Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
Biochemistry. 2024 Jun 4;63(11):1505-1512. doi: 10.1021/acs.biochem.4c00182. Epub 2024 May 14.
rhodopsin (ESR) functions as a light-driven proton pump utilizing Lys96 for proton uptake and maintaining its activity over a wide pH range. Using a combination of methodologies including the linear Poisson-Boltzmann equation and a quantum mechanical/molecular mechanical approach with a polarizable continuum model, we explore the microscopic mechanisms underlying its pumping activity. Lys96, the primary proton uptake site, remains deprotonated owing to the loss of solvation in the ESR protein environment. Asp85, serving as a proton acceptor group for Lys96, does not form a low-barrier H-bond with His57. Instead, deprotonated Asp85 forms a salt-bridge with protonated His57, and the proton is predominantly located at the His57 moiety. Glu214, the only acidic residue at the end of the H-bond network exhibits a p value of ∼6, slightly elevated due to solvation loss. It seems likely that the H-bond network [Asp85···His57···HO···Glu214] serves as a proton-conducting pathway toward the protein bulk surface.
视紫红质（ESR）作为一种光驱动质子泵，利用 Lys96 进行质子摄取，并在较宽的 pH 范围内保持其活性。我们使用包括线性泊松-玻尔兹曼方程和带有极化连续体模型的量子力学/分子力学方法的组合，探索了其泵送活性的微观机制。主要质子摄取位点 Lys96 由于在 ESR 蛋白质环境中失去溶剂化作用而保持去质子化。作为 Lys96 的质子接受基团的 Asp85 与 His57 没有形成低势垒氢键。相反，去质子化的 Asp85 与质子化的 His57 形成盐桥，质子主要位于 His57 部分。作为氢键网络末端唯一的酸性残基，Glu214 的 p 值约为 6，由于溶剂化损失略有升高。似乎氢键网络 [Asp85···His57···HO···Glu214] 充当质子向蛋白质体表面的传导途径。
