Simulation of Protein Folding Process

尽管蛋白质有很大的构象自由度，但它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Barnase和蛋白质G进行了热诱导去折叠模拟。对于Barnase，我们在498K下进行了十次分子动力学模拟，描述了去折叠过程的共同特征。天然状态中的疏水核心和二级结构逐渐被破坏，直到它们最终都消失了，除了一些非常局部的区域保持着它们类似天然的构象。这与已知的实验结果是一致的。我们的新发现是，由紧凑的亚结构组成的天然层级结构，称为模块，在如此广泛的展开状态下被很好地维持，即使整个蛋白质结构在很大程度上膨胀，但与天然模块相对应的节段区仍保持相对紧凑的构象。此外，TE…之间的疏水相互作用对于蛋白质G，虽然早期的模拟结果与已知的实验结果不一致，但重新考虑模拟条件后发现，这个问题很可能是由于较高模拟温度下较低的介电常数造成的。然后，通过使用不太稳定的突变体或降低电荷的条件，我们得到了与实验一致的模拟结果。分析这些模拟数据，我们发现了与Barnase相似的去折叠特征，即由相对致密的亚结构组成的类自然层级结构在疏水核心发生较大破坏的情况下仍有保持的趋势，并且在展开过程中发生二级结构。因此，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，即减少天然结构需要搜索的构象空间的关键。较少

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