Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions

Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.

New insights into the proton pumping mechanism of ba3 cytochrome c oxidase: the functions of key residues and water

As the terminal oxidase of cell respiration in mitochondria and aerobic bacteria, the proton pumping mechanism of ba3-type cytochrome c oxidase (CcO) of Thermus thermophiles is still not fully understood. Especially, the functions of key residues which were considered as the possible proton loading sites (PLSs) above the catalytic center, as well as water located above and within the catalytic center, remain unclear. In this work, molecular dynamic simulations were performed on a set of designed mutants of key residues (Asp287, Asp372, His376, and Glu126II). The results showed that Asp287 may not be a PLS, but it could modulate the ability of the proton transfer pathway to transfer protons through its salt bridge with Arg225. Maintaining the closed state of the water pool above the catalytic center is necessary for the participation of inside water molecules in proton transfer. Water molecules inside the water pool can form hydrogen bond chains with PLS to facilitate proton transfer. Additional quantum cluster models of the Fe-Cu metal catalytic center are established, indicating that when the proton is transferred from Tyr237, it is more likely to reach the OCu atom directly through only one water molecule. This work provides a more profound understanding of the functions of important residues and specific water molecules in the proton pumping mechanism of CcO.

Protonation-State Dependence of Hydration and Interactions in the Two Proton-Conducting Channels of Cytochrome c Oxidase

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.

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.

Mechanical Allosteric Couplings of Redox-Induced Conformational Changes in Respiratory Complex I

We apply linear response theory to calculate mechanical allosteric couplings in respiratory complex I between the iron sulfur cluster N2, located in the catalytic cavity, and the membrane part of the enzyme, separated from it by more than 50 Å. According to our hypothesis, the redox reaction of ubiquinone in the catalytic cavity of the enzyme generates an unbalanced charge that via repulsion of the charged redox center N2 produces local mechanical stress that transmits into the membrane part of the enzyme where it induces proton pumping. Using coarse-grained simulations of the enzyme, we calculated mechanistic allosteric couplings that reveal the pathways of the mechanical transmission of the stress along the enzyme. The results shed light on the recent experimental studies where a stabilization of the enzyme with an introduced disulfide bridge resulted in the abolishing of proton pumping. Simulation of the disulfide bond action indicates a dramatic change of the mechanistic coupling pathways in line with experimental findings.

Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site

At the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction—due to a need for a rare opening of the bottleneck—of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction.

Electron Transfer Coupled to Conformational Dynamics in Cell Respiration

Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.

The allosteric protein interactions in the proton-motive function of mammalian redox enzymes of the respiratory chain

Insight into mammalian respiratory complexes defines the role of allosteric protein interactions in their proton-motive activity. In cytochrome c oxidase (CxIV) conformational change of subunit I, caused by O₂ binding to heme a₃²⁺-Cu_B⁺ and reduction, and stereochemical transitions coupled to oxidation/reduction of heme a and Cu_A, combined with electrostatic effects, determine the proton pumping activity. In ubiquinone-cytochrome c oxidoreductase (CxIII) conformational movement of Fe-S protein between cytochromes b and c₁ is the key element of the proton-motive activity. In NADH-ubiquinone oxidoreductase (CxI) ubiquinone binding and reduction result in conformational changes of subunits in the quinone reaction structure which initiate proton pumping.

Human Mitochondrial Pathologies of the Respiratory Chain and ATP Synthase: Contributions from Studies of Saccharomyces cerevisiae

The ease with which the unicellular yeast Saccharomyces cerevisiae can be manipulated genetically and biochemically has established this organism as a good model for the study of human mitochondrial diseases. The combined use of biochemical and molecular genetic tools has been instrumental in elucidating the functions of numerous yeast nuclear gene products with human homologs that affect a large number of metabolic and biological processes, including those housed in mitochondria. These include structural and catalytic subunits of enzymes and protein factors that impinge on the biogenesis of the respiratory chain. This article will review what is currently known about the genetics and clinical phenotypes of mitochondrial diseases of the respiratory chain and ATP synthase, with special emphasis on the contribution of information gained from pet mutants with mutations in nuclear genes that impair mitochondrial respiration. Our intent is to provide the yeast mitochondrial specialist with basic knowledge of human mitochondrial pathologies and the human specialist with information on how genes that directly and indirectly affect respiration were identified and characterized in yeast.

