STRUCTURE REFINEMENT & WATER PLACEMENT IN BACTERIORHODOPSIN

细菌视紫红质(BR)是一种跨膜蛋白，具有 作为盐生细菌细胞膜上的光驱动质子泵 萨利纳姆。这一功能是通过一个循环过程实现的 由一个光子的吸收引发[34]。泵的周期为 以一系列不同的中间体为特征的 从光谱和结构上看。附近的水分子 已知BR生色团在实验中起着重要作用 在蛋白质的功能上。最近，一种更好的解析结构 已报道[47]，但水分子的位置 仍然没有明确的定义。我们的工作*旨在将水 根据热力学标准确定的新结构中的分子 [74][中英文摘要]。计算了溶剂化自由能，计算了溶剂化的几率 一个(或多个)水占据质子通道中的空穴 分子(S)进行了计算。我们的模拟表明，在新的 结构，位于席夫碱附近的水分子，在 细胞外侧是非常稳定的，而水分子在 细胞质一侧稳定性较差。这些结果与以前的结果不同。 使用先前的结构[74]获得。我们计划继续这样做 研究和探索其他可能的补水地点。由此产生的模型 将用于主要的量子力学模拟 拍照活动。

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.