Bondar Ana-Nicoleta, Baudry Jerome, Suhai Sándor, Fischer Stefan, Smith Jeremy C
Computational Molecular Biophysics, IWR, University of Heidelberg, Heidelberg, Germany.
J Phys Chem B. 2008 Nov 27;112(47):14729-41. doi: 10.1021/jp801916f.
The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.
光驱动质子泵蛋白细菌视紫红质的功能机制取决于水分子在光循环各个阶段活性位点中的位置以及它们在质子转移步骤中的作用。在此，自由能计算表明，静电相互作用有利于在质子从视黄醛席夫碱转移至天冬氨酸85之前的状态下，有一个胞质侧水分子与视黄醛席夫碱形成氢键。然而，泵浦过程的非平衡性质意味着给定位点上水分子占据的概率既取决于在前一个光循环步骤中该水分子以及其他位点插入的自由能，也取决于这些位点在反应步骤时间尺度上的动力学可达性。胞质侧水分子的存在对质子转移机制有显著影响：质子在视黄醛的苏氨酸89一侧传递，而在天冬氨酸212一侧的转移则受到阻碍。反应路径模拟和分子动力学模拟表明，胞质侧水分子的存在允许形成一种低能量的细菌视紫红质构象异构体，其中水分子桥接扭曲的视黄醛席夫碱和质子受体天冬氨酸85。从这种低能量构象异构体开始，质子转移通过一种协同机制发生，其中水分子作为中间质子载体参与其中。
