dimensionless PMF obtained at different temperatures with the NVT scheme overlap almost perfectly in the region of the contact minimum and still very well in the regions of the desolvation maximum and the solvent-separated minimum, which suggests that the temperature-dependent hydrophobic interaction potentials at constant volume in united-residue force fields can be obtained by scaling the respective dimensionless potentials by RT, R being the universal gas constant. For the dimensionless potentials of mean force obtained with the NPT scheme, the depth of the contact minimum increases, whereas the height of the desolvation maximum and the depth of the solvent-separated minimum decrease with temperature, in agreement with results reported in the literature.