Respiratory complex I: Bottleneck at the entrance of quinone site requires conformational change for its opening

The structure of the entire respiratory complex I is now known at reasonably high resolution for many species - bacteria, yeast, and several mammals, including human. The structure reveals an almost 30 angstrom tunnel-like chamber for ubiquinone binding in the core part of the enzyme, at the joint between the membrane and hydrophilic arms of the enzyme. Here we characterize the geometric bottleneck forming the entrance of the quinone reaction chamber. Computer simulations of quinone/quinol passage through the bottleneck suggest that in all structures available, from bacterial to human, this bottleneck is too narrow for the quinone or quinol to pass and that a conformational change is required to open the channel. Moreover, the bottleneck is too narrow even for isoprenoid tail free passage. The closed structure can be an artifact of the crystallization packing forces, low temperature, or other unnatural conditions occurring in the structural data acquisition procedure that affect this flexible part of the enzyme. Two of the helices forming the bottleneck are in direct contact with the subunit (ND3) that was recently demonstrated to be involved in conformational changes during the redox proton pumping cycle, which indicates flexibility of that part of the enzyme. We conclude that the published structures are all locked in the unfunctional states and do not represent correctly the functional enzyme; we discuss possible ways to open the structure in the context of possible mechanisms of the enzyme.

Molecular machinery providing copper bioavailability for spermatozoa along the epididymial tubule in mouse

Progressive functional maturation of spermatozoa is completed during the transit of these cells through the epididymis, a tubule structure connecting a testicle to a vas deferens. Epididymal epithelial cells by means of their secretory and absorptive functions determine a highly specialized luminal microenvironment containing multiple organic and inorganic components. The latter include copper ions, which due to their redox properties are indispensable for critical homeostatic processes occurring in spermatozoa floating in different part of epididymis but can be potentially toxic. Main purpose of our study was to determine epididymal region-dependent expression and localization of copper transporters ensuring a tight control of copper concentration in epididymal fluid. We also aimed at identifying proteins responsible for copper uptake by spermatozoa and verifying whether this process is coordinated with copper supply to superoxide dismutase 1 (SOD1), a copper-dependent antioxidant enzyme. Our study identifies two ATPases-ATP7A, ATP7B and Slc31a1, major copper importers/exporters depending on their differential expression on epididymal polarized epithelial cells of the caput, corpus, and cauda. Next, ceruloplasmin seems to be a chief protein transporting copper in the epididymal fluid and providing this biometal to spermatozoa. The entry of copper to germ cells is mediated by Slc31a1 and is correlated with both expressions of copper chaperone for superoxide dismutase (CCS), copper chaperone directly providing copper ions to SOD1 and with the expression and activity of the latter. Our results outline a network of cooperating copper binding proteins expressed in epididymal epithelium and in spermatozoa that orchestrate bioavailability of this microelement for gametes and protect them against copper toxicity.

The redox-coupled proton-channel opening in cytochrome c oxidase

The interplay of cytochrome c oxidase's cofactor electrostatics, long-range conformational changes, H-bond rearrangement, and water dynamics enables transient proton-channel activation.

Explaining leak states in the proton pump of heme-copper oxidases observed in single-molecule experiments

Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Generally, these models associate, more or less directly, all translocation events with redox transitions. Although they can account for many phenomenological aspects of the pump, evidences from single-molecules experiments about leak states of the pump represent a formidable challenge. Disconnecting the redox-linked pK_a shifts of the proton loading site from the external barriers, we obtain a simple stochastic mechanism which behaves similarly to the real enzyme, able to reverse the flow of the proton transfer.

Allosteric Cooperativity in Proton Energy Conversion in A1-Type Cytochrome c Oxidase

Cytochrome c oxidase (CcO), the Cu_A, heme a, heme a₃, Cu_B enzyme of respiratory chain, converts the free energy released by aerobic cytochrome c oxidation into a membrane electrochemical proton gradient (ΔμH⁺). ΔμH⁺ derives from the membrane anisotropic arrangement of dioxygen reduction to two water molecules and transmembrane proton pumping from a negative (N) space to a positive (P) space separated by the membrane. Spectroscopic, potentiometric, and X-ray crystallographic analyses characterize allosteric cooperativity of dioxygen binding and reduction with protonmotive conformational states of CcO. These studies show that allosteric cooperativity stabilizes the favorable conformational state for conversion of redox energy into a transmembrane ΔμH⁺.

