School of Physics, Institute for Research in Fundamental Sciences, IPM, Tehran 19395-5531, Iran.
J Chem Phys. 2011 Sep 28;135(12):125101. doi: 10.1063/1.3641482.
Protein folding in confined media has attracted wide attention over the past decade due to its importance in both in vivo and in vitro applications. Currently, it is generally believed that protein stability increases by decreasing the size of the confining medium, if its interaction with the confining walls is repulsive, and that the maximum folding temperature in confinement occurs for a pore size only slightly larger than the smallest dimension of the folded state of a protein. Protein stability in pore sizes, very close to the size of the folded state, has not however received the attention that it deserves. Using detailed, 0.3-ms-long molecular dynamics simulations, we show that proteins with an α-helix native state can have an optimal folding temperature in pore sizes that do not affect the folded-state structure. In contradiction to the current theoretical explanations, we find that the maximum folding temperature occurs in larger pores for smaller α-helices. In highly confined pores the free energy surface becomes rough, and a new barrier for protein folding may appear close to the unfolded state. In addition, in small nanopores the protein states that contain the β structures are entropically stabilized, in contrast to the bulk. As a consequence, folding rates decrease notably and the free energy surface becomes rougher. The results shed light on many recent experimental observations that cannot be explained by the current theories, and demonstrate the importance of entropic effects on proteins' misfolded states in highly confined environments. They also support the concept of passive effect of chaperonin GroEL on protein folding by preventing it from aggregation in crowded environment of biological cells, and provide deeper clues to the α → β conformational transition, believed to contribute to Alzheimer's and Parkinson's diseases. The strategy of protein and enzyme stabilization in confined media may also have to be revisited in the case of tight confinement. For in silico studies of protein folding in confined media, use of non-Go potentials may be more appropriate.
蛋白质在受限介质中的折叠在过去十年中引起了广泛关注，因为它在体内和体外应用中都很重要。目前，人们普遍认为，如果受限介质与约束壁的相互作用是排斥的，那么蛋白质的稳定性会随着受限介质尺寸的减小而增加，并且在受限状态下蛋白质的最大折叠温度出现在孔尺寸稍大于蛋白质折叠状态的最小尺寸的情况下。然而，在非常接近折叠状态的孔尺寸下，蛋白质的稳定性并没有得到应有的重视。使用详细的、持续 0.3 毫秒的分子动力学模拟，我们表明具有α-螺旋天然状态的蛋白质可以在不影响折叠状态结构的孔尺寸下具有最佳折叠温度。与当前的理论解释相反，我们发现对于较小的α-螺旋，最大折叠温度出现在较大的孔中。在高度受限的孔中，自由能表面变得粗糙，并且可能在接近未折叠状态的地方出现新的蛋白质折叠障碍。此外，在小的纳米孔中，包含β结构的蛋白质状态在熵方面得到稳定，与体相相反。因此，折叠速率显著降低，自由能表面变得更加粗糙。这些结果阐明了许多最近的实验观察结果，这些结果无法用当前的理论来解释，并证明了在高度受限的环境中，熵效应对蛋白质错误折叠状态的重要性。它们还支持伴侣蛋白 GroEL 对蛋白质折叠的被动效应的概念，通过防止其在生物细胞拥挤环境中聚集，为阿尔茨海默病和帕金森病提供了更深层次的线索。在紧密受限的情况下，可能还需要重新考虑蛋白质和酶在受限介质中的稳定策略。对于受限介质中蛋白质折叠的计算机模拟研究，使用非-Go 势可能更为合适。
