Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea.
Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea.
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DOI：
10.1021/bi970096i
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发表时间：
1997-06
期刊：
影响因子：
2.9
通讯作者：
J. Tirado-Rives;Modesto Orozco;William L. Jorgensen
中科院分区：
文献类型：
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作者：
J. Tirado-Rives;Modesto Orozco;William L. Jorgensen
芽孢杆菌RNA酶的分子动力学模拟已在水和8 M尿素溶液中进行，25℃下500ps，85℃下2000ps。室温下水模拟的最终结构与NMR获得的结构以及实验观察到的同位素交换保护非常匹配。对 85 摄氏度水模拟生成的结构进行比较，揭示了由几何相关结构组组成的轨迹，这些结构被结构快速变化的狭窄区域分隔开。第一个区域显示主链 rmsd 对晶体结构和溶剂可及区域的变化，暗示过渡态，而在模拟的最后 300 ps 期间观察到的特性与稳定的中间体一致。这些分配通过使用基于线性响应方法的经验方程计算“沿着反应坐标的进展”phi值来确认。以这种方式定义的解折叠途径在过渡态和中间体的二级结构含量方面与定点诱变的实验结果非常吻合，并且再现了二级结构的不同元素的相对稳定性。尿素的模拟结果表明了其在分子水平上增强蛋白质变性的机制。径向分布函数的分析表明，相对于本体溶剂，蛋白质的第一溶剂化壳富含尿素。水分子的置换使得疏水性侧链更多地暴露，这一点在较高温度下对溶剂可及的表面积的分析中尤其可见。几乎所有第一壳中的尿素分子都与蛋白质形成至少一个氢键。它们为剩余水分子的容纳提供了更有利的环境，并且它们通过充当先前形成蛋白内氢键的基团之间的桥梁来促进二级结构元素的分离。
Molecular dynamics simulations of barnase have been conducted both in water and in 8 M urea solution for 500 ps at 25 degrees C and for 2000 ps at 85 degrees C. The final structure of the aqueous simulation at room temperature matches closely the structure obtained by NMR and the experimentally observed protections from isotopic exchange. The comparison of the structures generated by the aqueous simulation at 85 degrees C reveals a trajectory composed of groups of geometrically related structures separated by narrow regions of rapid change in structure. The first of these regions displays changes in backbone rmsd to the crystal structure and solvent-accessible area suggestive of a transition state, while the properties observed during the final 300 ps of the simulation are consistent with a stable intermediate. These assignments were confirmed by calculation of the "progress along the reaction coordinate" phi-values using an empirical equation based on a linear response method. The pathway of unfolding defined in this fashion agrees well with the experimental results of site-directed mutagenesis in terms of secondary structure content of the transition state and the intermediate and reproduces the relative stability of the different elements of secondary structure. The results of the simulations in urea suggest a mechanism at the molecular level for its well-known enhancement of the denaturation of proteins. The analysis of radial distribution functions shows that the first solvation shell of the protein is enriched in urea relative to the bulk solvent. The displacement of water molecules allows greater exposure of hydrophobic side chains, as witnessed particularly in the analysis of solvent-accessible surface areas at the higher temperature. Almost all urea molecules in the first shell form at least one hydrogen bond with the protein. They provide a more favorable environment for accommodation of the remaining water molecules, and they facilitate the separation of secondary structure elements by acting as a bridge between groups previously forming intraprotein hydrogen bonds.