Proton-coupled electron transfer in cytochrome oxidase

Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex

Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.

Elementary Reactions in the Functional Triads of the Blue-Light Photoreceptor BLUF Domain

The blue light using the flavin (BLUF) domain is one of the smallest photoreceptors in nature, which consists of a unique bidirectional electron-coupled proton relay process in its photoactivation reaction cycle. This perspective summarizes our recent efforts in dissecting the photocycle into three elementary processes, including proton-coupled electron transfer (PCET), proton rocking, and proton relay. Using ultrafast spectroscopy, we have determined the temporal sequence, rates, kinetic isotope effects (KIEs), and concertedness of these elementary steps. Our findings provide important implications for illuminating the photoactivation mechanism of the BLUF domain and suggest an engineering platform to characterize intricate reactions involving proton motions that are ubiquitous in nonphotosensitive protein machines.

Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase

Cytochrome c oxidase (CcO) is part of the respiratory chain and contributes to the electrochemical membrane gradient in mitochondria as well as in many bacteria, as it uses the energy released in the reduction of oxygen to pump protons across an energy-transducing biological membrane. Here, we use time-resolved serial femtosecond crystallography to study the structural response of the active site upon flash photolysis of carbon monoxide (CO) from the reduced heme a3 of ba3-type CcO. In contrast with the aa3-type enzyme, our data show how CO is stabilized on CuB through interactions with a transiently ordered water molecule. These results offer a structural explanation for the extended lifetime of the CuB-CO complex in ba3-type CcO and, by extension, the extremely high oxygen affinity of the enzyme.

Theoretical Insights into the Generation Mechanism of the Tyr122 Radical Catalyzed by Intermediate X in Class Ia Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr122β ↔ [Trp48β]? ↔ Tyr356β ↔ Tyr731α ↔ Tyr730α ↔ Cys439α. The formation of the Y122• radical initiates this long-range radical transfer process. However, the generation mechanism of Y122• is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y122• generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y122• radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y122 and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y122 hydroxyl group to the terminal hydroxide ligand of Fe1III and simultaneously electron transfer from the side chain of Y122 to Fe2IV. These findings provide an insight into the formation mechanism of Y122• catalyzed by the double-iron center of the β subunit of class Ia RNR.

The catalytic reaction of cytochrome c oxidase probed by in situ gas titrations and FTIR difference spectroscopy

Cytochrome c oxidase (CcO) is a transmembrane heme‑copper metalloenzyme that catalyzes the reduction of O2 to H2O at the reducing end of the respiratory electron transport chain. To understand this reaction, we followed the conversion of CcO from Rhodobacter sphaeroides between several active-ready and carbon monoxide-inhibited states via attenuated total reflection Fourier-transform infrared (ATR FTIR) difference spectroscopy. Utilizing a novel gas titration setup, we prepared the mixed-valence, CO-inhibited R2CO state as well as the fully-reduced R4 and R4CO states and induced the "active ready" oxidized state OH. These experiments are performed in the dark yielding FTIR difference spectra exclusively triggered by exposure to O2, the natural substrate of CcO. Our data demonstrate that the presence of CO at heme a3 does not impair the catalytic oxidation of CcO when the cycle starts from the fully-reduced states. Interestingly, when starting from the R2CO state, the release of the CO ligand upon purging with inert gas yield a product that is indistinguishable from photolysis-induced states. The observed changes at heme a3 in the catalytic binuclear center (BNC) result from the loss of CO and are unrelated to electronic excitation upon illumination. Based on our experiments, we re-evaluate the assignment of marker bands that appear in time-resolved photolysis and perfusion-induced experiments on CcO.

Reactivities and Electronic Structures of μ-1,2-Peroxo and μ-1,2-Superoxo CoIIICoIII Complexes: Electrophilic Reactivity and O2 Release Induced by Oxidation

Peroxo complexes are key intermediates in water oxidation catalysis (WOC). Cobalt plays an important role in WOC, either as oxides CoOx or as {CoIII(μ-1,2-peroxo)CoIII} complexes, which are the oldest peroxo complexes known. The oxidation of {CoIII(μ-1,2-peroxo)CoIII} complexes had usually been described to form {CoIII(μ-1,2-superoxo)CoIII} complexes; however, recently the formation of {CoIV(μ-1,2-peroxo)CoIII} species were suggested. Using a bis(tetradentate) dinucleating ligand, we present here the synthesis and characterization of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} and {CoIII(μ-OH)2CoIII} complexes. Oxidation of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} at -40 °C in CH3CN provides the stable {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} species and activates electrophilic reactivity. Moreover, {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} catalyzes water oxidation, not molecularly but rather via CoOx films. While {CoIII(μ-1,2-peroxo)(μ-OH)CoIII} can be reversibly deprotonated with DBU at -40 °C in CH3CN, {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} undergoes irreversible conversions upon reaction with bases to a new intermediate that is also the decay product of {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} in aqueous solution at pH > 2. Based on a combination of experimental methods, the new intermediate is proposed to have a {CoII(μ-OH)CoIII} core formed by the release of O2 from {CoIII(μ-1,2-superoxo)(μ-OH)CoIII} confirmed by a 100% yield of O2 upon photocatalytic oxidation of {CoIII(μ-1,2-peroxo)(μ-OH)CoIII}. This release of O2 by oxidation of a peroxo intermediate corresponds to the last step in molecular WOC.