Geometric and Electronic Structure Contributions to O-O Cleavage and the Resultant Intermediate Generated in Heme-Copper Oxidases

This study investigates the mechanism of O-O bond cleavage in heme-copper oxidase (HCO) enzymes, combining experimental and computational insights from enzyme intermediates and synthetic models. It is determined that HCOs undergo a proton-initiated O-O cleavage mechanism where a single water molecule in the active site enables proton transfer (PT) from the cross-linked tyrosine to a peroxo ligand bridging the heme Fe^III and Cu^II, and multiple H-bonding interactions lower the tyrosine p K_a. Due to sterics within the active site, the proton must either transfer initially to the O(Fe) (a high-energy intermediate), or from another residue over a ∼10 Å distance to reach the O(Cu) atom directly. While the distance between the H⁺ donor (Tyr) and acceptor (O(Cu)) results in a barrier to PT, this separation is critical for the low barrier to O-O cleavage as it enhances backbonding from Fe into the O₂^2- σ* orbital. Thus, PT from Tyr precedes O-O elongation and is rate-limiting, consistent with available kinetic data. The electron transfers from tyrosinate after the barrier via a superexchange pathway provided by the cross-link, generating intermediate P_M. P_M is evaluated using available experimental data. The geometric structure contains an Fe^IV═O that is H-bonded to the Cu^II-OH. The electronic structure is a singlet, where the Fe^IV and Cu^II are antiferromagnetically coupled through the H-bond between the oxo(Fe) and hydroxo(Cu) ligands, while the Cu^II and Tyr^• are ferromagnetically coupled due their delocalization into orthogonal magnetic orbitals on the cross-linked His residue. These findings provide critical insights into the mechanism of efficient O₂ reduction in HCOs, and the nature of the P_M intermediate that couples this reaction to proton pumping.

Electric field modulated redox-driven protonation and hydration energetics in energy converting enzymes

Biological energy conversion is catalysed by proton-coupled electron transfer (PCET) reactions that form the chemical basis of respiratory and photosynthetic enzymes. Despite recent advances in structural, biophysical, and computational experiments, the mechanistic principles of these reactions still remain elusive. Based on common functional features observed in redox enzymes, we study here generic mechanistic models for water-mediated long-range PCET reactions. We show how a redox reaction within a buried protein environment creates an electric field that induces hydration changes between the proton acceptor and donor groups, and in turn, lowers the reaction barrier and increases the thermodynamic driving forces for the water-mediated PCET process. We predict linear free energy relationships, and discuss the proposed mechanism in context of PCET in cytochrome c oxidase.

A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii

The biological route for nitrogen gas entering the biosphere is reduction to ammonia by the nitrogenase enzyme, which is inactivated by oxygen. Three types of nitrogenase exist, the least-studied of which is the iron-only nitrogenase. The Anf3 protein in the bacterium Rhodobacter capsulatus is essential for diazotrophic (i.e. nitrogen-fixing) growth with the iron-only nitrogenase, but its enzymatic activity and function are unknown. Here, we biochemically and structurally characterize Anf3 from the model diazotrophic bacterium Azotobacter vinelandii Determining the Anf3 crystal structure to atomic resolution, we observed that it is a dimeric flavocytochrome with an unusually close interaction between the heme and the FAD cofactors. Measuring the reduction potentials by spectroelectrochemical redox titration, we observed values of -420 ± 10 and -330 ± 10 mV for the two FAD potentials and -340 ± 1 mV for the heme. We further show that Anf3 accepts electrons from spinach ferredoxin and that Anf3 consumes oxygen without generating superoxide or hydrogen peroxide. We predict that Anf3 protects the iron-only nitrogenase from oxygen inactivation by functioning as an oxidase in respiratory protection, with flavodoxin or ferredoxin as the physiological electron donors.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Tyrosine-Rich Peptides as a Platform for Assembly and Material Synthesis

