Fourier transform infrared analysis of the interaction of azide with the active site of oxidized and reduced bovine Cu,Zn superoxide dismutase

Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase

Biological carbon dioxide (CO2 ) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.

Protein dynamics of [Cu-Zn] superoxide dismutase (SOD1): How protein motions at the global and local levels impact the reactivity of SOD1

This work explores the pivotal role that protein mobility plays in facilitating the catalytic activity of Copper-Zinc superoxide dismutase (SOD1). Through both localized active site distortions and correlated domain movement, these motions enable the enzyme to adopt the conformations necessary to achieve both substrate delivery and efficient catalytic transformation. Structural and computational studies of a biomimetic model complex are used to probe the localized interactions between substrate and secondary sphere residues that play a role in guiding substrate to the active site, as well as facilitating the conformational changes necessary for substrate turnover. Normal mode analysis (NMA) of SOD1 demonstrates how collective domain motion influences key residues of the electrostatic loop (ESL), guiding substrate to the active site and facilitating the delivery of the conserved water network necessary for proton transfer.

Determination of oxidative stress levels and some antioxidant enzyme activities in prostate cancer

In this study, the antioxidant enzyme activities such as (SOD, GSH, and CAT) and malondialdehyde (MDA) level which is the end product of lipid peroxidation, were determined from the serum samples taken from patients diagnosed with prostate cancer Van Yuzuncu Yıl University Medical Faculty of Educational Research and Training Hospital and İstanbul Bagcilar Education Research Hospital. The SOD, GSH, and CAT activity of patient groups was found significantly lower than the healthy control group in patients with prostate cancer (p < .05). Serum MDA level is found significantly high when compared to control groups. MDA levels increased in patients that suffer prostate cancer disorder. Whereas, firstly antioxidant enzymes activity of SOD, GSH and CAT have been decreased in control groups. Thus, we concluded that the cause of development of prostate cancer may be the result of an imbalance between the antioxidants and oxidative stress. As a result, SOD, CAT, GSH, and MDA may play an important role in the etiopathogenesis of prostate cancer.

Structural evidence for a copper-bound carbonate intermediate in the peroxidase and dismutase activities of superoxide dismutase

Copper-zinc superoxide dismutase (SOD) is of fundamental importance to our understanding of oxidative damage. Its primary function is catalysing the dismutation of superoxide to O(2) and H(2)O(2). SOD also reacts with H(2)O(2), leading to the formation of a strong copper-bound oxidant species that can either inactivate the enzyme or oxidise other substrates. In the presence of bicarbonate (or CO(2)) and H(2)O(2), this peroxidase activity is enhanced and produces the carbonate radical. This freely diffusible reactive oxygen species is proposed as the agent for oxidation of large substrates that are too bulky to enter the active site. Here, we provide direct structural evidence, from a 2.15 Å resolution crystal structure, of (bi)carbonate captured at the active site of reduced SOD, consistent with the view that a bound carbonate intermediate could be formed, producing a diffusible carbonate radical upon reoxidation of copper. The bound carbonate blocks direct access of substrates to Cu(I), suggesting that an adjunct to the accepted mechanism of SOD catalysed dismutation of superoxide operates, with Cu(I) oxidation by superoxide being driven via a proton-coupled electron transfer mechanism involving the bound carbonate rather than the solvent. Carbonate is captured in a different site when SOD is oxidised, being located in the active site channel adjacent to the catalytically important Arg143. This is the probable route of diffusion from the active site following reoxidation of the copper. In this position, the carbonate is poised for re-entry into the active site and binding to the reduced copper.

Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand

Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.

Measured rates of fluoride/metal association correlate with rates of superoxide/metal reactions for Fe(III)EDTA(H2O)- and related complexes

