Probing protonation/deprotonation of tyrosine residues in cytochrome ba3 oxidase from Thermus thermophilus by time-resolved step-scan Fourier transform infrared spectroscopy

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.

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.

Membrane Protein Activity Induces Specific Molecular Changes in Nanodiscs Monitored by FTIR Difference Spectroscopy

It is well known that lipids neighboring integral membrane proteins directly influence their function. The opposite effect is true as well, as membrane proteins undergo structural changes after activation and thus perturb the lipidic environment. Here, we studied the interaction between these molecular machines and the lipid bilayer by observing changes in the lipid vibrational bands via FTIR spectroscopy. Membrane proteins with different functionalities have been reconstituted into lipid nanodiscs: Microbial rhodopsins that act as light-activated ion pumps (the proton pumps NsXeR and UmRh1, and the chloride pump NmHR) or as sensors (NpSRII), as well as the electron-driven cytochrome c oxidase RsCcO. The effects of the structural changes on the surrounding lipid phase are compared to mechanically induced lateral tension exerted by the light-activatable lipid analogue AzoPC. With the help of isotopologues, we show that the ν(C = O) ester band of the glycerol backbone reports on changes in the lipids’ collective state induced by mechanical changes in the transmembrane proteins. The perturbation of the nanodisc lipids seems to involve their phase and/or packing state. ¹³C-labeling of the scaffold protein shows that its structure also responds to the mechanical expansion of the lipid bilayer.

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.

Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations

Cytochrome c oxidase (CcO) is a transmembrane protein complex that reduces molecular oxygen to water while translocating protons across the mitochondrial membrane. Changes in the redox states of its cofactors trigger both O₂ reduction and vectorial proton transfer, which includes a proton-loading site, yet unidentified. In this work, we exploited carbon monoxide (CO) as a vibrational Stark effect (VSE) probe at the binuclear center of CcO from Rhodobacter sphaeroides. The CO stretching frequency was monitored as a function of the electrical potential, using Fourier transform infrared (FTIR) absorption spectroelectrochemistry. We observed three different redox states (R₄CO, R₂CO, and O), determined their midpoint potential, and compared the resulting electric field to electrostatic calculations. A change in the local electric field strength of +2.9 MV/cm was derived, which was induced by the redox transition from R₄CO to R₂CO. We performed potential jump experiments to accumulate the R₂CO and R₄CO species and studied the FTIR difference spectra in the protein fingerprint region. The comparison of the experimental and computational results reveals that the key glutamic acid residue E286 is protonated in the observed states, and that its hydrogen-bonding environment is disturbed upon the redox transition of heme a₃. Our experiments also suggest propionate A of heme a₃ changing its protonation state in concert with the redox state of a second cofactor, heme a. This supports the role of propionic acid side chains as part of the proton-loading site.

Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain

DNA Gyrase is a type II topoisomerase that utilizes the energy of ATP hydrolysis for introducing negative supercoils in DNA. The protein comprises two subunits GyrA and GyrB that form a GyrA₂GyrB₂ heterotetramer. GyrB subunit contains the N-terminal domain (GBNTD) for ATPase activity and the C-terminal domain (GBCTD) for interaction with GyrA and DNA. Earlier structural studies have revealed three different conformational states for GBNTD during ATP hydrolysis defined as open, semi-open, and closed. Here we report, the three-dimensional structure of a new transient closed conformation of GBNTD from Salmonella Typhi (StGBNTD) at 1.94 Å resolution. Based on the structural analysis of this transient closed conformation, we propose the role of protein in the mechanism of ATP hydrolysis. We further explored the effect of pH on ATPase activity and structural stability of the GBNTD using CD and fluorescence spectroscopy at varying pH environment. Kinetic parameters obtained from the ATPase assay were correlated with its secondary and tertiary structure at their respective pH environment. The protein possessed maximum ATPase activity and structural stability at optimum pH 8. At acidic pH, a remarkable decrease in both enzymatic activity and structural stability was observed whereas at alkaline pH there was no significant change. The structural analysis of StGBNTD reveals the role of polar interactions in stabilizing the overall dimeric conformation of the protein.

