Javidpour Leili, Tabar M Reza Rahimi, Sahimi Muhammad
Department of Physics, Sharif University of Technology, Tehran 11155-9161, IranInstitute of Physics, Carl von Ossietzky University, Oldenburg D-26111, Germany.
J Chem Phys. 2009 Feb 28;130(8):085105. doi: 10.1063/1.3080770.
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the alpha-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the experimental data, the computed diffusivities under the bulk conditions are of the correct order of magnitude. The diffusivities both in the bulk and in the pores follow a power law in the length [script-l] of the proteins and are larger in pores with repulsive walls. D(+)/D(-), the ratio of the diffusivities in pores with attractive and repulsive walls, exhibits two local maxima in its dependence on the pore size h, which are attributed to the pore sizes and protein configurations that induce long-lasting simultaneous interactions with both walls of the pores. Far from the folding temperature T(f), D increases about linearly with T, but due to the thermal fluctuations and their effect on the proteins' structure near T(f), the dependence of D on T in this region is nonlinear. We propose a novel and general "phase diagram," consisting of four regions, that describes qualitatively the effect of h, T, and interaction potentials with the walls on the diffusivity D of a protein.
一种将非连续分子动力学与朗之万方程相结合的新方法，连同蛋白质的中等分辨率模型，被用于进行长时间（几微秒）模拟，以研究蛋白质在纳米孔中的传输。我们模拟了具有α - 螺旋天然结构的单结构域蛋白质。考虑了蛋白质与孔壁之间的吸引和排斥相互作用势。不仅在本体条件下计算蛋白质的扩散系数D，还将其作为蛋白质“长度”（氨基酸基团数量）、温度T、孔径以及与壁的相互作用势的函数来计算。与实验数据相比，在本体条件下计算得到的扩散系数具有正确的数量级。本体和孔中的扩散系数在蛋白质长度[script - l]上都遵循幂律，并且在具有排斥壁的孔中更大。D(+)/D(-)，即具有吸引壁和排斥壁的孔中扩散系数的比值，在其对孔径h的依赖关系中表现出两个局部最大值，这归因于能诱导与孔的两壁同时产生持久相互作用的孔径和蛋白质构型。远离折叠温度T(f)时，D随T大致呈线性增加，但由于热涨落及其对T(f)附近蛋白质结构的影响，该区域中D对T的依赖是非线性的。我们提出了一个新颖且通用的“相图”，由四个区域组成，定性地描述了h、T以及与壁的相互作用势对蛋白质扩散系数D的影响。
