Graduate Program in Biophysics and Department of Chemistry, University of Wisconsin, University Avenue, Madison, Wisconsin 53706, USA.
Biochemistry. 2010 Mar 9;49(9):1954-62. doi: 10.1021/bi9020082.
To improve our understanding of the effects of small solutes on protein stability, we conducted atomistic simulations to quantitatively characterize the interactions between two broadly used small solutes, urea and glycine betaine (GB), and a triglycine peptide, which is a good model for a protein backbone. Multiple solute concentrations were analyzed, and each solute-peptide-water ternary system was studied with approximately 200-300 ns of molecular dynamics simulations with the CHARMM force field. The comparison between calculated preferential interaction coefficients (Gamma(23)) and experimentally measured values suggests that semiquantitative agreement with experiments can be obtained if care is exercised to balance interactions among the solute, protein, and water. On the other hand, qualitatively incorrect (i.e., wrong sign in Gamma(23)) results can be obtained if a solute model is constructed by directly taking parameters for chemically similar groups from an existing force field. Such sensitivity suggests that small solute thermodynamic data can be valuable in the development of accurate force field models of biomolecules. Further decomposition of Gamma(23) into group contributions leads to additional insights regarding the effects of small solutes on protein stability. For example, use of the CHARMM force field predicts that urea preferentially interacts with not only amide groups in the peptide backbone but also aliphatic groups, suggesting a role for these interactions in urea-induced protein denaturation; quantitatively, however, it is likely that the CHARMM force field overestimates the interaction between urea and aliphatic groups. The results with GB support a simple thermodynamic model that assumes additivity of preferential interaction between GB and various biomolecular surfaces.
为了深入了解小分子溶质对蛋白质稳定性的影响，我们进行了原子模拟，以定量描述两种广泛使用的小分子溶质（尿素和甘氨酸甜菜碱）与三肽之间的相互作用，三肽是蛋白质主链的良好模型。分析了多个溶质浓度，并使用 CHARMM 力场对每个溶质-肽-水三元体系进行了大约 200-300ns 的分子动力学模拟研究。计算的优先相互作用系数（Gamma(23)）与实验测量值的比较表明，如果谨慎平衡溶质、蛋白质和水之间的相互作用，可以获得与实验的半定量一致性。另一方面，如果通过直接从现有力场中为化学相似基团采用参数来构建溶质模型，则可能会得到定性错误（即 Gamma(23)中的符号错误）的结果。这种敏感性表明小分子热力学数据可用于开发生物分子准确力场模型。将 Gamma(23)进一步分解为基团贡献，可以进一步了解小分子对蛋白质稳定性的影响。例如，CHARMM 力场的预测表明，尿素不仅优先与肽主链中的酰胺基团相互作用，而且还与脂肪族基团相互作用，这表明这些相互作用在尿素诱导的蛋白质变性中起作用；然而，从定量的角度来看，CHARMM 力场可能高估了尿素与脂肪族基团之间的相互作用。GB 的结果支持一个简单的热力学模型，该模型假设 GB 与各种生物分子表面之间的优先相互作用是可加的。
