Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto, 615-8245, Japan.
Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo, 169-8555, Japan.
Chemphyschem. 2022 Nov 18;23(22):e202200109. doi: 10.1002/cphc.202200109. Epub 2022 Aug 23.
In bacteriorhodopsin, representative light-driven proton pump, five proton transfers yield vectorial active proton translocation, resulting in a proton gradient in microbes. Third proton transfer occurs from Asp96 to the Schiff base on the photocycle, which is expected to be a long-range proton transfer via the Grotthuss mechanism through internal water molecules. Here, large-scale quantum molecular dynamics simulations are performed for the third proton transfer, where all the atoms (∼50000 atoms) are treated quantum-mechanically. The simulations demonstrate that two reaction paths exist along the water wire, namely, via hydronium and via hydroxide ions. The free energy analysis confirms that the path via hydroxide ions is considerably favorable and consistent with the observed lifetime of the transient water wire. Therefore, the proposed hydroxide ion mechanism, as in the first proton transfer, is responsible for the third long-range proton transfer.
在细菌视紫红质中，这一具有代表性的光驱动质子泵通过五次质子转移实现了定向的主动质子转运，从而在微生物中产生质子梯度。第三次质子转移发生在 Asp96 到光循环中的席夫碱之间，预计这是一个通过质子扩散机制通过内部水分子进行的长程质子转移。在这里，对第三次质子转移进行了大规模的量子分子动力学模拟，其中所有原子（约 50000 个原子）都被量子力学处理。模拟表明，存在两条沿着水线的反应路径，即通过水合氢离子和氢氧根离子。自由能分析证实，通过氢氧根离子的路径是相当有利的，并且与观察到的瞬态水线的寿命一致。因此，与第一个质子转移一样，所提出的氢氧根离子机制负责第三次长程质子转移。