Reversible temperature-dependent high- to low-spin transition in the heme Fe–Cu binuclear center of cytochrome ba3 oxidase

A reversible temperature-dependent high-spin to low-spin transition with T_1/2 = −60 °C has been observed in the resonance Raman spectra of the equilibrium reduced and photoreduced heme a₃ of the thermophilic ba₃ heme–copper oxidoreductase. The transition is based on the frequency shifts of the spin-state marker bands ν₂ (C_bC_b) and ν₁₀ (C_aC_m) and is attributed to the displacement of the heme iron along the heme normal as a consequence of the Fe–Np repulsion at temperature below −40 °C which will increase the ligand field strength forcing the pairing of d electrons into the lower energy orbitals.

A reversible temperature-dependent high- to low-spin transition with T_1/2 = −60 °C has been observed in the resonance Raman spectra of the equilibrium reduced and photoreduced heme a₃ of the thermophilic ba₃ heme–copper oxidoreductase.

The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation

Cytochrome c oxidase (CcO) is a membrane protein of the respiratory chain that catalytically reduces molecular oxygen (O2) to water while translocating protons across the membrane. The enzyme hosts two copper and two heme iron moieties (heme a/heme a3). The atomic details of the sequential steps that go along with this redox-driven proton translocation are a matter of debate. Particularly for the reductive phase of CcO that precedes oxygen binding experimental data are scarce. Here, we use CcO under anaerobic conditions where carbon monoxide (CO) is bound to heme a3 which in tandem with CuB forms the binuclear center (BNC). Fourier-transform infrared (FTIR) absorption spectroscopy is combined with electro-chemistry to probe different redox and protonation states populated by variation of the external electrostatic potential. With this approach, the redox behavior of heme a and the BNC could be separated and the corresponding redox potentials were determined. We also infer the protonation of one of the propionate side chains of heme a3 to correlate with the oxidation of heme a. Experimental changes in the local electric field surrounding CO bound to heme a3 are determined by their vibrational Stark effect and agree well with electrostatic computations. The comparison of experimental and computational results indicates that changes of the heme a3/CuB redox state are coupled to proton transfer towards heme a3. The latter supports the role of the heme a3 propionate D as proton loading site.

Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O2 Reduction in Heme-Copper Oxidases

This study evaluates the reaction of a biomimetic heme-peroxo-copper complex, {[(DCHIm)(F8)FeIII]-(O22-)-[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O-O bond that produces FeIV═O, CuII-OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme-copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O-O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O-O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O-O homolysis mechanism. The consequences of these findings are discussed in relation to O-O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e- required for O-O cleavage derive from the cross-linked Tyr residue present at the active site.

Splitting of the O-O bond at the heme-copper catalytic site of respiratory oxidases

Heme-copper oxidases catalyze the four-electron reduction of O₂ to H₂O at a catalytic site that is composed of a heme group, a copper ion (Cu_B), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (P_R ; Fe⁴⁺=O^2-, Cu_B²⁺-OH^-). We show that with the Thermus thermophilus ba₃ oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the P_R ferryl (τ ≅110 μs), which indicates that O₂ is reduced before the splitting of the O-O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe³⁺-O^--O^-(H⁺)], which is formed before the P_R ferryl. The rates of heme b oxidation and P_R ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O₂ reduction by heme-copper oxidases.

ns-μs Time-Resolved Step-Scan FTIR of ba₃ Oxidoreductase from Thermus thermophilus: Protonic Connectivity of w941-w946-w927

Time-resolved step-scan FTIR spectroscopy has been employed to probe the dynamics of the ba₃ oxidoreductase from Thermus thermophilus in the ns-μs time range and in the pH/pD 6–9 range. The data revealed a pH/pD sensitivity of the D372 residue and of the ring-A propionate of heme a₃. Based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the D372 and the ring-A propionate of heme a₃ is described.