The self-assembly of biomolecules can provide a new approach for the design of functional systems with a diverse range of hierarchical nanoarchitectures and atomically defined structures. In this regard, peptides, particularly short peptides, are attractive building blocks because of their ease of establishing structure-property relationships, their productive synthesis, and the possibility of their hybridization with other motifs. Several assembling peptides, such as ionic-complementary peptides, cyclic peptides, peptide amphiphiles, the Fmoc-peptide, and aromatic dipeptides, are widely studied. Recently, studies on material synthesis and the application of tyrosine-rich short peptide-based systems have demonstrated that tyrosine units serve as not only excellent assembly motifs but also multifunctional templates. Tyrosine has a phenolic functional group that contributes to π-π interactions for conformation control and efficient charge transport by proton-coupled electron-transfer reactions in natural systems. Here, the critical roles of the tyrosine motif with respect to its electrochemical, chemical, and structural properties are discussed and recent discoveries and advances made in tyrosine-rich short peptide systems from self-assembled structures to peptide/inorganic hybrid materials are highlighted. A brief account of the opportunities in design optimization and the applications of tyrosine peptide-based biomimetic materials is included.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Atomistic insights into cardiolipin binding sites of cytochrome c oxidase

Mitochondrial cytochrome c oxidase couples the reduction of oxygen to proton pumping. Despite an overall good understanding of its molecular mechanism, the role of cardiolipin in protein function is not understood. Here, we have studied the cardiolipin-protein interactions in a dynamic context by means of atomistic molecular dynamics simulations performed on the entire structure of monomeric and dimeric forms of the enzyme. Several microseconds of simulation data reveal that the crystallographic cardiolipin molecules that glue two monomers together bind weakly in hybrid and single-component lipid bilayers and dissociate rapidly. Atomistic simulations performed in the absence of tightly bound cardiolipin molecules strongly perturb the structural integrity of subunits III and VIIa, thereby highlighting an indispensable nature of lipid-protein interactions in enzyme function such as proton uptake and oxygen channeling. Our results demonstrate the strength of molecular simulations in providing direct atomic description of lipid-protein processes that are difficult to achieve experimentally.

Redox-Driven Proton Pumps of the Respiratory Chain

In aerobic cells, the proton gradient that drives ATP synthesis is created by three different proton pumps-membrane enzymes of the respiratory electron transport chain known as complex I, III, and IV. Despite the striking dissimilarity of structures and apparent differences in molecular mechanisms of proton pumping, all three enzymes have much in common and employ the same universal physical principles of converting redox energy to proton pumping. In this study, we describe a simple mathematical model that illustrates the general principles of redox-driven proton pumps and discuss their implementation in complex I, III, and IV of the respiratory chain.

Investigating the Many Roles of Internal Water in Cytochrome c Oxidase

Cytochrome c oxidase (C cO) is the terminal enzyme in the respiratory electron transport chain. As part of its catalytic cycle, C cO transfers protons to its Fe-Cu binuclear center (BNC) to reduce oxygen, and in addition, it pumps protons across the mitochondrial inner, or bacterial, membrane where it is located. It is believed that this proton transport is facilitated by a network of water chains inside the enzyme. Here we present an analysis of the hydration of C cO, including the BNC region, using a semi-empirical hydration program, Dowser++, recently developed in our group. Using high-resolution X-ray data, we show that Dowser++ predictions match very accurately the water molecules seen in the D- and K-channels of C cO, as well as in the vicinity of its BNC. Moreover, Dowser++ predicts many more internal water molecules than is typically seen in the experiment. However, no significant hydration of the catalytic cavity in C cO described recently in the literature is observed. As Dowser++ itself does not account for structural changes of the protein, this result supports the earlier assessment that the proposed wetting transition in the catalytic cavity can only either be due to structural rearrangements of BNC, possibly induced by the charges during the catalytic cycle, or occur transiently, in concert with the proton transfer. Molecular dynamics simulations were performed to investigate the global dynamic nature of Dowser++ waters in C cO, and the results suggest a consistent explanation as to why some predicted water molecules would be missing in the experimental structures. Furthermore, in light of the significant protein hydration predicted by Dowser++, the dielectric constant of the hydrated cavities in C cO was also investigated using the Fröhlich-Kirkwood model; the results indicate that in the cavities where water is packed sufficiently densely the dielectric constant can approach values comparable even to that of bulk water.

