Time-resolved step-scan Fourier transform infrared investigation of heme-copper oxidases: implications for O2 input and H2O/H+ output channels

Application of double-pulse laser-induced breakdown spectroscopy (DP-LIBS), Fourier transform infrared micro-spectroscopy and Raman microscopy for the characterization of copper-sulfides

The combined application of the structure sensitive techniques Fourier transform infrared μ-spectroscopy and Raman microscopy in conjunction with different approaches of laser-induced breakdown spectroscopy (LIBS) including the two-color double pulse (DP-LIBS) have been applied towards the characterization of whole ore copper-sulfide minerals. Discrete information from the surface of the whole ore minerals that lead to the establishment of infrared marker bands and from the surface of bioleached samples that allow the monitoring of jarosite and biofilm formation are provided by FTIR mapping experiments. Raman data can provide information related to the type of the mineral and of the secondary minerals formed on the surface of the ore. Of the four different LIBS approaches applied towards the characterization of the composition of the whole ore minerals, the DP-LIBS shows the highest sensitivity with increasing signals for both the Fe and Cu metals in the whole ore samples.

Raman and FTIR microspectroscopies, laser induced breakdown spectroscopy (LIBS) and DP-LIBS have been applied towards our understanding of the characterization of the structure and structure–function relationship in copper-sulfide minerals.

Extracellular electron uptake from carbon-based π electron surface-donors: oxidation of graphite sheets by Sulfobacillus thermosulfidooxidans probed by Raman and FTIR spectroscopies

In this work we report Raman and FTIR evidence for extracellular electron uptake by Sulfobacillus thermosulfidooxidans from the solid phase carbon-based π-electron donor surface of graphite sheets. The primary step in the reaction is the intercalation of water on the surface of graphite followed by the formation of EPS and proceeds to form graphite oxide (GO) with a Raman I D/I G = 0.3 ratio which represents the highest defect content in the carbon lattice reported by bio-oxidation process. We propose and discuss a direct extracellular electron transfer mechanism via outer membrane redox proteins for the electron transfer.

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.

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.

Probing the Role of the Heme Distal and Proximal Environment in Ligand Dynamics in the Signal Transducer Protein HemAT by Time-Resolved Step-Scan FTIR and Resonance Raman Spectroscopy

HemAT is a heme-containing oxygen sensor protein that controls aerotaxis. Time-resolved step-scan FTIR studies were performed on the isolated sensor domain and full-length HemAT proteins as well as on the Y70F (B-helix), L92A (E-helix), T95A (E-helix), and Y133F (G-helix) mutants to elucidate the effect of the site-specific mutations on the ligand dynamics subsequent to CO photolysis. The mutations aimed to perturb H-bonding and electrostatic interactions near the heme Fe-bound gaseous ligand (CO) and the heme proximal environment. Rebinding of CO to the heme Fe is biphasic in the sensor domain and full-length HemAT as well as in the mutants, with the exception of the Y133F mutant protein. The monophasic rebinding of CO in Y133F suggests that in the absence of the H-bond between Y133 and the heme proximal H123 residue the ligand rebinding process is significantly affected. The role of the proximal environment is also probed by resonance Raman photodissociation experiments, in which the Fe-His mode of the photoproduct of sensor domain HemAT-CO is detected at a frequency higher than that of the deoxy form in the difference resonance Raman spectra. The role of the conformational changes of Y133 (G-helix) and the role of the distal L92 and T95 residues (E-helix) in regulating ligand dynamics in the heme pocket are discussed.

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.

Kinetics of cytochrome c oxidase from R. sphaeroides initiated by direct electron transfer followed by tr-SEIRAS

Time-resolved surface-enhanced IR-absorption spectroscopy (tr-SEIRAS) has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. The enzyme was converted electrochemically into the fully reduced state. Thereafter, in the presence of oxygen, the potential was switched to open circuit potential (OCP). Under these conditions, the enzyme is free to undergo enzymatic oxidation in the absence of an external electric field. Tr-SEIRAS was performed using the step-scan technique, triggered by periodic potential pulses switching between - 800mV and OCP. Single bands were resolved in a broad band in the amide I region using phase sensitive detection. Amplitudes of these bands were analyzed as a function of time. Time constants in the ms time scale were considered in terms of conformational changes of the protein secondary structures associated with the enzymatic turnover of the protein.

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.

Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy

We present time-resolved step-scan FTIR evidence for the role of the distal Y43 and L65 residues in controlling the ligand dynamics in the signal transducer protein YddV.

