Simulation of Protein Folding Process

尽管有巨大的构象自由度，蛋白质可以在生理时间尺度内折叠成其特定的天然结构。为了阐明其机制，我们对藤壶酶和蛋白质g进行了热诱导展开模拟。对于藤壶酶，在498 K下进行了10次分子动力学模拟，我们表征了展开过程的共同特征。天然状态下的疏水核心和二级结构逐渐被破坏，直到最终全部消失，只有一些非常局部的区域保留了它们的天然构象。这与已知的实验结果一致。我们的新发现是，由紧密的亚结构（称为模块）组成的天然层次结构在如此广泛的展开状态下得到很好的维持，在某种意义上，与天然模块对应的片段区域保持相对紧凑的构象，尽管整个蛋白质结构很大程度上膨胀。此外，两者之间的疏水相互作用很大程度上保留了更多的模块，这将是稳定模块结构的主要因素。对于蛋白质G，尽管早期的模拟结果与已知的实验不一致，但重新考虑模拟条件表明，问题可能归因于较高模拟温度下较低的介电常数。然后，在不稳定的突变或减荷条件下，我们得到了与实验一致的模拟结果。通过分析这些模拟数据，我们发现了与藤本酶相似的展开特征，即由相对紧凑的亚结构组成的类似天然的层次结构倾向于持续存在，尽管疏水核心和二级结构在展开过程中发生了大的破坏。综上所述，在折叠过程的早期形成模块结构可能是解决折叠问题的关键，即减少寻找原生结构的构象空间的关键。少

Despite huge degree of conformational freedom, protein can fold into its specific native structure within a physiological time scale. To elucidate its mechanism, we performed heat-induced unfolding simulations of barnase and protein G.For barnase, performing ten runs of molecular dynamics simulations at 498 K, we characterized a common feature on unfolding processes. Hydrophobic cores and secondary structures seen in the native state were gradually disrupted until they were all eventually lost except some very local regions kept their native-like conformations. This is consistent with known experimental results. Our novel finding is that the native hierarchical structure composed of compact substructures, called modules, were well sustained in such extensive unfolded states in a sense that segmental regions corresponding to the native modules kept relatively compact conformations despite the whole protein structure largely inflated. Furthermore, hydrophobic interactions between both te … More rmini of modules were retained with high probability, which would be a main factor to stabilize module structures.For protein G, although early simulation results were inconsistent with known experiments, reconsidering simulation conditions revealed that the problem was likely ascribed to lower dielectric constants at higher simulation temperatures. And then, by using a less stable mutant or reduced-charge conditions, we obtained simulation results consistent with the experiments. Analyzing these simulation data, we found a similar unfolding feature to that of barnase, that is, native-like hierarchical structures composed of relatively compact substructures had a tendency to be sustained despite large disruption of hydrophobic cores and secondary structures occurred as unfolding proceeded.In conclusion, formation of module structures in an early stage of folding process could be a key to solve the folding problem, that is, a key to reduce conformational space to be searched for the native structure. Less