Solvation free energies of alanine peptides: the effect of flexibility.
Solvation free energies of alanine peptides: the effect of flexibility.
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丙氨酸肽的溶剂化自由能：灵活性的影响。
DOI：
10.1021/jp409693p
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Pettitt,BMontgomery
中科院分区：
文献类型：
--
作者：
Kokubo,Hironori;Harris,RobertC;Asthagiri,Dilipkumar;Pettitt,BMontgomery
计算了长度（n）为1 ~ 10个单体的10个丙氨酸肽的静电（ΔGel）、货车德瓦耳斯空穴形成（ΔGvdw）和总（ΔG）溶剂化自由能。自由能是在肽的固定、扩展构象下以及在没有限制的情况下对一些肽进行计算的。发现溶剂化自由能ΔGel和组分ΔGvdw和ΔG与ln呈线性关系，最佳拟合线的斜率分别为γel、γvdw和γ。γ和γ对固定肽和柔性肽均为阴性，γ vdw对固定肽为阴性。γ vdw为负值令人惊讶，因为烷烃的实验数据、理论模型以及小分子和模型系统的分子动力学计算通常表明γ vdw应为正值。负的γ vdw似乎与Δ Gvdw通过有利于具有小表面积的构象来驱动蛋白质折叠时的初始塌陷的概念相矛盾。当我们计算柔性肽的Δ Gvdw，从而使肽呈现更紧凑构象的自然集合时，γ vdw为正。由于大多数蛋白质不呈现伸展构象，因此随表面积增加而增加的Δ Gvdw可能是球状蛋白质的典型特征。另一种假设是，塌缩是由分子内相互作用驱动的。我们发现很少的分子内H-键，但表明，分子内的货车德瓦尔斯相互作用能是更有利的灵活比扩展肽，似乎有利于这一假设。vdw能量的大波动可能使得将肽的塌陷归因于这种分子内能量变得困难。
The electrostatic (ΔGel), van der Waals cavity-formation (ΔGvdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1 to 10 monomers were calculated. The free energies were computed both with fixed, extended conformations of the peptides and again for some of the peptides without constraints. The solvation free energies, ΔGel, and components ΔGvdw, and ΔG, were found to be linear inn, with the slopes of the best-fit lines being γel, γvdw, and γ, respectively. Both γeland γ were negative for fixed and flexible peptides, and γvdwwas negative for fixed peptides. That γvdwwas negative was surprising, as experimental data on alkanes, theoretical models, and MD computations on small molecules and model systems generally suggest that γvdwshould be positive. A negative γvdwseemingly contradicts the notion that ΔGvdwdrives the initial collapse of the protein when it folds by favoring conformations with small surface areas. When we computed ΔGvdwfor the flexible peptides, thereby allowing the peptides to assume natural ensembles of more compact conformations, γvdwwas positive. Because most proteins do not assume extended conformations, a ΔGvdwthat increases with increasing surface area may be typical for globular proteins. An alternative hypothesis is that the collapse is driven by intramolecular interactions. We find few intramolecular H-bonds but show that the intramolecular van der Waals interaction energy is more favorable for the flexible than for the extended peptides, seemingly favoring this hypothesis. The large fluctuations in the vdw energy may make attributing the collapse of the peptide to this intramolecular energy difficult.
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