The Redox-Active Tyrosine Is Essential for Proton Pumping in Cytochrome c Oxidase

Structural and functional mechanisms of cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain in mitochondria. It catalyzes the four-electron reduction of O2 to H2O and harnesses the redox energy to drive unidirectional proton translocation against a proton electrochemical gradient. A great deal of research has been conducted to comprehend the molecular properties of CcO. However, the mechanism by which the oxygen reduction reaction is coupled to proton translocation remains poorly understood. Here, we review the chemical properties of a variety of key oxygen intermediates of bovine CcO (bCcO) revealed by time-resolved resonance Raman spectroscopy and the structural features of the enzyme uncovered by serial femtosecond crystallography, an innovative technique that allows structural determination at room temperature without radiation damage. The implications of these data on the proton translocation mechanism are discussed.

Reduction of molecular oxygen in flavodiiron proteins - Catalytic mechanism and comparison to heme-copper oxidases

The family of flavodiiron proteins (FDPs) plays an important role in the scavenging and detoxification of both molecular oxygen and nitric oxide. Using electrons from a flavin mononucleotide cofactor molecular oxygen is reduced to water and nitric oxide is reduced to nitrous oxide and water. While the mechanism for NO reduction in FDPs has been studied extensively, there is very little information available about O2 reduction. Here we use hybrid density functional theory (DFT) to study the mechanism for O2 reduction in FDPs. An important finding is that a proton coupled reduction is needed after the O2 molecule has bound to the diferrous diiron active site and before the OO bond can be cleaved. This is in contrast to the mechanism for NO reduction, where both NN bond formation and NO bond cleavage occurs from the same starting structure without any further reduction, according to both experimental and computational results. This computational result for the O2 reduction mechanism should be possible to evaluate experimentally. Another difference between the two substrates is that the actual OO bond cleavage barrier is low, and not involved in rate-limiting the reduction process, while the barrier connected with bond cleavage/formation in the NO reduction process is of similar height as the rate-limiting steps. We suggest that these results may be part of the explanation for the generally higher activity for O2 reduction as compared to NO reduction in most FDPs. Comparisons are also made to the O2 reduction reaction in the family of heme‑copper oxidases.

Biomolecular investigations into BBI reveal an enzymatic mechanism for PUFA isomerisation in bifidobacterium CFA bioconversion strains

Multiple species of Bifidobacterium exhibit the ability to bioconvert conjugated fatty acids (CFAs), which is considered an important pathway for these strains to promote host health. However, there has been limited progress in understanding the enzymatic mechanism of CFA bioconversion by bifidobacteria, despite the increasing number of studies identifying CFA-producing strains. The protein responsible for polyunsaturated fatty acid (PUFA) isomerization in B. breve CCFM683 has recently been discovered and named BBI, providing a starting point for exploring Bifidobacterium isomerases (BIs). This study presents the sequence classification of membrane-bound isomerases from four common Bifidobacterium species that produce CFA. Heterologous expression, purification, and enzymatic studies of the typical sequences revealed that all possess a single c9, t11 isomer as the product and share common features in terms of enzymatic properties and catalytic kinetics. Using molecular docking and alanine scanning, Lys84, Tyr198, Asn202, and Leu245 located in the binding pocket were identified as critical to the catalytic activity, a finding further confirmed by site-directed mutagenesis-based screening assays. Overall, these findings provide insightful knowledge concerning the molecular mechanisms of BIs. This will open up additional opportunities for the use of bifidobacteria and CFAs in probiotic foods and precision nutrition.

Reaction pathways, proton transfer, and proton pumping in ba3 class cytochrome c oxidase: perspectives from DFT quantum chemistry and molecular dynamics

After drawing comparisons between the reaction pathways of cytochrome c oxidase (CcO, Complex 4) and the preceding complex cytochrome bc1 (Complex 3), both being proton pumping complexes along the electron transport chain, we provide an analysis of the reaction pathways in bacterial ba3 class CcO, comparing spectroscopic results and kinetics observations with results from DFT calculations. For an important arc of the catalytic cycle in CcO, we can trace the energy pathways for the chemical protons and show how these pathways drive proton pumping of the vectorial protons. We then explore the proton loading network above the Fe heme a3-CuB catalytic center, showing how protons are loaded in and then released by combining DFT-based reaction energies with molecular dynamics simulations over states of that cycle. We also propose some additional reaction pathways for the chemical and vector protons based on our recent work with spectroscopic support.

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.

Structural insights into functional properties of the oxidized form of cytochrome c oxidase

Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.

