Physik Department, Technische Universität München 85748 Garching, Germany.
J Phys Chem A. 2011 Jun 16;115(23):6125-36. doi: 10.1021/jp1110086. Epub 2011 Mar 1.
Many proteins denature when they are transferred to concentrated urea solutions. Three mechanisms for urea's denaturing ability have been proposed: (i) direct binding to polar parts of the protein surface, (ii) direct binding to nonpolar parts of the protein surface, and (iii) an indirect effect mediated by modifications of the bulk water properties. The disentanglement of these three processes has been the goal of many experimental and computational studies, yet there is no final agreement on the relative importance of the three contributions. The separation of the two direct mechanisms, albeit conceptually clear, is difficult in experimental studies and in simulations depends subtly on how the discrimination between polar and nonpolar groups is accomplished. Indirect effects, embodied in the change of solution activity as urea is added, are rarely monitored in urea/peptide simulations and thus have remained elusive in numerical studies. In this paper we establish a rigorous separation of all three contributions to the solvation thermodynamics of stretched peptide chains. We contrast this scenario with two commonly used model systems: the air/water interface and the interface between water and a hydrophobic alkane self-assembled monolayer. Together with bulk thermodynamic properties of urea/water mixed solvents, a complete thermodynamic description of the urea/water/peptide system is obtained: urea avoids the air/water interface but readily adsorbs at the oil-water interface and at hydrophobic as well as hydrophilic peptide chains, in accordance with experimental results. Simple thermodynamic arguments show that the indirect contribution to urea's denaturing capability is negligibly small, although urea strongly changes the water bulk properties as judged by the number of hydrogen bonds formed. Urea's tendency to bind to proteins is correctly reproduced with several force field combinations, but the quantitative binding strength as well as the relative importance of direct and indirect effects vary drastically between different force fields used for urea and the peptides.
许多蛋白质在转移到高浓度尿素溶液中时会变性。已经提出了尿素变性能力的三种机制：（i）直接结合蛋白质表面的极性部分，（ii）直接结合蛋白质表面的非极性部分，以及（iii）通过对体相水分子性质的修饰的间接影响。这些过程的分离一直是许多实验和计算研究的目标，但对于三种贡献的相对重要性仍没有最终共识。尽管概念上很清楚，但在实验研究和模拟中，两种直接机制的分离是困难的，并且取决于如何完成极性和非极性基团之间的区分，这在模拟中是微妙的。间接影响体现在添加尿素时溶液活度的变化，在尿素/肽模拟中很少被监测，因此在数值研究中仍然难以捉摸。在本文中，我们建立了一种严格分离伸展肽链溶剂化热力学的所有三种贡献的方法。我们将这种情况与两种常用的模型系统进行对比：空气/水界面和水与疏水烷烃自组装单层之间的界面。与尿素/水混合溶剂的体相热力学性质一起，我们得到了尿素/水/肽体系的完整热力学描述：尿素避免了空气/水界面，但很容易在油/水界面以及疏水和亲水肽链上吸附，这与实验结果一致。简单的热力学论证表明，尽管尿素强烈改变了体相水分子的性质（通过形成氢键的数量来判断），但间接贡献对尿素变性能力的影响可以忽略不计。尿素与蛋白质结合的趋势可以通过几种力场组合正确重现，但不同力场对尿素和肽的结合强度以及直接和间接影响的相对重要性存在很大差异。
