STRUCTURE REFINEMENT & WATER PLACEMENT IN BACTERIORHODOPSIN

结构细化

• 批准号: 6282415
• 负责人: JEROME BAUDRY
• 金额: $ 2.31万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-08-01 至 1999-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6282415
• 关键词: bioengineering /biomedical engineering; biomedical resource; eye; human tissue; proteins; structural biology

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.

细菌视紫红质 (bR) 是一种跨膜蛋白，其功能 作为盐杆菌细胞膜中的光驱动质子泵 盐池。 该功能是通过一个循环过程来实现的 由吸收光子引发[34]。 泵的循环周期为 其特征在于一系列不同的中间体 光谱和结构上。 附近的水分子 实验表明 bR 的发色团发挥着重要作用 在蛋白质的功能上。 最近，一个更好的解决结构 bR的位置已被报道[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 根据热力学标准的新结构中的分子 [74]。 计算溶剂化自由能，并计算概率 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，位于希夫碱附近的水分子， 细胞外侧非常稳定，而细胞外侧有一个水分子 细胞质一侧不太稳定。 这些结果与之前的结果不同 使用先前的结构获得[74]。 我们计划继续这样做 工作并探索其他可能的水合位点。 得到的模型 将用于初级的量子力学模拟 照片活动。