Simulation of the Functional Dynamics of Bacteriohodopsin in the Integral Purple Membrane

SchultenMCB 9982629通过膜的矢量质子移位是生物细胞中的基本能量转换过程。细菌视紫红质（bR）是盐生盐杆菌紫膜（PM）中的膜蛋白，其作为光驱动的电压敏感的质子泵，并且通过在其光循环中包括超快（~ 500 fs）、中间（微）和慢（~ 10 ms）过程的反应循环来实现其生物学功能。 为了解释泵浦机制，将对积分PM中bR光循环的光过程和第一中间体进行模拟。 参与质子泵的内部水是理解bR功能的基础。 几个水分子现在已经被晶体学解析了。 自由能微扰理论也被用来成功地将水分子在bR的建模研究。 模拟还显示，水分子在光循环过程中被置换。 后者的计算取决于水-肽相互作用的力场的质量，这仍然需要改进。该项目将（i）使用分子动力学（MD）工具并建立PM的真实模型，包括其所有蛋白质、脂质和水成分;（ii）应用新一代的水-肽势来描述bR的内部水;（iii）使用PM模型通过MD模拟来研究水合作用对PM结构特性的影响;（iv）为基态和激发态的bR的视网膜发色团提供多个势能面，作为相关内部坐标的函数并且包括与基态的圆锥相交;（vi）利用经典的分子动力学模拟方法对光循环中间体K、L和M进行了表征.与其他质子转运生物能蛋白相比，细菌视紫红质具有极其简单的性质，因此，它是研究反应过程的理想模型. 盐生盐杆菌的紫色膜是一种高度结构化的超分子组织，是细菌视紫红质在体内发挥功能的基础。

SchultenMCB 9982629Vectorial proton translocation through membranes is a fundamental energy conversion process in biological cells. Bacteriorhodopsin (bR) is a membrane protein that acts as a light-driven, voltage sensitive proton pump in the purple membrane (PM) of Halobacterium salinarium and achieves its biological function by cycling through a reaction that includes ultrafast (~ 500fs), intermediate (micro), and slow (~10ms) processes in its photo-cycle. The simulation of the photo-process and the first intermediates of bR's photo-cycle in the integral PM will be carried out in order to explain the pump mechanism. Internal water that participates in proton pumping is fundamental for an understanding of the function of bR. Several water molecules have been resolved now crystallographically. Free energy perturbation theory has also been used to successfully place water molecules in bR in modeling studies. Simulations have also revealed that water molecules become displaced during the photo-cycle. The latter calculations depend on the quality of the force fields for water-peptide interactions that still need to be improved. This project will (i) use molecular dynamics (MD) tools and build a realistic model of the PM, including all of its protein, lipid and water components; (ii) apply a new generation of water-peptide potentials to describe bR's internal water; (iii) use the PM model to investigate through MD simulations the influence of hydration on structural properties of the PM; (iv) furnish multiple potential energy surfaces for the retinal chromophore of bR in the ground and excited state, as a function of relevant internal coordinates and including conical intersection to the ground state; (v) carry out quantum dynamical calculations of the primary photoreaction; and (vi) characterize the photocycle intermediates K, L and M using classical molecular dynamics simulations.Bacteriorhodopsin is of utmost simplicity in comparison with other proton translocating bioenergetic proteins and, therefore, constitutes an ideal model for the study of the reaction process. The purple membrane of Halobacterium salinarium involves a highly structured supramolecular organization, and is fundamental for the in vivo functioning of Bacteriorhodopsin.