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

2020 ◽  
Vol 124 (39) ◽  
pp. 8524-8539
Author(s):  
Junichi Ono ◽  
Minori Imai ◽  
Yoshifumi Nishimura ◽  
Hiromi Nakai
Keyword(s):  
Proton Transfer ◽  
Primary Proton ◽  
Proton Pumps ◽  
Hydroxide Ion ◽  
Ion Carrier

scholarly journals Hydroxide Ion Carrier for Proton Pump in Bacteriorhodopsin: Primary Proton Transfer

2019 ◽  
Author(s):  
M. Imai ◽  
J. Ono ◽  
Y. Nishimura ◽  
H. Nakai
Keyword(s):  
Proton Transfer ◽  
Energy Conversion ◽  
Quantum Mechanical ◽  
Primary Proton ◽  
Proton Pumps ◽  
Microscopic Mechanism ◽  
Hydroxide Ion ◽  
Time Resolved ◽  
Internal Water ◽  
Dynamics Simulations

ABSTRACTBacteriorhodopsin (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.SIGNIFICANCEBacteriorhodopsin (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.

scholarly journals Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Stephan Hirschi ◽  
David Kalbermatter ◽  
Zöhre Ucurum ◽  
Thomas Lemmin ◽  
Dimitrios Fotiadis
Keyword(s):  
Proton Translocation ◽  
Functional Characterization ◽  
Green Light ◽  
Proton Donor ◽  
Molecular Organization ◽  
Primary Proton ◽  
Proton Pumps ◽  
Model Protein ◽  
Dynamics Simulations ◽  
And Function

AbstractThe green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.

Proton transfer from imidazole, benzimidazole, and their 1-alkyl derivatives. FMO analysis of the effect of methyl and benzo substitution

1986 ◽  
Vol 64 (6) ◽  
pp. 1240-1245 ◽  
Author(s):  
Erwin Buncel ◽  
Helen A. Joly ◽  
John R. Jones
Keyword(s):  
Proton Transfer ◽  
Reaction Scheme ◽  
Frontier Molecular Orbital ◽  
Neutral Species ◽  
Ph Profile ◽  
Hydroxide Ion ◽  
Methyl Substitution ◽  
Rate Determining Step ◽  
Alkyl Derivatives ◽  
Conjugate Acid

The rate–pH profile for detritiation from the C-2 position of 1-methylimidazole has been determined in aqueous solution at 85 °C. The profile is consistent with a mechanism involving attack by hydroxide ion on the conjugate acid of the substrate to give an ylid intermediate in the rate-determining step. At higher pH, hydroxide-catalyzed exchange of the neutral species becomes increasingly important. Comparison of the second-order rate constants derived from the rate–pH profiles of imidazole, 1-methylimidazole, benzimidazole, and 1-methylbenzimidazole showed that methyl substitution caused the rate to increase by 2-to 3-fold while benzo annelation increased the rate by 10- to 20-fold. Frontier molecular orbital (FMO) analysis of the reaction scheme for proton transfer from imidazole, benzimidazole, and their 1-alkyl derivatives has been used to explain the rate-accelerating effect of methyl substitution and benzo annelation in these processes.

scholarly journals Photocycle-dependent conformational changes in the proteorhodopsin cross-protomer Asp–His–Trp triad revealed by DNP-enhanced MAS-NMR

2019 ◽  
Vol 116 (17) ◽  
pp. 8342-8349 ◽  
Author(s):  
Jakob Maciejko ◽  
Jagdeep Kaur ◽  
Johanna Becker-Baldus ◽  
Clemens Glaubitz
Keyword(s):  
Proton Transfer ◽  
Conformational Changes ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Proton Acceptor ◽  
Primary Proton ◽  
Magic Angle ◽  
Drastic Effect ◽  
Microbial Rhodopsin ◽  
Angle Spinning

Proteorhodopsin (PR) is a highly abundant, pentameric, light-driven proton pump. Proton transfer is linked to a canonical photocycle typical for microbial ion pumps. Although the PR monomer is able to undergo a full photocycle, the question arises whether the pentameric complex formed in the membrane via specific cross-protomer interactions plays a role in its functional mechanism. Here, we use dynamic nuclear polarization (DNP)-enhanced solid-state magic-angle spinning (MAS) NMR in combination with light-induced cryotrapping of photointermediates to address this topic. The highly conserved residue H75 is located at the protomer interface. We show that it switches from the (τ)- to the (π)-tautomer and changes its ring orientation in the M state. It couples to W34 across the oligomerization interface based on specific His/Trp ring orientations while stabilizing the pKaof the primary proton acceptor D97 within the same protomer. We further show that specific W34 mutations have a drastic effect on D97 and proton transfer mediated through H75. The residue H75 defines a cross-protomer Asp–His–Trp triad, which potentially serves as a pH-dependent regulator for proton transfer. Our data represent light-dependent, functionally relevant cross talk between protomers of a microbial rhodopsin homo-oligomer.

Base-catalyzed Isotopic Exchange of Molecular Hydrogen. II. Rate Dependence on Basicity in the Dimethyl Sulfoxide–Water System

1973 ◽  
Vol 51 (11) ◽  
pp. 1673-1681 ◽  
Author(s):  
E. Allan Symons ◽  
Erwin Buncel
Keyword(s):  
Proton Transfer ◽  
Dimethyl Sulfoxide ◽  
Molecular Hydrogen ◽  
Isotopic Exchange ◽  
Water System ◽  
Medium Composition ◽  
Hydroxide Ion ◽  
Hydride Ion ◽  
Low Sensitivity ◽  
Concerted Reaction

Isotopic exchange of D2 has been determined in mixtures of dimethyl sulfoxide and water under catalysis by hydroxide ion. The rate of exchange increases by ca. 104 as the medium composition is changed from 0% DMSO to 99.6% DMSO at 65 °C. The unusually low sensitivity to medium basicity is reflected in abnormally low slope values for the plots of log kobs υs. H− or J−. When [Me4NOH] is varied at a given medium composition, the apparent order with respect to [Me4NOH] is greater than unity.These results are discussed in terms of (1) rate determining proton transfer from D2 to OH− with formation of hydride ion; (2) a concerted reaction of OH−, D2, and H2O; (3) addition of OH− to D2 to yield an intermediate adduct, [HODD]−; (4) a 6-centered process involving cation participation and electrophilic assistance by H2O in the reaction of OH− with D2.L'échange isotopique de D2 a été étudié dans des mélanges de sulfoxyde de diméthyle et d'eau sous l'effet d'une catalyse par l'ion hydroxyle. Le taux d'échange augmente d'environ 104 alors que la composition du milieu change de 0% en DMSO à 99.6% en DMSO à 65 °C. La sensitivité anormalement faible à la basicité du milieu est réflétée par des valeurs anormalement faibles de la pente dans les graphiques du log kobs υs. H− ou J−. Quand la concentration de Me4NOH est changée pour une composition donnée du milieu, l'ordre apparent en ce qui a trait à la [Me4NOH] est plus élevé que l'unité.

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