Dewetting transitions coupled to K-channel activation in cytochrome c oxidase

Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.

Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane. CcO employs the so-called D- and K-channels for proton uptake, but the molecular mechanism for activation of the K-channel has remained elusive for decades. We show here by combining large-scale atomistic molecular simulations with graph-theoretical water network analysis, and hybrid quantum/classical (QM/MM) free energy calculations, that the K-channel is activated by formation of a reactive oxidized intermediate in the binuclear heme a₃/Cu_B active site. This state induces electrostatic, hydration, and conformational changes that lower the barrier for proton transfer along the K-channel by dewetting pathways that connect the D-channel with the active site. Our combined results reconcile previous experimental findings and indicate that water dynamics plays a decisive role in the proton pumping machinery in CcO.

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase

This review focuses on the type A cytochrome c oxidases (CcO), which are found in all mitochondria and also in several aerobic bacteria. CcO catalyzes the respiratory reduction of dioxygen (O₂) to water by an intriguing mechanism, the details of which are fairly well understood today as a result of research for over four decades. Perhaps even more intriguingly, the membrane-bound CcO couples the O₂ reduction chemistry to translocation of protons across the membrane, thus contributing to generation of the electrochemical proton gradient that is used to drive the synthesis of ATP as catalyzed by the rotary ATP synthase in the same membrane. After reviewing the structure of the core subunits of CcO, the active site, and the transfer paths of electrons, protons, oxygen, and water, we describe the states of the catalytic cycle and point out the few remaining uncertainties. Finally, we discuss the mechanism of proton translocation and the controversies in that area that still prevail.

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations

Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment. The majority of residues in the H channel do not undergo large conformational fluctuations. Its upper and middle regions have adequate hydration and H-bonding residues to form potential proton-conducting channels, and Asp51 exhibits conformational fluctuations that have been observed crystallographically. In contrast, throughout the simulations, we do not observe transient water networks that could support proton transfer from the N phase toward heme a via neutral His413, regardless of a labile H bond between Ser382 and the hydroxyethylfarnesyl group of heme a In fact, the region around His413 only became sufficiently hydrated when His413 was fixed in its protonated imidazolium state, but its calculated pK_a is too low for this to provide the means to create a proton transfer pathway. Our simulations show that the electric dipole moment of residues around heme a changes with the redox state, hence suggesting that the H channel could play a more general role as a dielectric well.

Cavity hydration dynamics in cytochrome c oxidase and functional implications

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O₂ reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O₂ reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively [Formula: see text]4 [Formula: see text]s) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a₃ and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of [Formula: see text]2-[Formula: see text]s trajectories suggests that hydration-level change occurs on the timescale of 100-200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

MtDNA depletion influences the transition of CD44 subtypes in human prostate cancer DU145 cells

Our earlier study revealed that long-term ethidium bromide application causes mitochondrial DNA depletion in human prostate cancer DU145 cell line (DU145MtDP), and this DU145MtDP subline appears to have expanded CD44Bright cell population than its parental wild type DU145 cells (DU145WT). Increasing evidence suggests that CD44Bright cells are highly cancer stem cell like, but it is not clear about their dynamic transition between CD44Dim and CD44Bright phenotypes in prostate cancer cells, and how it is affected by mitochondrial DNA depletion. To address these questions, four cell subpopulations were isolated from both DU145WT and DU145MtDP cell lines based on their CD44 expression level and mitochondrial membrane potential. The cell motility and colony formation capability of the fluorescence activated cell sorting–sorted cell subpopulations were further examined. It was discovered in the DU145WT cells that CD44Dim cells could transit into both CD44Dim and CD44Bright phenotypes and that CD44Bright cells were prone to sustain their CD44Bright phenotype as renewal. However, such transition principle was altered in the DU145MtDP cells, in which CD44Bright cells showed similar capability to sustain a CD44Bright phenotype, while the transition of CD44Dim cells to CD44Bright were suppressed. It is concluded that mitochondrial DNA depletion in the human prostate cancer DU145 cells influences their renewal and CD44 subphenotype transition. Such alterations may be the driving force for the enrichment of CD44Bright DU145 cells after the mitochondrial DNA depletion, although the molecular mechanisms remain unclear.

Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease

Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen. COX consists of 14 subunits, three and eleven encoded, respectively, by the mitochondrial and nuclear DNA. Tissue- and condition-specific isoforms have only been reported for COX but not for the other oxidative phosphorylation complexes, suggesting a fundamental requirement to fine-tune and regulate the essentially irreversible reaction catalyzed by COX. This article briefly discusses the assembly of COX in mammals and then reviews the functions of the six nuclear-encoded COX subunits that are expressed as isoforms in specialized tissues including those of the liver, heart and skeletal muscle, lung, and testes: COX IV-1, COX IV-2, NDUFA4, NDUFA4L2, COX VIaL, COX VIaH, COX VIb-1, COX VIb-2, COX VIIaH, COX VIIaL, COX VIIaR, COX VIIIH/L, and COX VIII-3. We propose a model in which the isoforms mediate the interconnected regulation of COX by (1) adjusting basal enzyme activity to mitochondrial capacity of a given tissue; (2) allosteric regulation to adjust energy production to need; (3) altering proton pumping efficiency under certain conditions, contributing to thermogenesis; (4) providing a platform for tissue-specific signaling; (5) stabilizing the COX dimer; and (6) modulating supercomplex formation.

Testing for the Occurrence of Selective Episodes During the Divergence of Otophysan Fishes: Insights from Mitogenomics

How natural selection shapes biodiversity constitutes a topic of renewed interest during the last few decades. The division Otophysi comprises approximately two-thirds of freshwater fish diversity and probably underwent an extensive adaptive radiation derived from a single invasion of the supercontinent Pangaea, giving place to the evolution of the main five Otophysan lineages during a short period of time. Little is known about the factors involved in the processes that lead to lineage diversification among this group of fishes and identifying directional selection acting over protein-coding genes could offer clues about the processes acting on species diversification. The main objective of this study was to explore the otophysan mitochondrial genome evolution, in order to account for the possible signatures of selective events in this lineage, and to explore for the functional connotations of these molecular substitutions. Mainly, three different approaches were used: the "ω-based" BS-REL and MEME methods, implemented in the DATAMONKEY web server, and analysis of selection on amino acid properties, implemented in the software TreeSAAP. We found evidence of selective episodes along several branches of the evolutionary history of othophysan fishes. Analyses carried out using the BS-REL algorithm suggest episodic diversifying selection at basal branches of the otophysan lineage, which was also supported by analyses implemented in MEME and TreeSAAP. These results suggest that throughout the Siluriformes radiation, an important number of adaptive changes occurred in their mitochondrial genome. The metabolic consequences and ecological correlates of these molecular substitutions should be addressed in future studies.

Energy-Related Small Molecule Activation Reactions: Oxygen Reduction and Hydrogen and Oxygen Evolution Reactions Catalyzed by Porphyrin- and Corrole-Based Systems

Globally increasing energy demands and environmental concerns related to the use of fossil fuels have stimulated extensive research to identify new energy systems and economies that are sustainable, clean, low cost, and environmentally benign. Hydrogen generation from solar-driven water splitting is a promising strategy to store solar energy in chemical bonds. The subsequent combustion of hydrogen in fuel cells produces electric energy, and the only exhaust is water. These two reactions compose an ideal process to provide clean and sustainable energy. In such a process, a hydrogen evolution reaction (HER), an oxygen evolution reaction (OER) during water splitting, and an oxygen reduction reaction (ORR) as a fuel cell cathodic reaction are key steps that affect the efficiency of the overall energy conversion. Catalysts play key roles in this process by improving the kinetics of these reactions. Porphyrin-based and corrole-based systems are versatile and can efficiently catalyze the ORR, OER, and HER. Because of the significance of energy-related small molecule activation, this review covers recent progress in hydrogen evolution, oxygen evolution, and oxygen reduction reactions catalyzed by porphyrins and corroles.

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

The cytochrome (cyt) bc₁ complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q_i-site of the cyt bc₁ complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q_i-site to facilitate binding of half-protonated semiquinone – a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q_i-site.

