Cytochrome Spectra Research Articles

Integration of a Micro-Transparent heater-integrated electrochemical (μTHE) cell for investigation of the thermal stability of cytochrome c redox variants

Spectroelectrochemistry (SEC) is a powerful technique that combines spectroscopic and electrochemical properties to investigate the redox potential and spectral characterization of chemical or biological molecules. Recently, SEC has gained attention in quantitative analysis, particularly in exploring the role of redox-active proteins in electron transfer networks related to biological systems. The microfluidic technique is used to investigate the spectroelectrochemical properties of the redox potential of metalloproteins under accurate temperature environments. However, conventional heater systems suffer from long ramping times and the transparency of heat systems would influence the spectroscopic information. In this study, we fabricated a micro-transparent heater-integrated electrochemical (μTHE) cell. The μTHE cell allows for spectroelectrochemical studies to investigate the thermal stability of cytochrome c at specific temperatures and the transparent ITO heater integrated into the μTHE cell offers rapid and accurate temperature control during the measurements, avoiding interference with spectroscopic information. The μTHE cell could regulate the oxidation/reduction forms of cytochrome c by the electrochemical process, and the ITO heater provides the precise temperature control for the observation of the absorption spectrum of cytochrome c at different temperatures. By taking advantage of rapid heating and transparency, the μTHE cell offers a facile platform for investigating the spectroelectrochemical properties of redox-active molecules in a well-controlled environment.

A Comparative Multi-Frequency EPR Study of Dipolar Interaction in Tetra-Heme Cytochromes.

Distances between Fe ions in multiheme cytochromes are sufficiently short to make the intramolecular dipole-dipole interaction between hemes probable. In the analysis of EPR data from cytochromes, this interaction has thus far been ignored under the assumption that spectra are the simple sum of non-interacting components. Here, we use a recently developed low-frequency broadband EPR spectrometer to establish the extent of dipolar interaction in the example cytochromes, characterize its spectral signatures, and identify present limitations in the analysis. Broadband EPR spectra of Shewanella oneidensis MR-1 small tetraheme cytochrome (STC) have been collected over the frequency range of 0.45 to 13.11 GHz, and they have been compared to similar data from Desulfovibrio vulgaris Hildenborough cytochrome c3. The two cases are representative examples of two very different heme topologies and corresponding electron-transfer properties in tetraheme proteins. While in cytochrome c3, the six Fe-Fe distances can be sorted into two well-separated groups, those in STC are diffuse. Since the onset of dipolar interaction between Fe-Fe pairs is already observed in the X-band, the g values are determined in the simulation of the 13.11 GHz spectrum. Low-frequency spectra are analyzed with the inclusion of dipolar interaction based on available structural data on mutual distances and orientations between all hemes. In this procedure, all 24 possible assignments of individual heme spectra to heme topologies are sampled. The 24 configurations can be reduced to a few, but inspection falls short of a unique assignment, due to a remaining lack of understanding of the fine details of these complex spectra. In general, the EPR analysis suggests the four-heme system in c3 to be more rigid than that in STC, which is proposed to be related to different physiological roles in electron transfer.

Effect of solution acidity on cytochrome c conformations of alternating current electrospray ionization mass spectrometry

AbstractThis paper reports notable observations regarding the ion charge states of thermally stable cytochrome c, generated using an alternating current (AC) electrospray ionization (ESI) device. An AC ESI sprayer entrains low‐mobility ions to accumulate at the meniscus cone tip prior to the ejection of detached aerosols to produce analyte ions. Therefore, as the solvent acidity varies, protein ions entrained in the AC cone tip are found to change conformation less significantly compared with those in the direct current (DC) cone. We acquired the AC ESI mass spectra of cytochrome c at pH range from 2 to 4. Unlike the DC ESI mass spectra showing clear conformation changes due to denaturing, the AC spectra indicated that only partial denaturing occurs even at extremely acidic pH 2. More native cytochrome c in lower charge states therefore remained. Moreover, with a solvent mixture of aqueous buffer and acetonitrile (70:30), partially denatured cytochrome c was still preserved at pH 2 by using AC ESI. Completely denatured proteins are observed at pH 2 by using DC ESI.

Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c.

We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300 nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723-13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.