Examination of 'high-energy' metastable state of the oxidized (OH) bovine cytochrome c oxidase: Proton uptake and reaction with H2O2

Reoxidized cytochrome c oxidase appears to be in a 'high-energy' metastable state (OH) in which part of the energy released in the redox reactions is stored. The OH is supposed to relax to the resting 'as purified' oxidized state (O) in a time exceeding 200 ms. The catalytic heme a3-CuB center of these two forms should differ in a protonation and ligation state and the transition of OH-to-O is suggested to be associated with a proton transfer into this center. Employing a stopped-flow and UV-Vis absorption spectroscopy we investigated a proton uptake during the predicted relaxation of OH. It is shown, using a pH indicator phenol red, that from the time when the oxidation of the fully reduced CcO is completed (∼25 ms) up to ∼10 min, there is no uptake of a proton from the external medium (pH 7.8). Moreover, interactions of the assumed OH, generated 100 ms after oxidation of the fully reduced CcO, and the O with H2O2 (1 mM), result in the formation of two ferryl intermediates of the catalytic center, P and F, with very similar kinetics and the amounts of the formed ferryl states in both cases. These results implicate that the relaxation time of the catalytic center during the OH-to-O transition is either shorter than 100 ms or there is no difference in the structure of heme a3-CuB center of these two forms.

Investigation of the Mechanism of Membrane Potential Generation by Heme-Copper Respiratory Oxidases in a Real Time Mode

Heme-copper respiratory oxidases are highly efficient molecular machines. These membrane enzymes catalyze the final step of cellular respiration in eukaryotes and many prokaryotes: the transfer of electrons from cytochromes or quinols to molecular oxygen and oxygen reduction to water. The free energy released in this redox reaction is converted by heme-copper respiratory oxidases into the transmembrane gradient of the electrochemical potential of hydrogen ions H+). Heme-copper respiratory oxidases have a unique mechanism for generating H+, namely, a redox-coupled proton pump. A combination of direct electrometric method for measuring the kinetics of membrane potential generation with the methods of prestationary kinetics and site-directed mutagenesis in the studies of heme-copper oxidases allows to obtain a unique information on the translocation of protons inside the proteins in real time. The review summarizes the data of studies employing time-resolved electrometry to decipher the mechanisms of functioning of these important bioenergetic enzymes.

Tyrosine residues initiated photopolymerization in living organisms

Towards intracellular engineering of living organisms, the development of new biocompatible polymerization system applicable for an intrinsically non-natural macromolecules synthesis for modulating living organism function/behavior is a key step. Herein, we find that the tyrosine residues in the cofactor-free proteins can be employed to mediate controlled radical polymerization under 405 nm light. A proton-coupled electron transfer (PCET) mechanism between the excited-state TyrOH* residue in proteins and the monomer or the chain transfer agent is confirmed. By using Tyr-containing proteins, a wide range of well-defined polymers are successfully generated. Especially, the developed photopolymerization system shows good biocompatibility, which can achieve in-situ extracellular polymerization from the surface of yeast cells for agglutination/anti-agglutination functional manipulation or intracellular polymerization inside yeast cells, respectively. Besides providing a universal aqueous photopolymerization system, this study should contribute a new way to generate various non-natural polymers in vitro or in vivo to engineer living organism functions and behaviours.

Electronic coupling and electron transfer in hydrogen-bonded mixed-valence compounds

Electron transfer provided by hydrogen bonds represents a unique and highly significant area of research, as it has a crucial role to play in a wide variety of chemical and biological systems. The hydrogen-bonded mixed-valence system, in the form of donor-hydrogen bond-acceptor, provides an ideal platform for exploring thermally-induced electron transfer across this non-covalent unit. Over the past decades, ongoing progress has been made in this field. Here we critically assess some studies on the qualitative and quantitative evaluation of electronic coupling and thermal electron transfer across hydrogen bond interface. Additionally, selected experimental examples are discussed in terms of intervalence charge transfer, with particular attention paid to the proton-coupled and often overlooked proton-uncoupled electron transfer pathway in hydrogen-bonded mixed-valence systems. We further highlight the major limitations of this research area and suggest potential directions for future exploration.

Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers

Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the Q_B site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to Q_B. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with Q_B^•- are compared with earlier results obtained with Q_B [Wei et. al Photosynthesis Research volume 152, pages153-165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation.

QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase

The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b₅₉₅. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b₅₉₅ to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b₅₉₅ to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.

Amine Groups in the Second Sphere of Iron Porphyrins Allow for Higher and Selective 4e-/4H+ Oxygen Reduction Rates at Lower Overpotentials

Iron porphyrins with one or four tertiary amine groups in their second sphere are used to investigate the electrochemical O₂ reduction reaction (ORR) in organic (homogeneous) and aqueous (heterogeneous) conditions. Both of these complexes show selective 4e^-/4H⁺ reduction of oxygen to water at rates that are 2-3 orders of magnitude higher than those of iron tetraphenylporphyrin lacking these amines in the second sphere. In organic solvents, these amines get protonated, which leads to the lowering of overpotentials, and the rate of the ORR is enhanced almost 75,000 times relative to rates expected from the established scaling relationship for the ORR by iron porphyrins. In the aqueous medium, the same trend of higher ORR rates at a lower overpotential is observed. In situ resonance Raman data under heterogeneous aqueous conditions show that the presence of one amine group in the second sphere leads to a cleavage of the O-O bond in a Fe^III-OOH intermediate as the rate-determining step (rds). The presence of four such amine groups enhances the rate of O-O bond cleavage such that this intermediate is no longer observed during the ORR; rather, the proton-coupled reduction of the Fe^III-O₂^- intermediate with a H/D isotope effect of 10.6 is the rds. These data clearly demonstrate changes in the rds of the electrochemical ORR depending on the nature of second-sphere residues and explain their deviation from linear scaling relationships.

Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides

Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.

A Contrasting Effect of Acid in Electron Transfer, Oxygen Atom Transfer, and Hydrogen Atom Transfer Reactions of a Nickel(III) Complex

There have been many examples of the accelerating effects of acids in electron transfer (ET), oxygen atom transfer (OAT), and hydrogen atom transfer (HAT) reactions. Herein, we report a contrasting effect of acids in the ET, OAT, and HAT reactions of a nickel(III) complex, [Ni^III(PaPy₃*)]²⁺ (1) in acetone/CH₃CN (v/v 19:1). 1 was synthesized by reacting [Ni^II(PaPy₃*)]⁺ (2) with magic blue or iodosylbenzene in the absence or presence of triflic acid (HOTf), respectively. Sulfoxidation of thioanisole by 1 and H₂O occurred in the presence of HOTf, and the reaction rate increased proportionally with increasing concentration of HOTf ([HOTf]). The rate of ET from diacetylferrocene to 1 also increased linearly with increasing [HOTf]. In contrast, HAT from 9,10-dihydroanthracene (DHA) to 1 slowed down with increasing [HOTf], exhibiting an inversely proportional relation to [HOTf]. The accelerating effect of HOTf in the ET and OAT reactions was ascribed to the binding of H⁺ to the PaPy₃* ligand of 2; the one-electron reduction potential (E_red) of 1 was positively shifted with increasing [HOTf]. Such a positive shift in the E_red value resulted in accelerating the ET and OAT reactions that proceeded via the rate-determining ET step. On the other hand, the decelerating effect of HOTf on HAT from DHA to 1 resulted from the inhibition of proton transfer from DHA^•+ to 2 due to the binding of H⁺ to the PaPy₃* ligand of 2. The ET reactions of 1 in the absence and presence of HOTf were well analyzed in light of the Marcus theory of ET in comparison with the HAT reactions.

Electric fields control water-gated proton transfer in cytochrome c oxidase

Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome c oxidase (CcO) functions as a terminal electron acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O₂ reduction into proton pumping. Here we show that CcO creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme a, leads to dissociation of an arginine (Arg438)-heme a₃ D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V Å^-1 along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.

Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ

Dioxygenases catalyze stereoselective oxygen atom transfer in metabolic pathways of biological, industrial, and pharmaceutical importance, but their precise chemical principles remain controversial. The α-ketoglutarate (αKG)-dependent dioxygenase AsqJ synthesizes biomedically active quinolone alkaloids via desaturation and subsequent epoxidation of a carbon-carbon bond in the cyclopeptin substrate. Here, we combine high-resolution X-ray crystallography with enzyme engineering, quantum-classical (QM/MM) simulations, and biochemical assays to describe a peroxidic intermediate that bridges the substrate and active site metal ion in AsqJ. Homolytic cleavage of this moiety during substrate epoxidation generates an activated high-valent ferryl (Fe^IV = O) species that mediates the next catalytic cycle, possibly without the consumption of the metabolically valuable αKG cosubstrate. Our combined findings provide an important understanding of chemical bond activation principles in complex enzymatic reaction networks and molecular mechanisms of dioxygenases.

Second-Sphere Hydrogen-Bond Donors and Acceptors Affect the Rate and Selectivity of Electrochemical Oxygen Reduction by Iron Porphyrins Differently

The factors that control the rate and selectivity of 4e^-/4H⁺ O₂ reduction are important for efficient energy transformation as well as for understanding the terminal step of respiration in aerobic organisms. Inspired by the design of naturally occurring enzymes which are efficient catalysts for O₂ and H₂O₂ reduction, several artificial systems have been generated where different second-sphere residues have been installed to enhance the rate and efficiency of the 4e^-/4H⁺ O₂ reduction. These include hydrogen-bonding residues like amines, carboxylates, ethers, amides, phenols, etc. In some cases, improvements in the catalysis were recorded, whereas in some cases improvements were marginal or nonexistent. In this work, we use an iron porphyrin complex with pendant 1,10-phenanthroline residues which show a pH-dependent variation of the rate of the electrochemical O₂ reduction reaction (ORR) over 2 orders of magnitude. In-situ surface-enhanced resonance Raman spectroscopy reveals the presence of different intermediates at different pH's reflecting different rate-determining steps at different pH's. These data in conjunction with density functional theory calculations reveal that when the distal 1,10-phenanthroline is neutral it acts as a hydrogen-bond acceptor which stabilizes H₂O (product) binding to the active Fe^II state and retards the reaction. However, when the 1,10-phenanthroline is protonated, it acts as a hydrogen-bond donor which enhances O₂ reduction by stabilizing Fe^III-O₂^.- and Fe^III-OOH intermediates and activating the O-O bond for cleavage. On the basis of these data, general guidelines for controlling the different possible rate-determining steps in the complex multistep 4e^-/4H⁺ ORR are developed and a bioinspired principle-based design of an efficient electrochemical ORR is presented.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Proton-Coupled Electron-Transfer Reduction of Dioxygen: The Importance of Precursor Complex Formation between Electron Donor and Proton Donor

The proton-coupled electron transfer (PCET) reaction has drawn extensive attention for its widespread occurrence in chemistry, biology, and materials science. The mechanistic studies via model systems such as tyrosine and phenol oxidation have gradually deepened the understanding of PCET reactions, which was widely accepted and applied to bond activation and transformation. However, direct PCET activation of nonpolar bonds such as the C-H bond, O₂, and N₂ has yet to be explored. Herein, we report that the interaction between electron donor and proton donor could overcome the barrier of direct O₂ activation via a concerted electron-proton transfer mechanism. This work provides a new strategy for developing direct PCET activation of nonpolar bonds.