Impedimetric nano-collision Escherichia coli analysis based on Silver-Gold bimetallic nanoparticles

An impedimetric detection of E. coli was developed using chemically synthesised bimetallic Ag-Au (1:2) nanoparticles (NPs). The UV-visible spectra of the NPs had absorption bands at 470 and 580 nm for Ag NPs and Au NPs, respectively. In the presence of E. coli, a negative potential shift and a blue shift was observed in the voltammograms and spectra respectively. The complex formed had an oxidation potential at + 0.95 V. Technique choice was based on sensitivity comparison of Differential pulse voltammetry, cyclic voltammetry and impedance spectroscopy in 0.1 M PBS with Impedance being the best choice. Optimum sensing conditions of the NPs-E. coli complex for NPs concentration, incubation period, method modulation amplitude and applied potential were 5 mM, 20 min, 10 mV and + 0.5 V, respectively. The sensor's linearity range, lower limits of detection and quantification were found to be 10¹-10⁷, 1.88 × 10¹, 2.34 × 10² cells/mL, respectively. The sensor's applicability was validated by repeatability, stability and selectivity studies showing minimum changes in signal. Potential usage of the sensor in real samples was demonstrated by standard addition analysis of sea and River water samples as well as recovery of spiked water and fruit juices with acceptable % RSD < 2%.

Structural basis for functional properties of cytochrome c oxidase

Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis1. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes2. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation2,3. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX)4, we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state5,6, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO.

Dietary Copper Deficiency Leads to Changes in Gene Expression Indicating an Increased Demand for NADH in the Prefrontal Cortex of the Rat's Brain

Copper is an essential element to brain cells as it is a cofactor and a structural component of various enzymes involved in energy metabolism pathways. Accumulating evidence points to the pivotal role of copper deficiency in neurodegeneration resulting from impaired copper homeostasis. Despite the indisputable role of copper in mitochondrial respiration, its homeostasis regulation in the brain tissue remains unclear. The assessment of changes in the expression of genes encoding key pathways of energy metabolism can greatly benefit further studies exploring copper's role in neurodegeneration. Using a rat model, we investigate whether the replacement of the inorganic form of copper with metallic nanoparticles containing copper or complete deprivation of copper from the diet have an impact on the expression of genes involved in energy metabolism in the prefrontal cortex of the rats' brain. Herein, we indicate that removing inorganic copper from the normal standard diet or the replacement with copper nanoparticles can lead to programmed energy metabolism changes. It can be recognized that some of these changes indicate an increased demand for NADH in the prefrontal cortex of the rat's brain, probably as a result of adaptation effect.

Diversity of Cytochrome c Oxidase Assembly Proteins in Bacteria

Cytochrome c oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome c oxidase show diversity in bacteria. Using the model organisms Bacillus subtilis, Corynebacterium glutamicum, Paracoccus denitrificans, and Rhodobacter sphaeroides, the present review focuses on proteins for assembly of the heme a, heme a₃, Cu_B, and Cu_A metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome c oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria.

Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target

Cytochrome bd is a triheme copper-free terminal oxidase in membrane respiratory chains of prokaryotes. This unique molecular machine couples electron transfer from quinol to O₂ with the generation of a proton motive force without proton pumping. Apart from energy conservation, the bd enzyme plays an additional key role in the microbial cell, being involved in the response to different environmental stressors. Cytochrome bd promotes virulence in a number of pathogenic species that makes it a suitable molecular drug target candidate. This review focuses on recent advances in understanding the structure of cytochrome bd and the development of its selective inhibitors.

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.

Kinetic evidence for the transiently shifted acidity constant of histidine linked to paramagnetic tyrosine probed by intramolecular electron transfer in oxidized peptides

The kinetics of electron transfer (ET) from tyrosine (Tyr) to short-lived histidine (His) radicals in peptides of different structures was monitored using time-resolved chemically induced dynamic nuclear polarization (CIDNP) to follow the reduction of the His radicals using NMR detection of the diamagnetic hyperpolarized reaction products. In aqueous solution over a wide pH range, His radicals were generated in situ in the photo-induced reaction with the photosensitizer, 3,3',4,4'-tetracarboxy benzophenone. Model simulations of the CIDNP kinetics provided pH-dependent rate constants of intra- and intermolecular ET, and the pH dependencies of the reaction under study were interpreted in terms of protonation states of the reactants and the product, His with either protonated or neutral imidazole. In some cases, an increase of pKa of imidazole in the presence of the short-lived radical center at a nearby Tyr residue was revealed. Interpretation of the obtained pH dependencies made is possible to quantify the degree of paramagnetic shift of the acidity constant of the imidazole of the His residue in the peptides with a Tyr residue in its paramagnetic state, and to correlate this degree with the intramolecular ET rate constant - a higher intramolecular ET rate constant corresponded to a greater acidity constant shift.