Nanosecond ligand migration and functional protein relaxation in ba3 oxidoreductase: Structures of the B0, B1 and B2 intermediate states

Nanosecond time-resolved step-scan FTIR spectroscopy (nTRS (2) -FTIR) has been applied to literally probe the active site of the carbon monoxide (CO)-bound thermophilic ba3 heme-copper oxidoreductase as it executes its function. The nTRS (2) - snapshots of the photolysed heme a3 Fe-CO/CuB species captured a "transition state" whose side chains prevent the photolysed CO to enter the docking cavity. There are three sets of ba3 photoproduct bands of docked CO with different orientation exhibiting different kinetics. The trajectories of the "docked" CO at 2122, 2129 and 2137cm(-1) is referred to in the literature as B2, B1 and B0 intermediate states, respectively. The present data provided direct evidence for the role of water in controlling ligand orientation in an intracavity protein environment.

FTIR spectral signature of anticancer drugs. Can drug mode of action be identified?

Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.

Photobiochemical production of carbon monoxide by Thermus thermophilus ba3 -cytochrome c oxidase

We report the photobiochemical production of carbon monoxide by a terminal ba3 -cytochrome c oxidase from T. thermophilus HB8. FTIR and time-resolved step-scan FTIR spectroscopies were combined to probe this process and also monitor the concomitant binding of the produced gas to other intact ba3 molecules forming the ba3 -CO complex. The activation of this mechanism by ba3 -oxidase under visible excitation raises the question as to whether such a mechanism is physiologically relevant to the extreme environment in which it operates.

Detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba3-oxidoreductase

In this work we report FTIR data on the detection of functional hydrogen-bonded water molecules with protonated/deprotonated key carboxyl side chains in the respiratory enzyme ba₃-oxidoreductase.

Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase

The catalytic site of heme-copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Observation of ligand transfer in ba3 oxidase from Thermus thermophilus: simultaneous FTIR detection of photolabile heme a3(2+)-CN and transient Cu(B)(2+)-CN complexes

FTIR and light-minus-dark FTIR spectroscopy have been employed to investigate the reaction of oxidized and fully reduced ba(3) oxidase with cyanide. The characterization of the structures of the bound CN(-) in the binuclear heme Fe-Cu(B) center is essential, given that a central issue in the function of ba(3) oxidase is the extent to which the partially reduced substrates interact with the two metals. In the reaction of oxidized ba(3) oxidase with cyanide the initially formed heme a(3)(3+)-C≡N-Cu(B)(2+) species with ν(CN) frequency at 2152 cm(-1) was replaced by a photolabile complex with a frequency at 2075 cm(-1) characteristic of heme a(3)(2+)-CN(-). Photolysis of the heme a(3)(2+)-CN(-) adduct produced a band at 2146 cm(-1) attributed to the formation of a transient Cu(B)(2+)-CN(-) complex. All forms are pH independent between pH 5.5-9.5 and at pD 7.5 indicating the absence of ionizable groups that influence the properties of the cyanide complexes. In contrast to previous reports, our results show that CN(-) does not bind simultaneously to both heme a(3)(2+) and Cu(B)(2+) to form the mixed valence a(3)(2+)-CN·Cu(B)(2+)CN species. The photolysis products of the heme a(3)(2+)-CN(-)/Cu(B)(2+) and heme a(3)(2+)-CN(-)/Cu(B)(1+) species are different suggesting that relaxation dynamics in the binuclear center following ligand photodissociation are dependent on the oxidation state of Cu(B).

Spectroscopic analysis of immobilised redox enzymes under direct electrochemical control

This article reviews recent developments in spectroscopic analysis of electrode-immobilised enzymes under direct, unmediated electrochemical control. These methods unite the suite of spectroscopic methods available for characterisation of structural, electronic and coordination changes in proteins with the exquisite control over complex redox enzymes that can be achieved in protein film electrochemistry in which immobilised protein molecules exchange electrons directly with an electrode. This combination is particularly powerful in studies of highly active enzymes where redox states can be controlled even under fast electrocatalytic turnover. We examine examples in which UV-visible, IR, Raman and MCD spectroscopy have been combined with direct electrochemistry to probe redox-dependent chemistry, and consider future opportunities for 'direct' spectroelectrochemistry of immobilised enzymes.