Infrared and Raman spectroscopic investigation of the reaction mechanism of cytochrome c oxidase

Recent progress in studies on the proton-pumping and O₂reduction mechanisms of cytochrome c oxidase (CcO) elucidated by infrared (IR) and resonance Raman (rR) spectroscopy, is reviewed. CcO is the terminal enzyme of the respiratory chain and its O₂reduction reaction is coupled with H⁺ pumping activity across the inner mitochondrial membrane. The former is catalyzed by heme a3 and its mechanism has been determined using a rR technique, while the latter used the protein moiety and has been investigated with an IR technique. The number of H⁺ relative to e⁻ transferred in the reaction is 1:1, and their coupling is presumably performed by heme a and nearby residues. To perform this function, different parts of the protein need to cooperate with each other spontaneously and sequentially. It is the purpose of this article to describe the structural details on the coupling on the basis of the vibrational spectra of certain specified residues and chromophores involved in the reaction. Recent developments in time-resolved IR and Raman technology concomitant with protein manipulation methods have yielded profound insights into such structural changes. In particular, the new IR techniques that yielded the breakthrough are reviewed and assessed in detail. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

Time-resolved surface-enhanced IR-absorption spectroscopy of direct electron transfer to cytochrome c oxidase from R. sphaeroides

Time-resolved surface-enhanced IR-absorption spectroscopy triggered by electrochemical modulation has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. Single bands isolated from a broad band in the amide I region using phase-sensitive detection were attributed to different redox centers. Their absorbances changing on the millisecond timescale could be fitted to a model based on protonation-dependent chemical reaction kinetics established previously. Substantial conformational changes of secondary structures coupled to redox transitions were revealed.

Proton transfer and protein conformation dynamics in photosensitive proteins by time-resolved step-scan Fourier-transform infrared spectroscopy

Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as -10(-) (4), sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent.

Phase-sensitive detection in modulation excitation spectroscopy applied to potential induced electron transfer in cytochrome c oxidase

Cytochrome c oxidase (CcO) from Rhodobacter sphaeroides was investigated by modulated excitation surface-enhanced infrared-absorption spectroscopy (SEIRAS). Sequential electron transfer (ET) within CcO was initiated by electrochemical excitation. During modulated excitation by periodic potential pulses with frequencies between 20 and 500 Hz, time-resolved infrared spectra were measured by the step-scan technique, with time resolution in the millisecond range. Conformational changes of the protein structure as a result of ET lead to rather complex SEIRA spectra with many overlapping bands embedded in a broad background signal. Phase-sensitive detection (PSD) was used to separate single components within the broad band of overlapping structural bands in the amide I region. PSD is able to extract the periodic response of single components with the same frequency as the excitation from noise or from static background and therefore enhances the signal-to-noise ratio. Moreover, PSD enables validation of the fit model used for the deconvolution of overlapping bands by analyzing phase lags of single components acquired at different stimulation frequencies. Phase lags between the evaluated vibrational components and the modulated excitation increase with increasing excitation frequencies, an inherent prerequisite of this evaluation method.

Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system

X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O2 binding to the second heme (heme a3) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of α-helices of CcO in H2O medium. The present results indicate that migration of CO from heme a3 to CuB in the O2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including CuB, O2, heme a3, and two helix turns extending to Ser-382, CuB induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O2 transfer from CuB to heme a3.

Vibrational resonances and CuB displacement controlled by proton motion in cytochrome c oxidase

Cytochrome c oxidase (CcO), found in the inner mitochondrial membranes or in many bacteria, catalyzes the four-electron reduction of molecular oxygen to water. Four protons are pumped across the inner mitochondrial membrane through CcO. In this study, quantum mechanics/molecular mechanics and molecular dynamics calculations are used to probe the spectroscopic characteristics of the ferryl intermediates in the aa(3) CcO/O(2) reaction. These highly elaborate calculations, supported by several calculations on smaller model systems, demonstrate the sensitivity of vibrational frequencies on the Coulombic field of heme a(3) and their dependence on the distance of the adjacent Cu(B) to the heme a(3)-Fe atom. This distance seems to be associated with the protonation state of the heme a(3) propionate A, and we propose that it plays a crucial role on the mechanism of action of CcO. In detail, we link proton pumping activity in CcO enzyme (a) to a multiple (1:1:2) resonance among the frequencies of Fe(IV)=O bond stretching, the breathing mode of Histidine 411, and a bending mode of the His411-Fe(IV)=O species (aa(3) from Paracoccus denitrificans numbering) and (b) to Cu(B) displacement by electrostatic interactions toward the heme a(3) iron. We find that the vibrations of the His411-Fe(IV)=O unit become highly coupled depending on the protonation state of the heme a(3) ring A propionate/Asp399 pair, and we propose a mechanism for the resonance Raman enhancement of the bending mode delta(His411-Fe(IV)=O). Calculations on model systems demonstrate that the position of Cu(B) in relation to heme a(3) iron-oxo plays a crucial role in regulating that resonance. We also discuss the origin of the coupling between bending, delta(His411-Fe(IV)=O) and nu(Fe=O) stretching modes, and the role played by such vibrational coupling interactions or Cu(B) position in controlling functional properties of the enzyme, including electron/proton coupling as well as experimental spectra.

