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International Journal of Molecular... Jun 2023Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to...
Cytochrome c Oxidase (CcO), a membrane protein of the respiratory chain, pumps protons against an electrochemical gradient by using the energy of oxygen reduction to water. The ("chemical") protons required for this reaction and those pumped are taken up via two distinct channels, named D-channel and K-channel, in a step-wise and highly regulated fashion. In the reductive phase of the catalytic cycle, both channels transport protons so that the pumped proton passes the D-channel before the "chemical" proton has crossed the K-channel. By performing molecular dynamics simulations of CcO in the O→E redox state (after the arrival of the first reducing electron) with various combinations of protonation states of the D- and K-channels, we analysed the effect of protonation on the two channels. In agreement with previous work, the amount of water observed in the D-channel was significantly higher when the terminal residue E286 was not (yet) protonated than when the proton arrived at this end of the D-channel and E286 was neutral. Since a sufficient number of water molecules in the channel is necessary for proton transport, this can be understood as E286 facilitating its own protonation. K-channel hydration shows an even higher dependence on the location of the excess proton in the K-channel. Also in agreement with previous work, the K-channel exhibits a very low hydration level that likely hinders proton transfer when the excess proton is located in the lower part of the K-channel, that is, on the N-side of S365. Once the proton has passed S365 (towards the reaction site, the bi-nuclear centre (BNC)), the amount of water in the K-channel provides hydrogen-bond connectivity that renders proton transfer up to Y288 at the BNC feasible. No significant direct effect of the protonation state of one channel on the hydration level, hydrogen-bond connectivity, or interactions between protein residues in the other channel could be observed, rendering proton conductivity in the two channels independent of each other. Regulation of the order of proton uptake and proton passage in the two channels such that the "chemical" proton leaves its channel last must, therefore, be achieved by other means of communication, such as the location of the reducing electron.
Topics: Electron Transport Complex IV; Protons; Electron Transport; Oxidation-Reduction; Water; Rhodobacter sphaeroides
PubMed: 37445646
DOI: 10.3390/ijms241310464 -
Physica Medica : PM : An International... May 2014Suitable instrumentation for laser-accelerated proton (ion) beams is critical for development of integrated, laser-driven ion accelerator systems. Instrumentation aimed... (Review)
Review
Suitable instrumentation for laser-accelerated proton (ion) beams is critical for development of integrated, laser-driven ion accelerator systems. Instrumentation aimed at beam diagnostics and control must be applied to the driving laser pulse, the laser-plasma that forms at the target and the emergent proton (ion) bunch in a correlated way to develop these novel accelerators. This report is a brief overview of established diagnostic techniques and new developments based on material presented at the first workshop on 'Instrumentation for Diagnostics and Control of Laser-accelerated Proton (Ion) Beams' in Abingdon, UK. It includes radiochromic film (RCF), image plates (IP), micro-channel plates (MCP), Thomson spectrometers, prompt inline scintillators, time and space-resolved interferometry (TASRI) and nuclear activation schemes. Repetition-rated instrumentation requirements for target metrology are also addressed.
Topics: Lasers; Particle Accelerators; Protons; Spectrum Analysis
PubMed: 24100298
DOI: 10.1016/j.ejmp.2013.09.002 -
ELife Oct 2021Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels,...
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
Topics: Animals; Ligand-Gated Ion Channels; Markov Chains; Nuclear Pore; Protons; Xenopus laevis
PubMed: 34652272
DOI: 10.7554/eLife.68369 -
Nature Structural & Molecular Biology May 2022Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and...
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
Topics: Hydrogen Bonding; Proteins; Protons
PubMed: 35484235
DOI: 10.1038/s41594-022-00762-2 -
BioTechniques Feb 2011Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate... (Review)
Review
Fluorescent probes for monitoring mitochondrial membrane potential are frequently used for assessing mitochondrial function, particularly in the context of cell fate determination in biological and biomedical research. However, valid interpretation of results obtained with such probes requires careful consideration of numerous controls, as well as possible effects of non-protonic charges on dye behavior. In this context, we provide an overview of some of the important technical considerations, controls, and parallel complementary assays that can be employed to help ensure appropriate interpretation of results, thus providing a practical usage guide for monitoring mitochondrial membrane potentials with cationic probes. In total, this review will help illustrate both the strengths and potential pitfalls of common mitochondrial membrane potential dyes, and highlight best-usage approaches for their efficacious application in life sciences research.
Topics: Animals; Fluorescent Dyes; Humans; Membrane Potential, Mitochondrial; Mitochondria; Protons
PubMed: 21486251
DOI: 10.2144/000113610 -
Nature Communications Jul 2021The 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...
The 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.