Identification of Surf1 as an assembly factor of the cytochrome bc1-aa3 supercomplex of Actinobacteria

Respiration in aerobic Actinobacteria involves a cytochrome bc1-aa3 supercomplex with a diheme cytochrome c1, first isolated from Corynebacterium glutamicum. Synthesis of a functional cytochrome c oxidase requires incorporation of CuA, CuB, heme a, and heme a3. In contrast to eukaryotes and α-proteobacteria, this process is poorly understood in Actinobacteria. Here, we analyzed the role of a Surf1 homolog of C. glutamicum in the formation of a functional bc1-aa3 supercomplex. Deletion of the surf1 gene (cg2460) in C. glutamicum caused a growth defect and cytochrome spectra revealed reduced levels of cytochrome c and a and an increased level of cytochrome d. Membranes of the Δsurf1 strain had lost the ability to oxidize the artificial electron donor N,N,N′,N′-tetramethyl-p-phenylenediamine, suggesting that Surf1 is essential for the formation of a functional cytochrome aa3 oxidase. In contrast to the wild type, a bc1-aa3 supercomplex could not be purified from solubilized membranes of the Δsurf1 mutant. A transcriptome comparison revealed that the genes of the SigC regulon including those for cytochrome bd oxidase were upregulated in the Δsurf1 strain as well as the copper deprivation-inducible gene ctiP. Complementation studies showed that the Surf1 homologs of Corynebacterium diphtheriae, Mycobacterium smegmatis and Mycobacterium tuberculosis could at least partially abolish the growth defect of the C. glutamicum Δsurf1 mutant, suggesting that Surf1 is a conserved assembly factor for actinobacterial cytochrome aa3 oxidase.

Raman-Based in Situ Monitoring of Changes in Molecular Signatures during Mitochondrially Mediated Apoptosis.

Obtaining molecular information from inside cells is an important topic to understand the outcome of molecular interactions between potential drug molecules and biomolecules inside cells. To envision this goal, we investigated the surface-enhanced Raman scattering-based single-cell spectroscopic method to monitor changes in intracellular molecular signatures during mitochondrially mediated apoptosis in real time. Triphenylphosphine-modified gold nanoparticles were localized successfully to the mitochondria and greatly enhanced to obtain the intrinsic Raman scattering spectrum of mitochondria and cytochrome c in the live cell. Photothermally induced apoptosis showed a moderate decrease in the disulfide bond and a sharp increase in β-sheet structures depending on the input-laser power, along with morphological changes. However, chemical drug induced-apoptosis showed more subtle changes in the disulfide bond, as well as changes in Raman peaks corresponding to cytochrome c, and the appearance of a new peak at 1420 cm–1, which enabled us to study the molecular interactions within the mitochondria in real time from a single cell, following treatment with a novel pyruvate dehydrogenase kinase inhibitor.

Highly Efficient Desalting by Silica Isoporous Membrane-Based Microfluidic Chip for Electrospray Ionization Mass Spectrometry.

Nonvolatile buffers and inorganic salts used for isolation and stabilization of biological samples are essential to be cleaned up prior to mass spectrometry (MS) analysis because of their deleterious effects such as ion suppression and instrumental pollution. In this work, a centimeter-scale continuous silica isoporous membrane (SIM) was prepared and integrated into a facile microfluidic chip for the desalting of protein samples based on dialysis principle. Thanks to the uniform pore size (∼2.3 nm in diameter), ultrasmall thickness (90 nm) and high pore density (4.0 × 1012 pores cm-2, corresponding to a porosity of 16.7%) of SIM, the device achieved ∼99% desalting efficiency for the sample with 154 mM NaCl (isotonic saline) at a flow rate of 1 μL min-1, while protein loss was only 5%. High-quality electrospray ionization (ESI)-MS spectra of cytochrome c dissolved in isotonic saline was obtained after the desalting treatment. In addition, the SIM-based microfluidic device was successfully online-coupled with microchip ESI-MS for real-time desalting and characterization of proteins.

Comparison of redox and ligand binding behaviour of yeast and bovine cytochrome c oxidases using FTIR spectroscopy

Redox and CO photolysis FTIR spectra of yeast cytochrome c oxidase WT and mutants are compared to those from bovine and P. denitrificans CcOs in order to establish common functional features. All display changes that can be assigned to their E242 (bovine numbering) equivalent and to weakly H-bonded water molecules. The additional redox-sensitive band reported at 1736 cm−1 in bovine CcO and previously assigned to D51 is absent from yeast CcO and couldn't be restored by introduction of a D residue at the equivalent position of the yeast protein. Redox spectra of yeast CcO also show much smaller changes in the amide I region, which may relate to structural differences in the region around D51 and the subunit I/II interface.

Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase.

The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1.5+(CyS)2Cu1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.

