STRUCTURE REFINEMENT & WATER PLACEMENT IN BACTERIORHODOPSIN

细菌视紫红质（bR）是一种跨膜蛋白， 作为盐杆菌细胞膜中的光驱动质子泵 盐疗室。 该功能是通过循环过程实现的 由光子的吸收引发[34]。 泵周期 其特征在于一系列中间体， 光谱学和结构学。 水分子靠近 在实验上已知bR发色团起重要作用 蛋白质的功能。 最近，一个更好的解决结构， 已经报道了bR的位置[47]，但是水分子的位置 仍然没有很好的定义。 我们的工作 * 旨在将水 根据热力学标准， [74]. 计算了溶剂化自由能， 一种（或多种）水占据质子通道中的空腔 计算分子。 我们的模拟表明，在新的 结构，位于席夫碱附近的水分子， 细胞外侧非常稳定，而细胞外侧的水分子 细胞质侧不太稳定。 这些结果不同于 使用以前的结构[74]。 我们计划继续这样做 研究和探索其他可能的补水点 得到的模型 将被用于量子力学模拟的主要 照片事件。

Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in the cell membrane of Halobacterium salinarium. The function is achieved through a cyclic process initiated by the absorption of a photon [34]. The pump cycle is characterized by a series of intermediates that differ both spectroscopically and structurally. Water molecules near the chromophore of bR are experimentally known to play an important role in the function of the protein. Recently, a better resolved structure of bR has been reported [47], yet the position of the water molecules is still not well-defined. Our work* aims at placing the water molecules in the new structure according to thermodynamic criteria [74]. The free energy of solvation is calculated, and the probability of occupation of cavities in the proton channel by one (or more) water molecule(s) is calculated. Our simulations indicate that in the new structure, a water molecule located near the Schiff Base, on the extracellular side is very stable, while a water molecule on the cytoplasmic side is less stable. These results differ from the ones obtained using the previous structure [74]. We plan to continue this work and explore other possible hydration sites. The resulting model will be used for quantum mechanical simulations of the primary photo-event.