细菌紫红质中氢键相互作用和质子转移机理的分子模拟

Molecular Simulation of Hydrogen Bonding Interaction and Proton Transfer Mechanism in Bacteriorhodopsin

用CHARMM程序以细菌紫红质1R84晶体为模型,模拟了在等温定容条件下细菌紫红质在1ps过程中的变化,分析了与质子传递相关的ASP85,ASP212和水分子与视黄醛间氢键的结构变化情况.考虑到氨基酸残基和席夫碱质子的不同距离,考察了EC和PC两种结构的变化情况,探讨了紫红质中质子传递的可能途径.模拟结果表明1R84中可能的质子连续传递的机理是质子由席夫碱向水传递,再由水向ASP85传递.发现Asp212在模拟过程中保持EC结构,这样可能更有利于顺序质子传递.

The bacteriorhodopsin crystal structure from PDB （1R84） was taken as the model system to study the possible mechanism of the proton transfer by molecular simulations. The change of the system in 1 ps was simulated by using CHARMM package, under the conditions of constant temperature and volume. The proton transfers among Asp85, Asp212, water and retinal were analyzed through the change of separation distance. Two structures, EC and CP, which indicate different distance between the proton of Schiff base and the acid residues, were paid particular attention to. Simulations suggest a possible sequential mechanism for the proton transfer： the proton on Schiff base is transferred to oxygen of water molecule at first, and the proton transfer from water molecule to oxygen of Asp85 residue follows. During the simulation, Asp212 was found to retain the EC pattern, thus the sequential proton transfer was predicted favorably.