Coordination of metal center biogenesis in human cytochrome c oxidase

Mitochondrial cytochrome c oxidase (CcO) or respiratory chain complex IV is a heme aa₃-copper oxygen reductase containing metal centers essential for holo-complex biogenesis and enzymatic function that are assembled by subunit-specific metallochaperones. The enzyme has two copper sites located in the catalytic core subunits. The COX1 subunit harbors the Cu_B site that tightly associates with heme a₃ while the COX2 subunit contains the binuclear Cu_A site. Here, we report that in human cells the CcO copper chaperones form macromolecular assemblies and cooperate with several twin CX₉C proteins to control heme a biosynthesis and coordinate copper transfer sequentially to the Cu_A and Cu_B sites. These data on CcO illustrate a mechanism that regulates the biogenesis of macromolecular enzymatic assemblies with several catalytic metal redox centers and prevents the accumulation of cytotoxic reactive assembly intermediates.

Proton-electron-coupled functionalities of conductivity, magnetism, and optical properties in molecular crystals

Proton-electron-coupled reactions, specifically proton-coupled electron transfer (PCET), in biological and chemical processes have been extensively investigated for use in a wide variety of applications, including energy conversion and storage. However, the exploration of the functionalities of the conductivity, magnetism, and dielectrics by proton-electron coupling in molecular materials is challenging. Dynamic and static proton-electron-coupled functionalities are to be expected. This feature article highlights the recent progress in the development of functionalities of dynamic proton-electron coupling in molecular materials. Herein, single-unit conductivity by self-doping, quantum spin liquid state coupled with quantum fluctuation of protons, switching of conductivity and magnetism triggered by the disorder-order transition of deuterons, and their external responses under pressure and in the presence of an electric field are introduced. In addition, as for the functionalities of proton-d/π-electron coupling in metal dithiolene complexes, magnetic switching with multiple PCET and vapochromism induced by electron transfer through hydrogen-bond (H-bond) formation is introduced experimentally and theoretically. We also outlined the basic and applied issues and potential challenges for development of proton-electron-coupled molecular materials, functionalities, and devices.

Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling

One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH⁺/ne^-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH⁺/ne^- reactions. Such control can allow functional modeling of hydrogenases (H⁺ + e^- → 1/2 H₂), cytochrome c oxidase (O₂ + 4 e^- + 4 H⁺ → 2 H₂O), monooxygenases (RR'CH₂ + O₂ + 2 e^- + 2 H⁺ → RR'CHOH + H₂O) and dioxygenases (S + O₂ → SO₂; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.

Identification of Catalytic Active Sites for Durable Proton Exchange Membrane Fuel Cell: Catalytic Degradation and Poisoning Perspectives

Recent progress in synthetic strategies, analysis techniques, and computational modeling assist researchers to develop more active catalysts including metallic clusters to single-atom active sites (SACs). Metal coordinated N-doped carbons (M-N-C) are the most auspicious, with a large number of atomic sites, markedly performing for a series of electrochemical reactions. This perspective sums up the latest innovative and computational comprehension, while giving credit to earlier/pioneering work in carbonaceous assembly materials towards robust electrocatalytic activity for proton exchange membrane fuel cells via inclusive performance assessment of the oxygen reduction reaction (ORR). M-N_x -C_y are exclusively defined active sites for ORR, so there is a unique possibility to intellectually design the relatively new catalysts with much improved activity, selectivity, and durability. Moreover, some SACs structures provide better performance in fuel cells testing with long-term durability. The efforts to understand the connection in SACs based M-N_x -C_y moieties and how these relate to catalytic ORR performance are also conveyed. Owing to comprehensive practical application in the field, this study has covered very encouraging aspects to the current durability status of M-N-C based catalysts for fuel cells followed by degradation mechanisms such as macro-, microdegradation, catalytic poisoning, and future challenges.

Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers

The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the Q_A site cycles between quinone, Q_A, and anionic semiquinone, Q_A^·-, being reduced once and never binding protons. In the Q_B site, ubiquinone is reduced twice by Q_A^·-, binds two protons and is released into the membrane as the quinol, QH₂. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. Q_A is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to Q_B. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as AspM17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

Acid Catalysis in the Oxidation of Substrates by Mononuclear Manganese(III)-Aqua Complexes

Acids are known to enhance the reactivities of metal-oxygen intermediates, such as metal-oxo, -hydroperoxo, -peroxo, and -superoxo complexes, in biomimetic oxidation reactions. Although metal-aqua (and metal-hydroxo) complexes have been shown to be potent oxidants in oxidation reactions, acid effects on the reactivities of metal-aqua complexes have never been investigated previously. In this study, a mononuclear manganese(III)-aqua complex, [(dpaq^5NO2)Mn^III(OH₂)]²⁺ (1; dpaq^5NO2 = 2-[bis(pyridin-2-ylmethyl)]amino-N-quinolin-8-ylacetamidate with an NO₂ substituent at the 5 position), which is relatively stable in the presence of triflic acid (HOTf), is used in the investigation of acid-catalyzed oxidation reactions by metal-aqua complexes. As a result, we report a remarkable acid catalysis in the six-electron oxidation of anthracene by 1 in the presence of HOTf; anthraquinone is formed as the product. In the HOTf-catalyzed six-electron oxidation of anthracene by 1, the rate constant increases linearly with an increase of the HOTf concentration. Combined with the observed one-electron oxidation product, anthracene (derivative) radical cation, and the substitution effect at the 5 position of the dpaq ligand in 1 on the rate constants of the oxidation of anthracene, it is concluded that the oxidation of anthracene occurs via an acid-promoted electron transfer (APET) from anthracene to 1. The dependence of the rate constants of the APET from electron donors, including anthracene derivatives, to 1 on the driving force of electron transfer is also shown to be well fitted by the Marcus equation of outer-sphere electron transfer. To the best of our knowledge, this is the first example showing acid catalysis in the oxidation of substrates by metal(III)-aqua complexes.

Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II

Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O₂ into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn₄O₅Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyr_z (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca²⁺-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn₄O₅Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn₄O₅Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O₂ formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.

Second Sphere Effects on Oxygen Reduction and Peroxide Activation by Mononuclear Iron Porphyrins and Related Systems

Activation and reduction of O₂ and H₂O₂ by synthetic and biosynthetic iron porphyrin models have proved to be a versatile platform for evaluating second-sphere effects deemed important in naturally occurring heme active sites. Advances in synthetic techniques have made it possible to install different functional groups around the porphyrin ligand, recreating artificial analogues of the proximal and distal sites encountered in the heme proteins. Using judicious choices of these substituents, several of the elegant second-sphere effects that are proposed to be important in the reactivity of key heme proteins have been evaluated under controlled environments, adding fundamental insight into the roles played by these weak interactions in nature. This review presents a detailed description of these efforts and how these have not only demystified these second-sphere effects but also how the knowledge obtained resulted in functional mimics of these heme enzymes.

Mössbauer Property Calculations on Fea33+∙∙∙H2O∙∙∙CuB2+ Dinuclear Center Models of the Resting Oxidized as-Isolated Cytochrome c Oxidase

Mössbauer isomer shift and quadrupole splitting properties have been calculated using the OLYP‐D3(BJ) density functional method on previously obtained (W.‐G. Han Du, et al., Inorg Chem. 2020, 59, 8906–8915) geometry optimized Fe_a3³⁺−H₂O−Cu_B²⁺ dinuclear center (DNC) clusters of the resting oxidized (O state) “as‐isolated” cytochrome c oxidase (CcO). The calculated results are highly consistent with the available experimental observations. The calculations have also shown that the structural heterogeneities of the O state DNCs implicated by the Mössbauer experiments are likely consequences of various factors, particularly the variable positions of the central H₂O molecule between the Fe_a3³⁺ and Cu_B²⁺ sites in different DNCs, whether or not this central H₂O molecule has H‐bonding interaction with another H₂O molecule, the different spin states having similar energies for the Fe_a3³⁺ sites, and whether the Fe_a3³⁺ and Cu_B²⁺ sites are ferromagnetically or antiferromagnetically spin‐coupled.

The Cpx Stress Response Regulates Turnover of Respiratory Chain Proteins at the Inner Membrane of Escherichia coli

The Cpx envelope stress response is a major signaling pathway monitoring bacterial envelope integrity, activated both internally by excessive synthesis of membrane proteins and externally by a variety of environmental cues. The Cpx regulon is enriched with genes coding for protein folding and degrading factors, virulence determinants, and large envelope-localized complexes. Transcriptional repression of the two electron transport chain complexes, NADH dehydrogenase I and cytochrome bo₃, by the Cpx pathway has been demonstrated, however, there is evidence that additional regulatory mechanisms exist. In this study, we examine the interaction between Cpx-regulated protein folding and degrading factors and the respiratory complexes NADH dehydrogenase I and succinate dehydrogenase in Escherichia coli. Here we show that the cellular need for Cpx-mediated stress adaptation increases when respiratory complexes are more prevalent or active, which is demonstrated by the growth defect of Cpx-deficient strains on media that requires a functional electron transport chain. Interestingly, deletion of several Cpx-regulated proteolytic factors and chaperones results in similar growth-deficient phenotypes. Furthermore, we find that the stability of the NADH dehydrogenase I protein complex is lower in cells with a functional Cpx response, while in its absence, protein turnover is impaired. Finally, we demonstrated that the succinate dehydrogenase complex has reduced activity in E. coli lacking the Cpx pathway. Our results suggest that the Cpx two-component system serves as a sentry of inner membrane protein biogenesis, ensuring the function of large envelope protein complexes and maintaining the cellular energy status of the cell.

Outer-coordination sphere in multi-H+/multi-e-molecular electrocatalysis

Electrocatalysis is an indispensable technique for small-molecule transformations, which are essential for the sustainability of society. Electrocatalysis utilizes electricity as an energy source for chemical reactions. Hydrogen is considered the “fuel for the future,” and designing electrocatalysts for hydrogen production has thus become critical. Furthermore, fuel cells are promising energy solutions that require robust electrocatalysts for key fuel cell reactions such as the interconversion of oxygen to water. Concerns regarding the rising concentration of atmospheric carbon dioxide have prompted the search for CO₂ conversion methods. One promising approach is the electrochemical conversion of CO₂ into commodity chemicals and/or liquid fuels, but such chemistry is highly energy demanding because of the thermodynamic stability of CO₂. All of the above-mentioned electrocatalytic processes rely on the selective input of multiple protons (H⁺) and electrons (e^–) to yield the desired products. Biological enzymes evolved in nature to perform such redox catalysis and have inspired the design of catalysts at the molecular and atomic levels. While it is synthetically challenging to mimic the exact biological environment, incorporating functional outer coordination spheres into molecular catalysts has shown promise for advancing multi-H⁺ and multi-e^– electrocatalysis. From this Perspective, herein, catalysts with outer coordination sphere(s) are selected as the inspiration for developing new catalysts, particularly for the reductive conversion of H⁺, O₂, and CO₂, which are highly relevant to sustainability. The recent progress in electrocatalysis and opportunities to explore beyond the second coordination sphere are also emphasized.

