Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics–hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.

广泛的经典和量子力学/分子力学 (QM/MM) 分子动力学模拟用于建立细菌视紫红质 (bR) 中 O 态的结构特征及其向 bR 基态的转换。计算出的自由能面与 O 到 bR 转变的动力学和热力学的现有实验数据一致。模拟结果强调了质子释放基团（PRG，由 Glu194/204 组成）和保守的精氨酸 82 在调节蛋白质空腔水合水平中的重要性。特别是，在 O 状态下，PRG 的去质子化和 Arg82 的向下旋转导致水合水平升高以及将 PRG 与质子化的 Asp85 连接的连续水网络。∼0.1-μs 半经验 QM/MM 自由能模拟显示，通过该水网络的质子交换是通过质子空穴的生成和传播而发生的，该空穴由 Asp212 中继并由 Arg82 稳定。该机制为细菌视紫红质 D85S 突变体泵送氯离子的观察结果提供了解释。静电-水合耦合机制和水的所有滴定态的参与可能适用于参与生物能量转导的许多生物分子。