Spectroscopic study on the communication between a heme a3 propionate, Asp399 and the binuclear center of cytochrome c oxidase from Paracoccus denitrificans

The proton pumping mechanism of cytochrome c oxidase on a molecular level is highly disputed. Recently theoretical calculations and real time electron transfer measurements indicated the involvement of residues in the vicinity of the ring A propionate of heme a3, including Asp399 and the CuB ligands His 325, 326. In this study we probed the interaction of Asp399 with the binuclear center and characterize the protonation state of its side chain. Redox induced FTIR difference spectra of mutations at the site in direct comparison to wild type, indicate that below pH 5 Asp 399 displays signals typical for the deprotonation of the acidic residue with reduction of the enzyme. Interestingly at a pH higher than 5, no contributions from Asp 399 are evident. In order to probe the interaction of the site with the binuclear center we followed the rebinding of CO by infrared spectroscopy for mutations on residue Asp399 to Glu, Asn and Leu. Previously different CO conformers have been identified for bacterial cytochrome c oxidases, and its pH dependent behaviour discussed to be relevant for catalysis. Interestingly we observe the lack of this pH dependency and a strong influence on the observable conformers for all mutants studied here, clearly suggesting a communication of the site with the heme-copper center and the nearby histidine residues.

Reactivity studies on Fe(III)-(O2(2-))-Cu(II) compounds: influence of the ligand architecture and copper ligand denticity

Heme-Cu/O2 adducts are of interest in the elucidation of the fundamental metal-O2 chemistry occurring in heme-Cu enzymes which effect reductive O-O cleavage of dioxygen to water. In this report, the chemistry of four heme-peroxo-copper [FeIII-(O22-)-CuII]+ complexes (1-4), varying in their ligand architecture, copper-ligand denticity, or both and thus their structures and physical properties are compared in their reactivity toward CO, PPh3, acids, cobaltocene, and phenols. In 1 and 2, the copper(II) ligand is N4-tetradentate, and the peroxo unit is bound side-on to iron(III) and end-on to the copper(II). In contrast, 3 and 4 contain a N3-tridentate copper(II) ligand, and the peroxo unit is bound side-on to both metal ions. CO "displaces" the peroxo ligand from 2-4 to form reduced CO-FeII and CO-CuI species. PPh3 reacts with 3 and 4 displacing the peroxide ligand from copper, forming (porphyrinate)FeIII-superoxide plus CuI-PPh3 species. Complex 2 does not react with PPh3, and surprisingly, 1 reacts neither with PPh3 nor CO, exhibiting remarkable stability toward these reagents. The behavior of 1 and 2 compared to that of 3 and 4 correlates with the different denticity of the copper ligand (tetra vs tridentate). Complexes 1-4 react with HCl releasing H2O2, demonstrating the basic character of the peroxide ligand. Cobaltocene causes the two-electron reduction of 1-4 giving the corresponding micro-oxo [FeIII-(O2-)-CuII]+ complexes, in contrast to the findings for other heme-peroxo-copper species of different design. With t-butyl-substituted phenols, no reaction occurs with 1-4. The results described here emphasize how ligand design and variations influence and control not only the structure and physical properties but also the reactivity patterns for heme-Cu/O2 adducts. Implications for future investigations of protonated heme/Cu-peroxo complexes, low-spin analogues, and ultimately O-O cleavage chemistry are discussed.