Strategies for switching the mechanism of proton-coupled electron transfer reactions illustrated by mechanistic zone diagrams

The mechanism by which proton-coupled electron transfer (PCET) occurs is of fundamental importance and has great consequences for applications, e.g. in catalysis. However, determination and tuning of the PCET mechanism is often non-trivial. Here, we apply mechanistic zone diagrams to illustrate the competition between concerted and stepwise PCET-mechanisms in the oxidation of 4-methoxyphenol by Ru(bpy)₃³⁺-derivatives in the presence of substituted pyridine bases. These diagrams show the dominating mechanism as a function of driving force for electron and proton transfer (ΔG⁰_ET and ΔG⁰_PT) respectively [Tyburski et al., J. Am. Chem. Soc., 2021, 143, 560]. Within this framework, we demonstrate strategies for mechanistic tuning, namely balancing of ΔG⁰_ET and ΔG⁰_PT, steric hindrance of the proton-transfer coordinate, and isotope substitution. Sterically hindered pyridine bases gave larger reorganization energy for concerted PCET, resulting in a shift towards a step-wise electron first-mechanism in the zone diagrams. For cases when sufficiently strong oxidants are used, substitution of protons for deuterons leads to a switch from concerted electron–proton transfer (CEPT) to an electron transfer limited (ETPT_lim) mechanism. We thereby, for the first time, provide direct experimental evidence, that the vibronic coupling strength affects the switching point between CEPT and ETPT_lim, i.e. at what driving force one or the other mechanism starts dominating. Implications for solar fuel catalysis are discussed.

The mechanism by which proton-coupled electron transfer (PCET) occurs is of fundamental importance and has great consequences for applications, e.g. in catalysis.

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I

Biological energy conversion is catalyzed by membrane-bound proteins that transduce chemical or light energy into energy forms that power endergonic processes in the cell. At a molecular level, these catalytic processes involve elementary electron-, proton-, charge-, and energy-transfer reactions that take place in the intricate molecular machineries of cell respiration and photosynthesis. Recent developments in structural biology, particularly cryo-electron microscopy (cryoEM), have resolved the molecular architecture of several energy transducing proteins, but detailed mechanistic principles of their charge transfer reactions still remain poorly understood and a major challenge for modern biochemical research. To this end, multiscale molecular simulations provide a powerful approach to probe mechanistic principles on a broad range of time scales (femtoseconds to milliseconds) and spatial resolutions (10¹–10⁶ atoms), although technical challenges also require balancing between the computational accuracy, cost, and approximations introduced within the model. Here we discuss how the combination of atomistic (aMD) and hybrid quantum/classical molecular dynamics (QM/MM MD) simulations with free energy (FE) sampling methods can be used to probe mechanistic principles of enzymes responsible for biological energy conversion. We present mechanistic explorations of long-range proton-coupled electron transfer (PCET) dynamics in the highly intricate respiratory chain enzyme Complex I, which functions as a redox-driven proton pump in bacterial and mitochondrial respiratory chains by catalyzing a 300 Å fully reversible PCET process. This process is initiated by a hydride (H^–) transfer between NADH and FMN, followed by long-range (>100 Å) electron transfer along a wire of 8 FeS centers leading to a quinone biding site. The reduction of the quinone to quinol initiates dissociation of the latter to a second membrane-bound binding site, and triggers proton pumping across the membrane domain of complex I, in subunits up to 200 Å away from the active site. Our simulations across different size and time scales suggest that transient charge transfer reactions lead to changes in the internal hydration state of key regions, local electric fields, and the conformation of conserved ion pairs, which in turn modulate the dynamics of functional steps along the reaction cycle. Similar functional principles, which operate on much shorter length scales, are also found in some unrelated proteins, suggesting that enzymes may employ conserved principles in the catalysis of biological energy transduction processes.

Synergistic Dual-Atom Molecular Catalyst Derived from Low-Temperature Pyrolyzed Heterobimetallic Macrocycle-N4 Corrole Complex for Oxygen Reduction

A heterobimetallic corrole complex, comprising oxygen reduction reaction (ORR) active non-precious metals Co and Fe with a corrole-N4 center (PhFCC), is successfully synthesized and used to prepare a dual-atom molecular catalyst (DAMC) through subsequent low-temperature pyrolysis. This low-temperature pyrolyzed electrocatalyst exhibited impressive ORR performance, with onset potentials of 0.86 and 0.94 V, and half-wave potentials of 0.75 and 0.85 V, under acidic and basic conditions, respectively. During potential cycling, this DAMC displayed half-wave potential losses of only 25 and 5 mV under acidic and alkaline conditions after 3000 cycles, respectively, demonstrating its excellent stability. Single-cell Nafion-based proton exchange membrane fuel cell performance using this DAMC as the cathode catalyst showed a maximum power density of 225 mW cm^-2 , almost close to that of most metal-N4 macrocycle-based catalysts. The present study showed that preservation of the defined CoN4 structure along with the cocatalytic Fe-Cx site synergistically acted as a dual ORR active center to boost overall ORR performance. The development of DAMC from a heterobimetallic CoN4-macrocyclic system using low-temperature pyrolysis is also advantageous for practical applications.

