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Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer.
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-09-02 , DOI: 10.1021/acs.jpcb.0c05507 Junichi Ono 1, 2 , Minori Imai 3 , Yoshifumi Nishimura 1 , Hiromi Nakai 1, 2, 3
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-09-02 , DOI: 10.1021/acs.jpcb.0c05507 Junichi Ono 1, 2 , Minori Imai 3 , Yoshifumi Nishimura 1 , Hiromi Nakai 1, 2, 3
Affiliation
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Bacteriorhodopsin (BR) is a model protein for light-driven proton pumps, where the vectorial active proton transport results in light-energy conversion. To clarify the microscopic mechanism of primary proton transfer from retinal Schiff base (SB) to Asp85 in BR, herein, we performed quantum-mechanical metadynamics simulations with the isolated BR model (∼3750 atoms). The simulations showed a novel proton transfer mechanism, viz. the hydroxide ion mechanism, in which the deprotonation of specific internal water (Wat452) yields the protonation of Asp85 via Thr89, after which the resulting hydroxide ion accepts the remaining proton from retinal SB. Systematic investigations adopting four sequential snapshots obtained by the time-resolved serial femtosecond crystallography revealed that proton transfer took 2–5.25 μs on the photocycle. The presence of Wat401, which is the main difference between snapshots at 2 and 5.25 μs, is found to be essential in assisting the primary proton transfer. Furthermore, the hydroxide ion mechanism was confirmed by the minimum energy path for the primary proton transfer in BR obtained by the nudged elastic band calculations with the embedded BR model (10,119 atoms), in which BR was embedded within lipid membranes in between water solvents.
中文翻译：
细菌视紫红质中质子泵的氢氧化物离子载体：初次质子转移。
细菌视紫红质（BR）是光驱动质子泵的模型蛋白，其中矢量活性质子转运导致光能转换。为了阐明BR中从视网膜Schiff碱（SB）到Asp85的初级质子转移的微观机理，我们使用孤立的BR模型（〜3750个原子）进行了量子力学的元动力学模拟。模拟显示了一种新颖的质子转移机制，即。氢氧根离子机理，其中特定内部水的去质子化（Wat452）通过Thr89产生Asp85的质子化，然后所得的氢氧根离子接受来自视网膜SB的剩余质子。系统研究采用了时间分辨系列飞秒晶体学获得的四个连续快照，结果表明质子转移在光周期上花费了2–5.25μs。发现Wat401的存在（这是2和5.25μs时快照之间的主要区别）对于协助一次质子转移至关重要。此外，通过嵌入BR模型（10,119个原子）通过微动的弹性带计算获得的BR中一次质子转移的最小能量路径证实了氢氧离子的机理，其中BR嵌入在水溶剂之间的脂质膜中。
更新日期：2020-10-02
中文翻译：
细菌视紫红质中质子泵的氢氧化物离子载体：初次质子转移。
细菌视紫红质（BR）是光驱动质子泵的模型蛋白，其中矢量活性质子转运导致光能转换。为了阐明BR中从视网膜Schiff碱（SB）到Asp85的初级质子转移的微观机理，我们使用孤立的BR模型（〜3750个原子）进行了量子力学的元动力学模拟。模拟显示了一种新颖的质子转移机制，即。氢氧根离子机理，其中特定内部水的去质子化（Wat452）通过Thr89产生Asp85的质子化，然后所得的氢氧根离子接受来自视网膜SB的剩余质子。系统研究采用了时间分辨系列飞秒晶体学获得的四个连续快照，结果表明质子转移在光周期上花费了2–5.25μs。发现Wat401的存在（这是2和5.25μs时快照之间的主要区别）对于协助一次质子转移至关重要。此外，通过嵌入BR模型（10,119个原子）通过微动的弹性带计算获得的BR中一次质子转移的最小能量路径证实了氢氧离子的机理，其中BR嵌入在水溶剂之间的脂质膜中。
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