Practical aspects of the maximum entropy inversion of the laplace transform for the quantitative analysis of multi-exponential data

The number, position, area, and width of the bands in a lifetime distribution give the number of exponentials present in time-resolved data and their time constants, amplitudes, and heterogeneities. The maximum entropy inversion of the Laplace transform (MaxEnt-iLT) provides a lifetime distribution from time-resolved data, which is very helpful in the analysis of the relaxation of complex systems. In some applications both positive and negative values for the lifetime distribution amplitudes are physical, but most studies to date have focused on positive-constrained solutions. In this work, we first discuss optimal conditions to obtain a sign-unrestricted maximum entropy lifetime distribution, i.e., the selection of the entropy function and the regularization value. For the selection of the regularization value we compared four methods: the chi2 criterion and Bayesian inference (already used in sign-restricted MaxEnt-iLT), and the L-curve and the generalized cross-validation methods (not yet used in MaxEnt-iLT to our knowledge). Except for the frequently used chi2 criterion, these methods recommended similar regularization values, providing close to optimum solutions. However, even when an optimal entropy function and regularization value are used, a MaxEnt lifetime distribution will contain noise-induced errors, as well as systematic distortions induced by the entropy maximization (regularization-induced errors). We introduce the concept of the apparent resolution function in MaxEnt, which allows both the noise and regularization-induced errors to be estimated. We show the capability of this newly introduced concept in both synthetic and experimental time-resolved Fourier transform infrared (FT-IR) data from the bacteriorhodopsin photocycle.

Characterization of a Bimetallic-Bridging Intermediate in the Reduction of NO to N2O: a Density Functional Theory Study

We have applied density functional theory to characterize the bimetallic-bridging intermediate in the reduction of NO to N2O by heme-copper oxidoreductases. The present study provides information of the electronic and vibrational structure of the putative intermediate, and thus, it forms the basis for a quantitative accurate atomic-level description of the key steps in the N-N bond formation and the N-O bond cleavage mechanism.

Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus

Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a(3)(2+)-NO species formed in the reaction of ba(3)-oxidase with NO from resonance Raman spectroscopy. We have identified the His-heme a(3)(2+)-NO/Cu(B)(1+) species by its characteristic Fe-NO and N-O stretching frequencies at 539 and 1620 cm(-)(1), respectively. The Fe-NO and N-O frequencies in ba(3)-oxidase are 21 and 7 cm(-)(1) lower and higher, respectively, than those observed in Mb-NO. From these results and earlier Raman and FTIR measurements, we demonstrate that the protein environment of the proximal His384 that is part of the Q-proton pathway controls the strength of the Fe-His384 bond upon ligand (CO vs NO) binding. We also show by time-resolved FTIR spectroscopy that Cu(B)(1+) has a much lower affinity for NO than for CO. We suggest that the reduction of NO to N(2)O by ba(3)-oxidase proceeds by the fast binding of the first NO molecule to heme a(3) with high-affinity, and the second NO molecule binds to Cu(B) with low-affinity, producing the temporal co-presence of two NO molecules in the heme-copper center. The low-affinity of Cu(B) for NO binding also explains the NO reductase activity of the ba(3)-oxidase as opposed to other heme-copper oxidases. With the identification of the His-heme a(3)(2+)-NO/Cu(B)(1+) species, the structure of the binuclear heme a(3)-Cu(B)(1+) center in the initial step of the NO reduction mechanism is known.

Photoinduced carbon monoxide migration in a synthetic heme-copper complex

Time-resolved infrared (TRIR) flash photolytic techniques have been employed to initiate and observe the efficient dissociation of CO from a synthetic heme-CO/copper complex, [((6)L)Fe(II)(CO)..Cu(I)](+) (2), in CH(3)CN and acetone at room temperature. In CH(3)CN, a significant fraction of the photodissociated CO molecules transiently bind to copper (nu(CO)(Cu) = 2091 cm(-)(1)) giving [((6)L)Fe(II)..Cu(I)(CO)](+) (4), with an observed rate constant, k(1) = 1.5 x 10(5) s(-)(1). That is followed by a slower direct transfer of CO from the copper moiety back to the heme (nu(CO)(Fe) = 1975 cm(-)(1)) with k(2) = 1600 s(-)(1). Additional transient absorption (TA) UV-vis spectroscopic experiments have been performed monitoring the CO-transfer reaction by following the Soret band. Eyring analysis of the temperature-dependent data yields DeltaH(double dagger) = 43.9 kJ mol(-)(1) for the 4-to-2 transformation, similar to that for CO dissociation from [Cu(I)(tmpa)(CO)](+) in CH(3)CN (DeltaH(double dagger) = 43.6 kJ mol(-)(1)), suggesting CO dissociation from copper regulates the binding of small molecules to the heme within [((6)L)Fe(II)..Cu(I)](+)(3). Our observations are analagous to those observed for the heme(a3)/Cu(B) active site of cytochrome c oxidase, where photodissociated CO from the heme(a3) site immediately (ps) transfers to Cu(B) followed by millisecond transfer back to the heme.