Rejigging Electron and Proton Transfer to Transition between Dioxygenase, Monooxygenase, Peroxygenase, and Oxygen Reduction Activity: Insights from Bioinspired Constructs of Heme Enzymes

Nature has employed heme proteins to execute a diverse set of vital life processes. Years of research have been devoted to understanding the factors which bias these heme enzymes, with all having a heme cofactor, toward distinct catalytic activity. Among them, axial ligation, distal super structure, and substrate binding pockets are few very vividly recognized ones. Detailed mechanistic investigation of these heme enzymes suggested that several of these enzymes, while functionally divergent, use similar intermediates. Furthermore, the formation and decay of these intermediates depend on proton and electron transfer processes in the enzyme active site. Over the past decade, work in this group, using in situ surface enhanced resonance Raman spectroscopy of synthetic and biosynthetic analogues of heme enzymes, a general idea of how proton and electron transfer rates relate to the lifetime of different O2 derived intermediates has been developed. These findings suggest that the enzymatic activities of all these heme enzymes can be integrated into one general cycle which can be branched out to different catalytic pathways by regulating the lifetime and population of each of these intermediates. This regulation can further be achieved by tuning the electron and proton transfer steps. By strategically populating one of these intermediates during oxygen reduction, one can navigate through different catalytic processes to a desired direction by altering proton and electron transfer steps.

Beating Heart of Cytochrome c Oxidase: The Shared Proton of Heme a3 Propionates

Cytochrome c oxidase (CcO) pumps protons from the N-side to the P-side and consumes electrons from the P-side of the mitochondrial membrane driven by energy gained from reduction of dioxygen to water. ATP synthesis uses the resulting proton gradient and electrostatic potential difference. Since the distance a proton travels through CcO is too large for a one-step transfer process, proton-loading sites (PLS) that can carry protons transiently are necessary. One specific pump-active PLS couples to the redox reaction, thus energizing the proton to move across the membrane against electric potential and proton gradient. The PLS should also prevent proton backflow. Therefore, the propionates of the two redox-active hemes in CcO were suggested as PLS candidates although, according to CcO crystal structures, none of the four propionates can be protonated on account of strong H-bonds. Here, we show that modeling the local structure around heme a₃ propionates enhances significantly their capability of carrying a proton jointly. This was not possible for the propionates of heme a. The modeled structures are stable in molecular dynamics simulations (MDS) and are energetically similar to the crystal structure. Precise electrostatic energy computations of MDS data are used to estimate the pK_A values of all titratable residues in CcO. For the modeled structures, the heme a₃ propionates have pK_A values high enough to host a proton transiently but not too high to fix the proton permanently. The change in pK_A throughout the redox reaction is sufficient to push the proton to the P-side of the membrane and to provide the protons with the necessary amount of energy for ATP synthesis.

Proton-Coupled Electron Transfer (PCET) with 1,4-Bisguanidino-Benzene Derivatives: Comparative Study and Use in Acid-Initiated C-H Activation

Proton‐coupled electron transfer (PCET) is of key importance in modern synthetic chemistry. Redox‐active guanidines were established by our group as valuable alternatives to toxic high‐potential benzoquinones in a variety of different PCET reactions. In this work, the PCET reactivity of a series of 1,4‐bisguanidino‐benzenes varying in their redox potentials and proton affinities is evaluated. The relevant redox and protonation states are fully characterized, and the compounds sorted with respect to their PCET reactivity by comparative PCET experiments supplemented by quantum‐chemical calculations. Depending on the studied reactions, the driving force is either electron transfer or proton transfer; thereby the influence of both processes on the overall reactivity could be assessed. Then, two of the PCET reagents are applied in representative oxidative aryl‐aryl coupling reactions, namely the intramolecular coupling of 3,3’’‐4,4’’‐tetramethoxy‐o‐terphenyl to give the corresponding triphenylene, the intermolecular coupling of N‐ethylcarbazole to give N,N’‐diethyl‐3,3’‐bicarbazole, and in the oxidative lactonization of 2‐[(4‐methoxyphenyl)methyl]‐benzoic acid. Under mild conditions, the reactions proceed fast and efficient. Only small amounts of acid are needed, in clear contrast to the corresponding coupling reactions with traditional high‐potential benzoquinones such as DDQ or chloranil requiring a large excess of a strong acid.

Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes

In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.

Deactivation blocks proton pathways in the mitochondrial complex I

The electron transport chain of mitochondria is initiated by the respiratory complex I that converts chemical energy into a proton motive force to power synthesis of adenosine triphosphate. On a chemical level, complex I catalyzes elementary electron and proton transfer processes that couple across large molecular distances of >300 Å. However, under low oxygen concentrations, the respiratory chain operates in reverse mode and produces harmful reactive oxygen species. To avoid cell damage, the mitochondrial complex I transitions into a deactive state that inhibits turnover by molecular principles that remain elusive. By combining large-scale molecular simulations with cryo-electron microscopy data, we show here that complex I deactivation blocks the communication between proton pumping and redox modules by conformational and hydration changes.

Cellular respiration is powered by membrane-bound redox enzymes that convert chemical energy into an electrochemical proton gradient and drive the energy metabolism. By combining large-scale classical and quantum mechanical simulations with cryo-electron microscopy data, we resolve here molecular details of conformational changes linked to proton pumping in the mammalian complex I. Our data suggest that complex I deactivation blocks water-mediated proton transfer between a membrane-bound quinone site and proton-pumping modules, decoupling the energy-transduction machinery. We identify a putative gating region at the interface between membrane domain subunits ND1 and ND3/ND4L/ND6 that modulates the proton transfer by conformational changes in transmembrane helices and bulky residues. The region is perturbed by mutations linked to human mitochondrial disorders and is suggested to also undergo conformational changes during catalysis of simpler complex I variants that lack the “active”-to-“deactive” transition. Our findings suggest that conformational changes in transmembrane helices modulate the proton transfer dynamics by wetting/dewetting transitions and provide important functional insight into the mammalian respiratory complex I.

