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ConditionalSolvation Thermodynamics of Isoleucinein Model Peptides and the Limitations of the Group-Transfer Model

机译：有条件的异亮氨酸的溶剂化热力学肽中的氨基酸和群转移模型的局限性

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摘要

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute–solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration andthe conflation of background contributions with energetics attributedto the side chain limit the ability of a single scaling factor, suchas the fractional solvent exposure of the group in the protein, tomap the component energetic contributions of the model-compound datato their value in the protein. But ignoring the origin of cancellationsin the underlying components the group-transfer model may appear toprovide a reasonable estimate of the free energy for a given errortolerance.
机译：氨基酸X相对于参考G（甘氨酸）的水合热力学或X侧链的小分子类似物的水合热力学通常用于模拟X对蛋白质稳定性和溶液热力学的贡献。我们通过计算和比较两性离子异亮氨酸，扩展的五肽和螺旋十肽中的异亮氨酸侧链的条件过量自由能，焓和水合熵，来考虑这种方法成功的原因和局限性。 gauche构象的丁烷用作异亮氨酸侧链的小分子类似物。解析侧链对水合的疏水和亲水作用表明，水合的这两个方面都是上下文相关的。此外，分析溶质-溶剂相互作用对侧链的条件过量焓的贡献表明，名义上被认为是侧链性质的物质包括背景的完全不明显的贡献。疏水和亲水水合的背景敏感性背景贡献与归因于能量学的混合侧链限制单个缩放因子的能力，例如作为蛋白质中基团的部分溶剂暴露，映射模型复合数据的组件能量贡献他们在蛋白质中的价值。但是忽略取消的起源在基础组件中，组转移模型可能看起来像提供给定误差的自由能的合理估计公差。

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