Mechanism of electron transport during thiosulfate oxidation in an obligately mixotrophic bacterium Thiomonas bhubaneswarensis strain S10 (DSM 18181T).

This study describes the thiosulfate-supported respiratory electron transport activity of Thiomonas bhubaneswarensis strain S10 (DSM 18181T). Whole-genome sequence analysis revealed the presence of complete sox (sulfur oxidation) gene cluster (soxCDYZAXB) including the sulfur oxygenase reductase (SOR), sulfide quinone reductase (SQR), sulfide dehydrogenase (flavocytochrome c (fcc)), thiosulfate dehydrogenase (Tsd), sulfite dehydrogenase (SorAB), and intracellular sulfur oxidation protein (DsrE/DsrF). In addition, genes encoding respiratory electron transport chain components viz. complex I (NADH dehydrogenase), complex II (succinate dehydrogenase), complex III (ubiquinone-cytochrome c reductase), and various types of terminal oxidases (cytochrome c and quinol oxidase) were identified in the genome. Using site-specific electron donors and inhibitors and by analyzing the cytochrome spectra, we identified the shortest thiosulfate-dependent electron transport chain in T. bhubaneswarensis DSM 18181T. Our results showed that thiosulfate supports the electron transport activity in a bifurcated manner, donating electrons to quinol (bd) and cytochrome c (Caa 3 ) oxidase; these two sites (quinol oxidase and cytochrome c oxidase) also showed differences in their phosphate esterification potential (oxidative phosphorylation efficiency (P/O)). Further, it was evidenced that the substrate-level phosphorylation is the major contributor to the total energy budget in this bacterium.

Structural Re-arrangement and Peroxidase Activation of Cytochrome c by Anionic Analogues of Vitamin E, Tocopherol Succinate and Tocopherol Phosphate

Cytochrome c is a multifunctional hemoprotein in the mitochondrial intermembrane space whereby its participation in electron shuttling between respiratory complexes III and IV is alternative to its role in apoptosis as a peroxidase activated by interaction with cardiolipin (CL), and resulting in selective CL peroxidation. The switch from electron transfer to peroxidase function requires partial unfolding of the protein upon binding of CL, whose specific features combine negative charges of the two phosphate groups with four hydrophobic fatty acid residues. Assuming that other endogenous small molecule ligands with a hydrophobic chain and a negatively charged functionality may activate cytochrome c into a peroxidase, we investigated two hydrophobic anionic analogues of vitamin E, α-tocopherol succinate (α-TOS) and α-tocopherol phosphate (α-TOP), as potential inducers of peroxidase activity of cytochrome c. NMR studies and computational modeling indicate that they interact with cytochrome c at similar sites previously proposed for CL. Absorption spectroscopy showed that both analogues effectively disrupt the Fe-S(Met(80)) bond associated with unfolding of cytochrome c. We found that α-TOS and α-TOP stimulate peroxidase activity of cytochrome c. Enhanced peroxidase activity was also observed in isolated rat liver mitochondria incubated with α-TOS and tBOOH. A mitochondria-targeted derivative of TOS, triphenylphosphonium-TOS (mito-VES), was more efficient in inducing H2O2-dependent apoptosis in mouse embryonic cytochrome c(+/+) cells than in cytochrome c(-/-) cells. Essential for execution of the apoptotic program peroxidase activation of cytochrome c by α-TOS may contribute to its known anti-cancer pharmacological activity.

Low-level laser therapy on skeletal muscle inflammation: evaluation of irradiation parameters.

We evaluated the effect of different irradiation parameters in low-level laser therapy (LLLT) for treating inflammation induced in the gastrocnemius muscle of rats through cytokines concentration in systemic blood and analysis of muscle tissue. We used continuous (830 and 980 nm) and pulsed illuminations (830 nm). Animals were divided into five groups per wavelength (10, 20, 30, 40, and 50 mW), and a control group. LLLT was applied during 5 days with a constant irradiation time and area. TNF-α, IL-1β, IL-2, and IL-6 cytokines were quantified by ELISA. Inflammatory cells were counted using microscopy. Identical methodology was used with pulsed illumination. Average power (40 mW) and duty cycle were kept constant (80%) at five frequencies (5, 25, 50, 100, and 200 Hz). For continuous irradiation, treatment effects occurred for all doses, with a reduction of TNF-α, IL-1β, and IL-6 cytokines and inflammatory cells. Continuous irradiation at 830 nm was more effective, a result explained by the action spectrum of cytochrome c oxidase (CCO). Best results were obtained for 40 mW, with data suggesting a biphasic dose response. Pulsed wave irradiation was only effective for higher frequencies, a result that might be related to the rate constants of the CCO internal electron transfer process.

