Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA.
Biophys J. 2011 Mar 16;100(6):1526-33. doi: 10.1016/j.bpj.2011.01.028.
Urea is a commonly used protein denaturant, and it is of great interest to determine its interaction with various protein groups to elucidate the molecular basis of its effect on protein stability. Using the Trp-cage miniprotein as a model system, we report what we believe to be the first computation of changes in the preferential interaction coefficient of the protein upon urea denaturation from molecular-dynamics simulations and examine the contributions from the backbone and the side-chain groups. The preferential interaction is obtained from reversible folding/unfolding replica exchange molecular-dynamics simulations of Trp-cage in presence of urea, over a wide range of urea concentration. The increase in preferential interaction upon unfolding is dominated by the side-chain contribution, rather than the backbone. Similar trends are observed in simulations using two different force fields, Amber94 and Amber99sb, for the protein. The magnitudes of the side-chain and backbone contributions differ in the two force fields, despite containing identical protein-solvent interaction terms. The differences arise from the unfolded ensembles sampled, with Amber99sb favoring conformations with larger surface area and lower helical content. These results emphasize the importance of the side-chain interactions with urea in protein denaturation, and highlight the dependence of the computed driving forces on the unfolded ensemble sampled.
尿素是一种常用的蛋白质变性剂，确定其与各种蛋白质基团的相互作用对于阐明其对蛋白质稳定性影响的分子基础非常重要。我们使用 Trp-cage 小蛋白作为模型系统，报告了我们认为首次通过分子动力学模拟计算尿素变性过程中蛋白质优先相互作用系数的变化，并考察了骨架和侧链基团的贡献。优先相互作用是通过在尿素存在下对 Trp-cage 进行可逆折叠/去折叠复制交换分子动力学模拟获得的，覆盖了广泛的尿素浓度范围。在去折叠过程中，优先相互作用的增加主要是由侧链贡献引起的，而不是由骨架贡献引起的。在使用两种不同力场（Amber94 和 Amber99sb）进行的模拟中，也观察到了类似的趋势。尽管两种力场都包含相同的蛋白质-溶剂相互作用项，但侧链和骨架贡献的大小在两种力场中有所不同。差异来自于所采样的无规卷曲构象，Amber99sb 倾向于具有更大表面积和更低螺旋含量的构象。这些结果强调了侧链与尿素相互作用在蛋白质变性中的重要性，并突出了计算驱动力对所采样的无规卷曲构象的依赖性。