Topics: Cryoelectron Microscopy; Gene Expression; Light; Molecular Dynamics Simulation; Physical Phenomena; Protein Conformation; Protons; Rhodopsin; Rhodopsins, Microbial
PubMed: 34226545
DOI: 10.1038/s41467-021-24429-6 -
Journal of the American Chemical Society Aug 2023The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZ) remains undetermined due to difficulties in measuring the net charge of...
The degree to which redox-driven proton pumps regulate net charge during electron transfer (ΔZ) remains undetermined due to difficulties in measuring the net charge of solvated proteins. Values of ΔZ can reflect reorganization energies or redox potentials associated with ET and can be used to distinguish ET from proton(s)-coupled electron transfer (PCET). Here, we synthesized protein "charge ladders" of a Rieske [2Fe-2S] subunit from (truncRp) and made 120 electrostatic measurements of ΔZ across pH. Across pH 5-10, truncRp is suspected of transitioning from ET to PCET, and then to two proton-coupled ET (2PCET). Upon reduction, we found that truncRp became more negative at pH 6.0 by one unit (ΔZ = -1.01 ± 0.14), consistent with single ET; was isoelectric at pH 8.8 (ΔZ = -0.01 ± 0.45), consistent with PCET; and became more positive at pH 10.6 (ΔZ = +1.37 ± 0.60), consistent with 2PCET. These ΔZ values are attributed to protonation of H154 and H134. Across pH, redox potentials of Rp (measured previously) correlated with protonation energies of H154 and H134 and ΔZ for truncRp, supporting a discrete proton pumping mechanism for Rieske proteins at the Fe-coordinating histidines.
Topics: Protons; Electrons; Electron Transport; Oxidation-Reduction; Proteins
PubMed: 37486967
DOI: 10.1021/jacs.3c03006 -
Advanced Science (Weinheim,... Jun 2022Despite the clinical potential, photodynamic therapy (PDT) relying on singlet oxygen ( O ) generation is severely limited by tumor hypoxia and endosomal entrapment....
Despite the clinical potential, photodynamic therapy (PDT) relying on singlet oxygen ( O ) generation is severely limited by tumor hypoxia and endosomal entrapment. Herein, a proton-driven transformable O -nanotrap (ANBDP NPs) with endosomal escape capability is presented to improve hypoxic tumor PDT. In the acidic endosomal environment, the protonated O -nanotrap ruptures endosomal membranes via a "proton-sponge" like effect and undergoes a drastic morphology-and-size change from nanocubes (≈94.1 nm in length) to nanospheres (≈12.3 nm in diameter). Simultaneously, anthracenyl boron dipyrromethene-derived photosensitizer (ANBDP) in nanospheres transforms to its protonated form (ANBDPH) and switches off its charge-transfer state to achieve amplified O photogeneration capability. Upon 730 nm photoirradiation, ANBDPH prominently produces O and traps generated- O in the anthracene group to form endoperoxide (ANOBDPH). Benefitting from the hypoxia-tolerant O -release property of ANOBDPH in the dark, the O -nanotrap brings about sustained therapeutic effect without further continuous irradiation, thereby achieving remarkable antitumor performance.
Topics: Humans; Hypoxia; Photochemotherapy; Photosensitizing Agents; Protons; Tumor Hypoxia
PubMed: 35435332
DOI: 10.1002/advs.202200128 -
Current Biology : CB Sep 2000Proton transfer into and out of proteins is important, both for many enzyme reaction mechanisms and proton pumping across membranes. Recent work on several proteins has... (Review)
Review
Proton transfer into and out of proteins is important, both for many enzyme reaction mechanisms and proton pumping across membranes. Recent work on several proteins has revealed stringent requirements for amino-acid side chains and subtle reorganisation of hydrogen-bond networks involving bound water molecules.
Topics: Hydrogen-Ion Concentration; Kinetics; Proteins; Protons
PubMed: 10996087
DOI: 10.1016/s0960-9822(00)00662-x -
Biochimica Et Biophysica Acta May 2000A brief summary of the principal notions of the quantum-mechanical theory of the charge transfer reactions has been presented. In the framework of this theory, the... (Review)
Review
A brief summary of the principal notions of the quantum-mechanical theory of the charge transfer reactions has been presented. In the framework of this theory, the mechanism of the proton transfer consists in the classical medium reorganization that equalizes the proton energy levels in the initial and final states, and a consequent proton transfer via a quantum-mechanical underbarrier transition. On the basis of this mechanism, factors influencing the proton transfer probability, and hence kinetic isotope effect, have been discussed; among them are the optimum tunneling distance, the involvement of the excited vibrational states, etc. Semi-classical and quantum-mechanical treatments of the Swain-Schaad relations have been compared. Some applications to enzymatic proton-transfer reactions have been described.
Topics: Energy Metabolism; Hydrogen Bonding; Models, Theoretical; Proton Pumps; Protons; Quantum Theory
PubMed: 10812022
DOI: 10.1016/s0005-2728(00)00057-8