Beck David A C, Bennion Brian J, Alonso Darwin O V, Daggett Valerie
Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
Methods Enzymol. 2007;428:373-96. doi: 10.1016/S0076-6879(07)28022-X.
Rarely is any solution simply solute and water. In vivo, solutes, such as proteins and nucleic acids, swim in a sea of water, salts, ions, small molecules, and lipids, not to mention other macromolecules. In vitro, virtually all solutions contain a mixture of aqueous solvents, or "cosolvents" [i.e., solvent(s) in addition to water], that can alter the dynamics, behavior, solubility, and stability of proteins and nucleic acids. We have developed models for a number of cosolvents, including the denaturant urea and the small chemical chaperone trimethylamine N-oxide (TMAO). This chapter examines the models for these two cosolvents in the context of experimental data. The direct and indirect effects of these molecules on water and protein are studied with molecular dynamics simulations. These observations and conclusions are drawn from simulations of these molecules in pure water and as a cosolvent for the protein chymotrypsin inhibitor 2. Urea-induced denaturation occurs initially through attack of the protein by water and hydration of hydrophobic protein moieties as a result of disruption of the hydrogen bonding network of water by urea. This indirect denaturing effect of urea is followed by more direct action as urea replaces some waters involved in the initial hydration of the hydrophobic core and subsequently binds to polar residues and the protein main chain to compete with the intraprotein hydrogen bonds. In the case of TMAO, we find that it encourages water-water interactions, thereby stabilizing the protein as a result of the increased penalty for the hydration of hydrophobic residues.
几乎没有任何溶液仅仅是溶质和水。在体内，诸如蛋白质和核酸等溶质，在水、盐、离子、小分子和脂质的海洋中“游动”，更不用说其他大分子了。在体外，几乎所有溶液都含有水性溶剂的混合物，即“共溶剂”（即除水之外的溶剂），这些共溶剂会改变蛋白质和核酸的动力学、行为、溶解性和稳定性。我们已经开发了多种共溶剂的模型，包括变性剂尿素和小分子化学伴侣氧化三甲胺（TMAO）。本章结合实验数据研究这两种共溶剂的模型。通过分子动力学模拟研究了这些分子对水和蛋白质的直接和间接影响。这些观察结果和结论来自于在纯水中以及作为蛋白质胰凝乳蛋白酶抑制剂2的共溶剂对这些分子的模拟。尿素诱导的变性最初是由于尿素破坏了水的氢键网络，导致水对蛋白质的攻击以及蛋白质疏水部分的水合作用。尿素的这种间接变性作用之后是更直接的作用，因为尿素取代了参与疏水核心初始水合作用的一些水分子，随后与极性残基和蛋白质主链结合，以竞争蛋白质内的氢键。在TMAO的情况下，我们发现它促进了水 - 水相互作用，从而由于疏水残基水合作用的增加而使蛋白质稳定。
