Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains.
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains.
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DOI：
10.1021/jp803896b
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发表时间：
2008-09-11
期刊：
影响因子：
--
通讯作者：
Scheraga HA
中科院分区：
文献类型：
--
作者：
Makowski M;Sobolewski E;Czaplewski C;Ołdziej S;Liwo A;Scheraga HA
模拟疏水性氨基酸侧链的分子的21个异二聚体的平均力的势：乙烷（丙氨酸），丙烷（脯氨酸），异丁烷（用于缬氨酸），异戊烷（对于亮氨酸和异亮氨酸），（用于苯丙氨酸），甲基丙基硫醚（对于甲硫氨酸），和吲哚（对异丁烷）确定了伞形采样分子动力学模拟在明确的水作为距离和方向的函数。由Gay-Berne项和空腔项组成的有效货车德瓦耳斯相互作用的解析表达式被拟合到平均力的势。接触最小值的位置和深度以及去溶剂化最大值的位置和高度，包括它们对分子取向的依赖性，通过所有系统的分析表达式很好地表示;对于涉及最小球形溶质的对，观察到MD确定的PMF和分析近似值之间的大偏差：在短距离的PMF是高的，因此，这些地区很少有人访问的甲基丙基硫醚，吲哚。当从PMF的数据只有10千卡/摩尔以上的全球最低被认为是，MD确定和拟合的PMF之间的标准偏差是从0.25至0.55千卡/摩尔（相对标准偏差为4%至8%），它是较大的对涉及非球形溶质分子。从PMF表面计算的接触的自由能是很好的相关性与那些确定从蛋白质晶体数据的斜率接近，有关的氨基酸（从水到正辛醇）的转移的自由能的平均接触自由能确定从蛋白质晶体数据。这些观察结果证明了未来使用的粗粒度蛋白质折叠模拟确定的潜力。
The potentials of mean force of 21 heterodimers of the molecules modeling hydrophobic amino acid side chains: ethane (for alanine), propane (for proline), isobutane (for valine), isopentane (for leucine and isoleucine), ethylbenzene (for phenylalanine), methyl propyl sulfide (for methionine), and indole (for tryptophane) were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation. Analytical expressions consisting of the Gay–Berne term to represent effective van der Waals interactions and the cavity term proposed in our earlier work were fitted to the potentials of mean force. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules, are well represented by the analytical expressions for all systems; large deviations between the MD-determined PMF and the analytical approximations are observed for pairs involving the least spheroidal solutes: ethylbenzene, indole, and methyl propyl sulfide at short distances at which the PMF is high and, consequently, these regions are rarely visited. When data from the PMF within only 10 kcal/mol above the global minimum are considered, the standard deviation between the MD-determined and the fitted PMF is from 0.25 to 0.55 kcal/mol (the relative standard deviation being from 4% to 8%); it is larger for pairs involving nonspherical solute molecules. The free energies of contact computed from the PMF surfaces are well correlated with those determined from protein–crystal data with a slope close to that relating the free energies of transfer of amino acids (from water to n-octanol) to the average contact free energies determined from protein–crystal data. These observations justify future use of the determined potentials in coarse-grained protein-folding simulations.
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影响因子：
3.3
作者：
Khalili, M;Liwo, A;Scheraga, HA
通讯作者：
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