Re-evaluation of the near infrared spectra of mitochondrial cytochrome c oxidase: Implications for non invasive in vivo monitoring of tissues

We re-determined the near infrared (NIR) spectral signatures (650–980nm) of the different cytochrome c oxidase redox centres, in the process separating them into their component species. We confirm that the primary contributor to the oxidase NIR spectrum between 700 and 980nm is cupric CuA, which in the beef heart enzyme has a maximum at 835nm. The 655nm band characterises the fully oxidised haem a3/CuB binuclear centre; it is bleached either when one or more electrons are added to the binuclear centre or when the latter is modified by ligands. The resulting ‘perturbed’ binuclear centre is also characterised by a previously unreported broad 715–920nm band. The NIR spectra of certain stable liganded species (formate and CO), and the unstable oxygen reaction compounds P and F, are similar, suggesting that the latter may resemble the stable species electronically. Oxidoreduction of haem a makes no contribution either to the 835nm maximum or the 715nm band. Our results confirm the ability of NIRS to monitor the CuA centre of cytochrome oxidase activity in vivo, although noting some difficulties in precise quantitative interpretations in the presence of perturbations of the haem a3/CuB binuclear centre.

The kinetics of the reaction of nitrogen dioxide with iron(II)- and iron(III) cytochrome c

The reactions of NO2 with both oxidized and reduced cytochrome c at pH 7.2 and 7.4, respectively, and with N-acetyltyrosine amide and N-acetyltryptophan amide at pH 7.3 were studied by pulse radiolysis at 23°C. NO2 oxidizes N-acetyltyrosine amide and N-acetyltryptophan amide with rate constants of (3.1±0.3)×105 and (1.1±0.1)×106M−1s−1, respectively. With iron(III)cytochrome c, the reaction involves only its amino acids, because no changes in the visible spectrum of cytochrome c are observed. The second-order rate constant is (5.8±0.7)×106M−1s−1 at pH 7.2. NO2 oxidizes iron(II)cytochrome c with a second-order rate constant of (6.6±0.5)×107M−1s−1 at pH 7.4; formation of iron(III)cytochrome c is quantitative. Based on these rate constants, we propose that the reaction with iron(II)cytochrome c proceeds via a mechanism in which 90% of NO2 oxidizes the iron center directly—most probably via reaction at the solvent-accessible heme edge—whereas 10% oxidizes the amino acid residues to the corresponding radicals, which, in turn, oxidize iron(II). Iron(II)cytochrome c is also oxidized by peroxynitrite in the presence of CO2 to iron(III)cytochrome c, with a yield of ~60% relative to peroxynitrite. Our results indicate that, in vivo, NO2 will attack preferentially the reduced form of cytochrome c; protein damage is expected to be marginal, the consequence of formation of amino acid radicals on iron(III)cytochrome c.

Analysis of Flexibility of Proteins by means of Positive and Negative Ion MALDI In-Source Decay Mass Spectrometry.

The amino acid residues susceptible to in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have been identified from both positive and negative ion ISD spectra of cytochrome c, myoglobin, thioredoxin and bovine serum albumin. Backbone cleavages at the N-Cα bonds of Xxx-Asp, Xxx-Asn, Xxx-Cys, and Gly-Xxx residues gave discontinuous intense peaks of c-ions, independent of positive and negative ion mode. The intensity values for c-ions, Int(c), were defined to allow estimation of the discontinuous intense peaks of c-ions. The identities of the high intensity value residues Asp, Asn, Cys, and Gly were compared with those identified using other measures of flexibility such as the B-factor, turn preferential factor and protection factor. The comparison indicates that Asp, Asn, and Gly residues are common to all measures. Thus, the intensity values of c-ions can be adopted as a measure of protein flexibility.

Sensing the dynamics of oxidative stress using enhanced absorption in protein-loaded random media.

Reactive oxygen species play a key role in cell signalling and oxidative stress mechanisms, therefore, sensing their production by living organisms is of fundamental interest. Here we describe a novel biosensing method for extracellular detection of endogenous hydrogen peroxide (H2O2). The method is based on the enhancement of the optical absorption spectrum of the hemoprotein cytochrome c when loaded into a highly scattering random medium. Such a configuration enables, in contrast to existing techniques, non-invasive and dynamic detection of the oxidation of cyt c in the presence of H2O2 with unprecedented sensitivity. Dynamic information on the modification of the cell oxidative status of Chlamydomonas reinhardtii, an aquatic green algae, was obtained under oxidative stress conditions induced by the presence of trace concentrations of Cd(II). Furthermore, the dynamics of H2O2 production was investigated under different lighting conditions confirming the impact of Cd(II) on the photosynthetic activity of those phytoplanktonic cells.