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H₃O⁺ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O₂ bound to heme a₃ To block backward proton movement, the water channel remains closed after O₂ binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O₂ binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg²⁺ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu¹⁹⁸, which bridges the Mg²⁺ and Cu_A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu_A-Glu¹⁹⁸-Mg²⁺ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg²⁺-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.

Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations

Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

A Protonated Water Cluster as a Transient Proton-Loading Site in Cytochrome c Oxidase

Cytochrome c oxidase (CcO) is a redox-driven proton pump that powers aerobic respiratory chains. We show here by multi-scale molecular simulations that a protonated water cluster near the active site is likely to serve as the transient proton-loading site (PLS) that stores a proton during the pumping process. The pKa of this water cluster is sensitive to the redox states of the enzyme, showing distinct similarities to other energy converting proton pumps.

Dowser++, a new method of hydrating protein structures

A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi-empirical modification of a popular program for protein hydration Dowser, and the usage of protocols AutoDock Vina, and WaterDock. The positions of water molecules predicted by Dowser++ were compared with experimental data for a set of 14 high-resolution crystal structures of oligopeptide-binding protein (OppA) containing a large number of resolved internal water molecules, as well as for the D- and K-channels of cytochrome c oxidase, and the recent data on PSII. Comparison is also made with the predictions of the original Dowser, and its improved version, Dowser+, described in our previous publication. We also present a model for quantitative estimation of the quality of water molecules placement made by a program, which includes an assumption of possible false negative data from the crystallographic analysis. The comparison of predictions made by Dowser++, Dowser and Dowser+ demonstrates significant improvement of predictive power of the new method. Proteins 2016; 84:1347-1357. © 2016 Wiley Periodicals, Inc.

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.

A simulation-guided fluorescence correlation spectroscopy tool to investigate the protonation dynamics of cytochrome c oxidase

Fluorescence correlation spectroscopy (FCS) is a single molecule based technique to temporally resolve rate-dependent processes by correlating the fluorescence fluctuations of individual molecules traversing through a confocal volume. In addition, chemical processes like protonation or intersystem crossing can be monitored in the sub-microsecond range. FCS thereby provides an excellent tool for investigations of protonation dynamics in proton pumps like cytochrome c oxidase (CcO). To achieve this, the pH-dependent fluorescent dye fluorescein was attached as a protonation probe to the CcO surface via site-specific labeling of single reactive cysteines that are located close to the entry point of a proton input channel (K-pathway). The analysis of protonation dynamics is complicated by overlapping triplet and protonation rates of the fluorophore. A Monte Carlo simulation based algorithm was developed to facilitate discrimination of these temporally overlapping processes thus allowing for improved protonation reaction rate determination. Using this simulation-guided approach we determined precise local proton association and dissociation rates and provide information about protein surface effects, such as proton collecting antennae, on the transport properties of proton transfer channels.

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations

Cytochrome c oxidases (CcOs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes reduce dioxygen (O(2)) to water and, simultaneously, generate a transmembrane electrochemical proton gradient. Despite their importance in the aerobic metabolism and the large amount of structural and biochemical data available for the A1-type CcO family, there is still no consensually accepted description of the molecular mechanisms operating in this protein. A substantial number of questions about the CcO's working mechanism remain to be answered, including how the protonation behavior of some key residues is modulated during a reduction cycle and how is the conformation of the protein affected by protonation. The main objective of this work was to study the protonation-conformation coupling in CcOs and identify the molecular factors that control the protonation state of some key residues. In order to directly capture the interplay between protonation and conformational effects, we have performed constant-pH MD simulations of an A1-type CcO inserted into a lipid bilayer in two redox states (oxidized and reduced) at physiological pH. From the simulations, we were able to identify several groups with unusual titration behavior that are highly dependent on the protein redox state, including the A-propionate from heme a and the D-propionate from heme a3, two key groups possibly involved in proton pumping. The protonation state of these two groups is heavily influenced by subtle conformational changes in the protein (notably of R481(I) and R482(I)) and by small changes in the hydrogen bond network.

