Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan.
Department of Physics, Tokyo University of Science, Noda, Chiba 278-8510, Japan.
Phys Rev Lett. 2021 Mar 26;126(12):128101. doi: 10.1103/PhysRevLett.126.128101.
Protein conformational fluctuations are highly complex and exhibit long-term correlations. Here, molecular dynamics simulations of small proteins demonstrate that these conformational fluctuations directly affect the protein's instantaneous diffusivity D_{I}. We find that the radius of gyration R_{g} of the proteins exhibits 1/f fluctuations that are synchronous with the fluctuations of D_{I}. Our analysis demonstrates the validity of the local Stokes-Einstein-type relation D_{I}∝1/(R_{g}+R_{0}), where R_{0}∼0.3 nm is assumed to be a hydration layer around the protein. From the analysis of different protein types with both strong and weak conformational fluctuations, the validity of the Stokes-Einstein-type relation appears to be a general property.
蛋白质构象波动高度复杂，表现出长程相关性。本文通过对小蛋白的分子动力学模拟表明，这些构象波动直接影响蛋白质的瞬时扩散系数 D_{I}。我们发现，蛋白质的转动半径 R_{g} 表现出 1/f 波动，与 D_{I} 的波动同步。我们的分析证明了局部斯道克斯-爱因斯坦关系 D_{I}∝1/(R_{g}+R_{0}) 的有效性，其中 R_{0}∼0.3 nm 被假定为蛋白质周围的水合层。通过对具有强和弱构象波动的不同蛋白质类型的分析，斯道克斯-爱因斯坦型关系的有效性似乎是一种普遍性质。
