Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer

Abstract

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 of the whole BR system (~3800 atoms). The simulations showed a novel proton transfer mechanism, viz. 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. Furthermore, 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. SIGNIFICANCE: Bacteriorhodopsin (BR), the benchmark of light-driven proton pumps, has attracted much attention from diverse areas in terms of energy conversion. Despite the significant experimental and theoretical efforts, the microscopic mechanism of the proton transfers in BR is not completely unveiled. In this study, quantum-mechanical molecular dynamics simulations of whole BR system were performed to elucidate the primary proton transfer in the L intermediate state with the latest snapshots obtained from X-ray free electron laser. As a result, it is found that the hydroxide ion originating from the specific internal water, which appears at the active site only in the L state, acts as a carrier for the primary proton transfer, demonstrating the importance of hydroxide ions in proton pumps.

Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models

“…Recently, the authors’ group reported a theoretical study on the primary proton transfer of BR based on XFEL crystal structures, which clarified the timing of proton transfer within four L intermediates. Furthermore, a novel proton transfer mechanism, namely, the hydroxide ion mechanism, was reported based on full quantum mechanical (QM) MD and metadynamics (MTD) − simulations using the entire BR system with retinal and internal water molecules containing ∼3750 atoms.…”

“…In this study, we investigated the microscopic mechanisms of proton storage and release processes in the secondary proton transfer stage by adopting the five time-resolved crystal structures in the M 1 -to-M 2 transition as well as one structure in the resting state observed by the XFEL experiment. The realistic models larger than those in our previous study 61 containing ∼20000 and ∼50000 atoms were fully quantum mechanically treated by the DC-DFTB-MD/MTD simulation technique.…”

Benchmarks of the density functional tight-binding method for redox, protonation and electronic properties of quinones

“…DFTB has been used extensively to study PT in chemical and biological systems. 94–106 Several methodological developments in DFTB over the years, including modification of the O-H repulsive potential, inclusion of third order terms in the Taylor series expansion and re-parameterization, have enhanced its accuracy for modeling PT. 21,22,95,98 However, the description of the energetics of PT between quinone molecules or between quinones and water by DFTB has not been investigated.…”

Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations

“…The QMD/MetaD simulations for large-scale systems including more than 10000 atoms can be achieved using the divide-and-conquer density-functional tight-binding (DC-DFTB) method [29] , [30] . Thus far, DC-DFTB-MD/MetaD simulations have been successfully applied to solutions [31] , [32] , batteries [33] , [34] , perovskites [35] , catalysts [36] , [37] , and biomolecular systems [38] , [39] . Here, the DC-DFTB-MD/MetaD and free energy analysis revealed that the functionally relevant IP state consistent with neutron crystallography [28] pre-exists even without ligands, and that this IP state is the most stable protonation state.…”