Monte Carlo Simulations of Glu-242 in Cytochrome c Oxidase

Monte Carlo (MC) simulations of conformational changes and protonation of Glu-242, a key residue that shuttles protons in cytochrome c oxidase (CcO), are reported. Previous studies suggest that this residue may play a role of the valve of the enzyme proton pump. Here we examine how sensitive the results of simulations are to the computational method used. We applied both molecular mechanic (MM) and hybrid quantum mechanic:molecular mechanic (QM:MM) methods and find that the results are qualitatively different. The results indicate that the mechanism for proton gating in CcO is still an open issue.

The role of the K-channel and the active-site tyrosine in the catalytic mechanism of cytochrome c oxidase

The active site of cytochrome c oxidase (CcO) comprises an oxygen-binding heme, a nearby copper ion (CuB), and a tyrosine residue that is covalently linked to one of the histidine ligands of CuB. Two proton-conducting pathways are observed in CcO, namely the D- and the K-channels, which are used to transfer protons either to the active site of oxygen reduction (substrate protons) or for pumping. Proton transfer through the D-channel is very fast, and its role in efficient transfer of both substrate and pumped protons is well established. However, it has not been fully clear why a separate K-channel is required, apparently for the supply of substrate protons only. In this work, we have analysed the available experimental and computational data, based on which we provide new perspectives on the role of the K-channel. Our analysis suggests that proton transfer in the K-channel may be gated by the protonation state of the active-site tyrosine (Tyr244) and that the neutral radical form of this residue has a more general role in the CcO mechanism than thought previously. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins

An important challenge in the simulation of biomolecular systems is a quantitative description of the protonation and deprotonation process of amino acid residues. Despite the seeming simplicity of adding or removing a positively charged hydrogen nucleus, simulating the actual protonation/deprotonation process is inherently difficult. It requires both the explicit treatment of the excess proton, including its charge defect delocalization and Grotthuss shuttling through inhomogeneous moieties (water and amino residues), and extensive sampling of coupled condensed phase motions. In a recent paper (J. Chem. Theory Comput. 2014, 10, 2729-2737), a multiscale approach was developed to map high-level quantum mechanics/molecular mechanics (QM/MM) data into a multiscale reactive molecular dynamics (MS-RMD) model in order to describe amino acid deprotonation in bulk water. In this article, we extend the fitting approach (called FitRMD) to create MS-RMD models for ionizable amino acids within proteins. The resulting models are shown to faithfully reproduce the free energy profiles of the reference QM/MM Hamiltonian for PT inside an example protein, the ClC-ec1 H(+)/Cl(-) antiporter. Moreover, we show that the resulting MS-RMD models are computationally efficient enough to then characterize more complex 2-dimensional free energy surfaces due to slow degrees of freedom such as water hydration of internal protein cavities that can be inherently coupled to the excess proton charge translocation. The FitRMD method is thus shown to be an effective way to map ab initio level accuracy into a much more computationally efficient reactive MD method in order to explicitly simulate and quantitatively describe amino acid protonation/deprotonation in proteins.

Catalytic reduction of dioxygen with modified Thermus thermophilus cytochrome c552

Efficient catalysis of the oxygen reduction reaction (ORR) is of central importance to function in fuel cells. Metalloproteins, such as laccase (Cu) or cytochrome c oxidase (Cu/Fe-heme) carry out the 4H(+)/4e(-) reduction quite efficiently, but using large, complex protein frameworks. Smaller heme proteins also can carry out ORR, but less efficiently. To gain greater insight into features that promote efficient ORR, we expressed, characterized, and investigated the electrochemical behavior of six new mutants of cytochrome c552 from Thermus thermophilus: V49S/M69A, V49T/M69A, L29D/V49S/M69A, P27A/P28A/L29D/V49S/M69A, and P27A/P28A/L29D/V49T/M69A. Mutation to V49 causes only minor shifts to Fe(III/II) reduction potentials (E°'), but introduction of Ser provides a hydrogen bond donor that slightly enhances oxygen reduction activity. Mutation of L29 to D induces small shifts in heme optical spectra, but not to E°' (within experimental error). Replacement of P27 and P28 with A in both positions induces a -50 mV shift in E°', again with small changes to the optical spectra. Both the optical spectra and reduction potentials have signatures consistent with peroxidase enzymes. The V49S and V49T mutations have the largest impact of ORR catalysis, suggesting that increased electron density at the Fe site does not improve O2 reduction chemistry.