IR signatures of the metal centres of bovine cytochrome c oxidase: assignments and redox-linkage

Assignments of IR bands of reduced minus oxidized IR difference spectra of bovine and related cytochrome c oxidases are reviewed and their linkages to specific metal centres are assessed. To aid this, redox-poised difference spectra in the presence of cyanide or carbon monoxide are presented. These ligands fix the redox states of either haem a3 alone or haem a3 and CuB respectively, while allowing redox cycling of the remaining centres.

Effect of red and near-infrared wavelengths on low-level laser (light) therapy-induced healing of partial-thickness dermal abrasion in mice

Low-level laser (light) therapy (LLLT) promotes wound healing, reduces pain and inflammation, and prevents tissue death. Studies have explored the effects of various radiant exposures on the effect of LLLT; however, studies of wavelength dependency in in vivo models are less common. In the present study, the healing effects of LLLT mediated by different wavelengths of light in the red and near-infrared (NIR) wavelength regions (635, 730, 810, and 980 nm) delivered at constant fluence (4 J/cm(2)) and fluence rate (10 mW/cm(2)) were evaluated in a mouse model of partial-thickness dermal abrasion. Wavelengths of 635 and 810 nm were found to be effective in promoting the healing of dermal abrasions. However, treatment using 730- and 980-nm wavelengths showed no sign of stimulated healing. Healing was maximally augmented in mice treated with an 810-nm wavelength, as evidenced by significant wound area reduction (p < 0.05), enhanced collagen accumulation, and complete re-epithelialization as compared to other wavelengths and non-illuminated controls. Significant acceleration of re-epithelialization and cellular proliferation revealed by immunofluorescence staining for cytokeratin-14 and proliferating cell nuclear antigen (p < 0.05) was evident in the 810-nm wavelength compared with other groups. Photobiomodulation mediated by red (635 nm) and NIR (810 nm) light suggests that the biological response of the wound tissue depends on the wavelength employed. The effectiveness of 810-nm wavelength agrees with previous publications and, together with the partial effectiveness of 635 nm and the ineffectiveness of 730 and 980 nm wavelengths, can be explained by the absorption spectrum of cytochrome c oxidase, the candidate mitochondrial chromophore in LLLT.

Evaluation of photodynamic treatment using aluminum phthalocyanine tetrasulfonate chloride as a photosensitizer: new approach

Photodynamic therapy (PDT) has been the subject of several clinical studies. Evidence to date suggests that direct cell death may involve apoptosis. T(24) cells (bladder cancer cells, ATCC-Nr. HTB-4) were subjected to PDT with aluminum phthalocyanine tetrasulfonate chloride (AlS(4)Pc-Cl) and red laser light at 670 nm. Morphological changes after PDT were visualized under confocal microscopy. Raman microspectroscopy is considered as one of the newly established methods used for the detection of cytochrome c as an apoptotic marker. Results showed that PDT treated T(24) cells seem to undergo apoptosis after irradiation with 3 J cm(-2). Cytochrome c could not be detected from cells incubated with AlS(4)Pc-Cl using Raman spectroscopy whereas AlS(4)Pc-Cl seems to interfere with the Raman spectrum of cytochrome c.

Complementary Surface-Enhanced Resonance Raman Spectroscopic Biodetection of Mixed Protein Solutions by Chitosan- and Silica-Coated Plasmon-Tuned Silver Nanoparticles

Silver nanoparticles with identical plasmonic properties but different surface functionalities are synthesized and tested as chemically selective surface-enhanced resonance Raman (SERR) amplifiers in a two-component protein solution. The surface plasmon resonances of the particles are tuned to 413 nm to match the molecular resonance of protein heme cofactors. Biocompatible functionalization of the nanoparticles with a thin film of chitosan yields selective SERR enhancement of the anionic protein cytochrome b(5), whereas functionalization with SiO(2) amplifies only the spectra of the cationic protein cytochrome c. As a result, subsequent addition of the two differently functionalized particles yields complementary information on the same mixed protein sample solution. Finally, the applicability of chitosan-coated Ag nanoparticles for protein separation was tested by in situ resonance Raman spectroscopy.