Tuning Oxygen Reduction Catalysis of Dinuclear Cobalt Polypyridyl Complexes by the Bridging Structure

The four-electron oxygen reduction reaction (4e^--ORR) is the mainstay in chemical energy conversion. Elucidation of factors influencing the catalyst's reaction rate and selectivity is important in the development of more active catalysts of 4e^--ORR. In this study, we investigated chemical and electrochemical 4e^--ORR catalyzed by Co₂(μ-O₂) complexes bridged by xanthene (1) and anthracene (3) and by a Co₂(OH)₂ complex bridged by anthraquinone (2). In the chemical ORR using Fe(CpMe)₂ as a reductant in acidic PhCN, we found that 1 showed the highest initial turnover frequency (TOF_init = 6.8 × 10² s^-1) and selectivity for 4e^--ORR (96%) in three complexes. The detailed kinetic analyses have revealed that the rate-determining steps (RDSs) in the catalytic cycles of 1-3 have the O₂ addition to [Co^II₂(OH₂)₂]⁴⁺ as an intermediate in common. In the only case that complex 1 was used as a catalyst, k_cat depended on proton concentration because the reaction rate of the O₂ addition to [Co^II₂(OH₂)₂]⁴⁺ was so fast as compared to that of the concerted PCET process of 1. Through X-ray, Raman, and electrochemical analyses and stoichiometric reactions, we found the face-to-face structure of 1 characterized by a slightly flexible xanthene was advantageous in capturing O₂ and stabilizing the Co₂(μ-O₂) structure, thus increasing both the reaction rate and selectivity for 4e^--ORR.

Proton-coupled electron transfer reactivities of electronically divergent heme superoxide intermediates: a kinetic, thermodynamic, and theoretical study

Heme superoxides are one of the most versatile metallo-intermediates in biology, and they mediate a vast variety of oxidation and oxygenation reactions involving O2(g). Overall proton-coupled electron transfer (PCET) processes they facilitate may proceed via several different mechanistic pathways, attributes of which are not yet fully understood. Herein we present a detailed investigation into concerted PCET events of a series of geometrically similar, but electronically disparate synthetic heme superoxide mimics, where unprecedented, PCET feasibility-determining electronic effects of the heme center have been identified. These electronic factors firmly modulate both thermodynamic and kinetic parameters that are central to PCET, as supported by our experimental and theoretical observations. Consistently, the most electron-deficient superoxide adduct shows the strongest driving force for PCET, whereas the most electron-rich system remains unreactive. The pivotal role of these findings in understanding significant heme systems in biology, as well as in alternative energy applications is also discussed.

The importance of exact exchange-A methodological investigation of NO reduction in heme-copper oxidases

Significant improvements of the density functional theory (DFT) methodology during the past few decades have made DFT calculations a powerful tool in studies of enzymatic reaction mechanisms. For metalloenzymes, however, there are still concerns about the reliability in the DFT-results. Therefore, a systematic study is performed where the fraction of exact exchange in a hybrid DFT functional is used as a parameter. By varying this parameter, a set of different but related functionals are obtained. The various functionals are applied to one of the reactions occurring in the enzyme family heme-copper oxidases, the reduction of nitric oxide (NO) to nitrous oxide (N₂O) and water. The results show that, even though certain parts of the calculated energetics exhibit large variations, the qualitative pictures of the reaction mechanisms are quite stable. Furthermore, it is found that the functional with 15% exact exchange (B3LYP^*) gives the best agreement with experimental data for the particular reactions studied. An important aspect of the procedure used is that the computational results are carefully combined with a few more general experimental data to obtain a complete description of the entire catalytic cycle of the reactions studied.

Trends in small organic fluorescent scaffolds for detection of oxidoreductase

Oxidoreductases are diverse class of enzymes engaged in modulating the redox homeostasis and cellular signaling cascades. Abnormal expression of oxidoreductases including thioredoxin reductase, azoreductase, cytochrome oxidoreductase, tyrosinase and monoamine oxidase leads to the initiation of numerous disorders. Thus, enzymes are the promising biomarkers of the diseased cells and their accurate detection has utmost significance for clinical diagnosis. The detection method must be extremely selective, sensitive easy to use, long self-life, mass manufacturable and disposable. Fluorescence assay approach has been developed potential substitute to conventional techniques used in enzyme's quantification. The fluorescent probes possess excellent stability, high spatiotemporal ratio and reproducibility represent applications in real sample analysis. Therefore, the enzymatic transformations have been monitored by small activatable organic fluorescent probes. These probes are generally integrated with enzyme's substrate/inhibitors to improve their binding affinity toward the enzyme's catalytic site. As the recognition unit bio catalyzed, the signaling unit produces the readout signals and provides novel insights to understand the biochemical reactions for diagnosis and development of point of care devices. Several structural modifications are required in fluorogenic scaffolds to tune the selectivity for a particular enzyme. Hence, the fluorescent probes with their structural features and enzymatic reaction mechanism of oxidoreductase are the key points discussed in this review. The basic strategies to detect each enzyme are discussed. The selectivity, sensitivity and real-time applications are critically compared. The kinetic parameters and futuristic opportunities are present, which would be enormous benefits for chemists and biologists to understand the facts to design and develop unique fluorophore molecules for clinical applications.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.