蛋白质在溶液中构象转换的分子动力学模拟

Molecular Dynamics Simulation of Protein Conformation Transition in Solution

将蛋白质的稳定和失活、折叠和去折叠等现象概括为蛋白质分子在溶液中的构象变化问题。采用非晶格模型和Langevin分子动力学方法研究了无限稀释溶液及不同尺度和不同表面亲/疏水性球形限制性空间内β模型蛋白的构象分布及其转换特性。模拟结果显示:尺寸适度的疏水性空间有利于蛋白质结构发生缩塌,而亲水性空间有利于缩塌态蛋白质结构的稳定,且表面亲/疏水性的影响作用随着空间半径的增大而减弱。计算结果与实验报道一致,为研究蛋白质分子在溶液中的折叠和稳定化提供了理论工具。

The conformational transitions of protein in a confined space were abstracted to represent the physical nature of the stabilization, destabilization, folding and unfolding of protein molecule in solution. A G6-1ike model was applied to investigate the conformation distribution and the conformational transition of an all β-sheet protein in spherical cages of different sizes and surface hydmphobicity using Langevin molecular dynamics. It was found that a cage of moderate size and hydmphobicity significantly enhanced protein collapsed whereas a hydmphilic cage with appropriate size stabilized the collapsed conformation. The effect of the surface property on the structural changes of protein decreases in response to the increase in the cage size. The simulation agrees well as experimental results reported elsewhere and has a high potential in the study of protein folding/infolding and stabilization in solution.