从封闭的（Gly）_n和环状双甘氨肽模型化合物探讨肽转移自由能的意义
Examining the meaning of the peptide transfer free energy obtained from blocked (Gly)_n and cyclic-diglycine model compounds
摘要：
在实验中，用（Gly）_n的转移自由能，加上自由能随n的恒定增量变化意味着每个附加单元对自由能的贡献是独立的这一假设，得到了肽基团从水到渗透剂溶液的转移自由能。在这里，我们测试这个假设，并揭示其局限性。连同环状双甘氨酸的结果，我们表明，在原则上，它是不可能获得独立的模型系统的肽基团转移自由能。本文计算了乙酰基-（Gly）_n-甲基酰胺（n=1. 7)肽在水和渗透剂溶液中以扩展构象建模，并发现水合自由能在n中是线性的，这表明独立的加性基团贡献。为了进一步探索所观察到的线性，我们研究了在第一水化壳层中失去水分子的溶质的水化。这种条件溶质在理论公式中自然产生，并帮助我们专注于水化效应，而不受短程溶质-水相互作用的复杂性的影响。我们细分成n+1肽组和甲基端基的条件溶质。这些基团中的每一个与溶剂的结合能是高斯分布的，但是近邻结合能本身是相关的：（i，i+1）相关性最强，并且倾向于降低独立基团情况下的自由能。我们发现，所观察到的线性可以解释的近邻相关性的相似性。基团添加剂转移自由能模型的影响。
英文摘要：
In experiments, the free energy of transferring the peptide group from water to an osmolyte solution is obtained using the transfer free energy of (Gly)_n with the added assumption that a constant incremental change in free energy with n implies that each additional unit makes an independent contribution to the free energy. Here we test this assumption and uncover its limitations. Together with results for cyclic-diglycine, we show that, in principle, it is not possible to obtain a peptide group transfer free energy that is independent of the model system. We calculate the hydration free energy of acetyl-(Gly)_n-methyl amide (n=1..7) peptides modeled in the extended conformation in water and osmolyte solutions and find that the hydration free energy is linear in n, suggestive of independent, additive group-contributions. To probe the observed linearity further, we study the hydration of the solute bereft of water molecules in the first hydration shell. This conditioned solute arises naturally in the theoretical formulation and helps us focus on hydration effects uncluttered by the complexities of short-range solute-water interactions. We subdivide the conditioned solute into n+1 peptide groups and a methyl end group. The binding energy of each of these groups with the solvent is Gaussian distributed, but the near neighbor binding energies are themselves correlated: the (i,i+1) correlation is the strongest and tends to lower the free energy over the independent group case. We show that the observed linearity can be explained by the similarity of near neighbor correlations. Implications for group additive transfer free energy models are indicated.
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