Biomolecular Structure and Design Program and Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17851-6. doi: 10.1073/pnas.1201809109. Epub 2012 Oct 22.
Molecular dynamics simulations of protein folding or unfolding, unlike most in vitro experimental methods, are performed on a single molecule. The effects of neighboring molecules on the unfolding/folding pathway are largely ignored experimentally and simply not modeled computationally. Here, we present two all-atom, explicit solvent molecular dynamics simulations of 32 copies of the Engrailed homeodomain (EnHD), an ultrafast-folding and -unfolding protein for which the folding/unfolding pathway is well-characterized. These multimolecule simulations, in comparison with single-molecule simulations and experimental data, show that intermolecular interactions have little effect on the folding/unfolding pathway. EnHD unfolded by the same mechanism whether it was simulated in only water or also in the presence of other EnHD molecules. It populated the same native state, transition state, and folding intermediate in both simulation systems, and was in good agreement with experimental data available for each of the three states. Unfolding was slowed slightly by interactions with neighboring proteins, which were mostly hydrophobic in nature and ultimately caused the proteins to aggregate. Protein-water hydrogen bonds were also replaced with protein-protein hydrogen bonds, additionally contributing to aggregation. Despite the increase in protein-protein interactions, the protein aggregates formed in simulation did not do so at the total exclusion of water. These simulations support the use of single-molecule techniques to study protein unfolding and also provide insight into the types of interactions that occur as proteins aggregate at high temperature at an atomic level.
与大多数体外实验方法不同，蛋白质折叠或展开的分子动力学模拟是在单个分子上进行的。实验中在很大程度上忽略了相邻分子对展开/折叠途径的影响，并且在计算上也没有建模。在这里，我们展示了两个全原子、显式溶剂的 Engrailed 同源域（EnHD）的分子动力学模拟，EnHD 是一种超快折叠和展开的蛋白质，其折叠/展开途径已经得到很好的描述。与单分子模拟和实验数据相比，这些多分子模拟表明，分子间相互作用对折叠/展开途径的影响很小。EnHD 以相同的机制展开，无论是在仅水存在的情况下还是在其他 EnHD 分子存在的情况下进行模拟。它在两个模拟系统中都占据了相同的天然状态、过渡态和折叠中间体，并且与每个状态的实验数据非常吻合。与相邻蛋白质的相互作用略微减缓了展开过程，这些相互作用主要是疏水性的，最终导致蛋白质聚集。蛋白质-水氢键也被蛋白质-蛋白质氢键取代，这也有助于聚集。尽管蛋白质-蛋白质相互作用增加，但在模拟中形成的蛋白质聚集体并没有完全排除水。这些模拟支持使用单分子技术来研究蛋白质展开，并且还提供了有关在高温下蛋白质聚集时发生的相互作用类型的深入了解。
