Solvation free energy of amino acids and side-chain analogues
Solvation free energy of amino acids and side-chain analogues
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DOI：
10.1021/jp0620163
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发表时间：
2007-03-01
影响因子：
3.3
通讯作者：
Sandler, Stanley I.
中科院分区：
文献类型：
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作者：
Chang, Jaeeon;Lenhoff, Abraham M.;Sandler, Stanley I.
用Monte Carlo模拟方法计算了氨基酸及其侧链类似物在水和环己烷中的溶剂化自由能。氨基酸分子间的相互作用采用OPLS-AA力场描述，水分子间的相互作用采用TIP 4P模型描述，自由能采用班尼特接受法确定.在环己烷和水中的侧链类似物的结果被用来评估的货车德瓦尔斯和静电相互作用，分别力场的性能。计算的氨基酸类似物和完整氨基酸的水合自由能的比较允许评估侧链对水合水分子的数量的贡献的加和性。中性氨基酸的水合自由能可以通过将其侧链的贡献加到甘氨酸的水合自由能上来合理地近似。然而，显着的非加和性的自由能被发现的两性离子形式的氨基酸与极性侧链。在丝氨酸和苏氨酸中，在极性侧链和主链基团之间形成分子内氢键，导致比甘氨酸更弱的溶剂化。相反，在酪氨酸中没有观察到这种非加和性，其中羟基与主链进一步分离，因此不能与主链形成分子内氢键。对于组氨酸，我们发现当极性基团和主链之间的分子内氢键断裂时，水分子可以形成桥。
The solvation free energies of amino acids and their side-chain analogues in water and cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are described by the OPLS-AA force field for the amino acids and the TIP4P model for water, and the free energies are determined by using the Bennett acceptance method. Results for the side-chain analogues in cyclohexane and in water are used to evaluate the performance of the force field for the van der Waals and the electrostatic interactions, respectively. Comparison of the calculated hydration free energies for the amino acid analogues and the full amino acids allows assessment of the additivity of the side chain contributions on the number of hydrating water molecules. The hydration free energies of neutral amino acids can be reasonably approximated by adding the contributions of their side chains to that of the hydration of glycine. However, significant nonadditivity in the free energy is found for the zwitterionic form of amino acids with polar side chains. In serine and threonine, intramolecular hydrogen bonds are formed between the polar side chains and backbone groups, leading to weaker solvation than for glycine. In contrast, such nonadditivity is not observed in tyrosine, in which the hydroxyl group is farther separated from, and therefore cannot form an intramolecular hydrogen bond with, the backbone. For histidine we find that a water molecule can form a bridge when the intramolecular hydrogen bond between the polar group and the backbone is broken.