Computer Simulation of Conformation-Coupled Proton Transfer in Bacteriorhodopsin

计算机模拟将进行细菌视紫红质光循环从光异构状态开始。这些模拟将使用最近确定的蛋白质在许多中间状态下的实验结构作为起始几何形状。计算将使用“分子运动学”方法，该方法确定已知终态结构之间的构型空间中的最小能量路径，并结合混合量子力学/分子力学建模。质子转移和结构变化的途径将被确定，这将是特别感兴趣的，以深入了解这两者是如何耦合。将进行额外的计算以了解盐视紫红质中的氯离子泵送。

Computer simulations will be performed of the bacteriorhodopsin photocycle starting from the photoisomerized state. These simulations will use as starting geometries recently determined experimental structures of the protein in a number of intermediate states. The calculations will use "molecular kinematics" methodology that determines minimum-energy pathways in configurational space between known end-state structures, in combination with hybrid quantum mechanical/molecular mechanical modeling. Pathways for proton transfer and for structural change will be determined, and it will be of particular interest to gain insight into how the two are coupled. Additional calculations will be performed to understand chloride ion pumping in halorhodopsin.