The effects of 10 paramagnetic metal complexes (Fe(III)EDTA(H2O)-, Fe(III)EDTA(OH)2-, Fe(III)PDTA-, Fe(III)DTPA2-, Fe(III)2O(TTHA)2-, Fe(III)(CN)6(3-), Mn(II)EDTA(H2O)2-, Mn(II)PDTA2-, Mn(II)beta-EDDADP2-, and Mn(II)PO4(-)) on F- ion 19F NMR transverse relaxation rates (R2 = 1/T2) were studied in aqueous solutions as a function of temperature. Consistent with efficient relaxation requiring formation of a metal/F- bond, only the substitution inert complexes Fe(III)(CN)6(3-) and Fe(III)EDTA(OH)2- had no measured effect on T2 relaxation of the F- 19F resonance. For the remaining eight complexes, kinetic parameters (apparent second-order rate constants and activation enthalpies) for metal/F- association were determined from the dependence of the observed relaxation enhancements on complex concentration and temperature. Apparent metal/F- association rate constants for these complexes (k(app,F-)) spanned 5 orders of magnitude. In addition, we measured the rates at which O2*- reacts with Fe(III)PDTA-, Mn(II)EDTA(H2O)2-, Mn(II)PDTA2-, and Mn(II)beta-EDDADP2- by pulse radiolysis. Although no intermediate is observed during the reduction of Fe(III)PDTA- by O2*-, each of the Mn(II) complexes reacts with formation of a transient intermediate presumed to form via ligand exchange. These reactivity patterns are consistent with literature precedents for similar complexes. With these data, both k(app,O2-) and k(app,F-) are available for each of the eight reactive complexes. A plot of log(k(app,O2-)) versus log(k(app,F-)) for these eight showed a linear correlation with a slope approximately 1. This correlation suggests that rapid metal/O2*- reactions of these complexes occur via an inner-sphere mechanism whereas formation of an intermediate coordination complex limits the overall rate. This hypothesis is also supported by the very low rates at which the substitution inert complexes (Fe(III)(CN)6(3-) and Fe(III)EDTA(OH)2-) are reduced by O2*-. These results suggest that F- 19F NMR relaxation can be used to predict the reactivities of other Fe(III) complexes toward reduction by O2*-, a key step in the biological production of reactive oxygen species.

Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation

We compare the role of a conformational switch and that of a point mutation in the thermodynamic stability of a protein solution and in the consequent propensity toward aggregation. We study sickle-cell hemoglobin (HbS), the beta6 Glu-Val point mutant of adult human hemoglobin (HbA), in its R (CO-liganded) conformation, and compare its aggregation properties to those of both HbS and HbA in their T (unliganded) conformation. Static and dynamic light scattering measurements performed for various hemoglobin concentrations showed critical divergences with mean field exponents as temperature was increased. This allowed determining spinodal data points T(S)(c) by extrapolation. These points were fitted to theoretical expressions of the T(S)(c) spinodal line, which delimits the region where the homogeneous solution becomes thermodynamically unstable against demixing in two sets of denser and dilute mesoscopic domains, while remaining still liquid. Fitting provided model-free numerical values of enthalpy and entropy parameters measuring the stability of solutions against demixing, namely, 93.2 kJ/mol and 314 J/ degrees K-mol, respectively. Aggregation was observed also for R-HbS, but in amorphous form and above physiological temperatures close to the spinodal, consistent with the role played in nucleation by anomalous fluctuations governed by the parameter epsilon = (T - T(S))/T(S). Fourier transform infrared (FTIR) and optical spectroscopy showed that aggregation is neither preceded nor followed by denaturation. Transient multiple interprotein contacts occur in the denser liquid domains for R-HbS, T-HbS, and T-HbA. The distinct effects of their specific nature and configurations, and those of desolvation on the demixing and aggregation thermodynamics, and on the aggregate structure are highlighted.

Copper−Zinc Superoxide Dismutase: Theoretical Insights into the Catalytic Mechanism

The mechanism for the toxic superoxide radical disproportionation to molecular oxygen and hydrogen peroxide by copper-zinc superoxide dismutase (CuZnSOD) has been studied using the B3LYP hybrid density functional. On the basis of the X-ray structure of the enzyme, the molecular system investigated includes the first-shell protein ligands of the two metal centers as well as the second-shell ligand Asp122. The substrates of the model reaction are two superoxide radical anions, approaching the copper center at the beginning of two half-reactions: the first part of the catalytic cycle involving Cu+ oxidation and the second part reducing Cu2+ back to its initial state. The quantitative free energy profile of the reaction is obtained and discussed in connection with the experimental data on the reduction potentials and CuZnSOD kinetics. The optimized structures are analyzed and compared to the experimental ones. The two transition states alternate the protonation state of His61 and correspond to histidine Cu-His61-Zn bridge rupture/reformation. Modifications applied to the initial model allow the importance of Asp122 for catalysis to be estimated.

Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

Cu,Zn-superoxide dismutase (Cu,Zn-SOD) is a ubiquitous enzyme with an essential role in antioxidant defense. To better understand structural factors at the origin of the highly efficient superoxide dismutation mechanism, we analyzed the consequence of copper reduction on the electronic properties of the backbone and individual amino acids by using electrochemistry coupled to Fourier transform infrared spectroscopy. Comparison of data recorded with bovine erythrocyte and recombinant chloroplastic Cu,Zn-SOD from Lycopersicon esculentum, expressed as a functional tetramer in Escherichia coli and (14)N- or fully (15)N-labeled, demonstrated that the infrared changes were dominated by reorganizations of peptide bonds and histidine copper ligands. Two main infrared modes of histidine side chain, markers of metal coordination, were identified by using Cu- and Zn-methylimidazole models: the nu(C(4)C(5))at 1605-1594 cm(-1) or approximately 1586 cm(-1) for Ntau or Npi coordination, and the nu(C(5)Ntau) at approximately 1113-1088 cm(-1). These modes, also identified in Cu,Zn-SOD by using (15)N labeling, showed that the electronic properties of the histidine Ntau ligands of copper are mostly affected upon copper reduction. A striking conclusion of this work is that peptide groups from loops and beta-sheet largely participate in charge redistribution upon copper reduction, and in contrast, electronic properties of polar and charged amino acids of the superoxide access channel remain unaffected. This is notably shown for the strictly conserved Arg-143 by site-directed mutagenesis on chloroplastic Cu,Zn-SOD. Charge compensation by the peptide backbone and preserved electronic properties of the superoxide access channel and docking site upon copper reduction may be the determinant factors for the high reaction kinetics of superoxide with both reduced and oxidized Cu,Zn-SOD.

Electrochemistry of immobilized CuZnSOD and FeSOD and their interaction with superoxide radicals

Copper, zinc superoxide dismutase (CuZnSOD) from bovine erythrocytes and iron superoxide dismutase from Escherichia coli (FeSOD) were immobilized on 3-mercaptopropionic acid (MPA)-modified gold electrodes, respectively. The characterization of the SOD electrodes showed a quasi-reversible, electrochemical redox behavior with a formal potential of 47+/-4 mV and -154+/-5 mV (vs. Ag/AgCl, 1 M KCl) for surface adsorbed CuZnSOD and FeSOD, respectively. The heterogeneous electron transfer rate constants were determined to be about 65 and 35/s, respectively. Covalent fixation of both SODs was also feasible with only slight changes in the formal potential. The interaction of superoxide radicals (O(2)(-)) with the SOD electrode was investigated. No catalytic current could be observed. However, due to the fast cyclic redox reaction of SOD with superoxide, the communication of the protein with the electrode was strongly influenced. The amperometric detection of superoxide radicals is discussed.

Local dynamic properties of the heme pocket in native and solvent-induced molten-globule-like states of cytochrome c

We report the Soret absorption band, down to cryogenic temperature, of native and molten-globule-like state of horse heart cytochrome c. The band profile is analyzed in terms of vibronic coupling of the heme normal modes to the electronic transition in the framework of the Franck-Condon approximation. From the temperature dependence of the Gaussian broadening and of the peak position, we obtain information on the 'bath' of low frequency harmonic motions of the heme group within the heme pocket. The reported data indicate that, compared to the native state, the less rigid tertiary structure of the molten globule is reflected in a higher flexibility of the heme pocket and in greater conformational disorder, allowing the transduction of large-amplitude motion of the protein to the dynamics of the heme pocket.

Anion protection of CuZnSOD during peroxidative activity with H(2)O(2)

The "peroxidase" activity of the copper-zinc superoxide dismutase is a poorly sustained activity because of the competing inactivation of the enzyme. New evidence suggests that the bound oxidant may be partitioning between oxidizing the enzyme or oxidizing small anions. At constant peroxide, nitrite and azide only partially protect the enzyme (50%) against loss of copper(I) and inactivation up to one anion per copper. Beyond that level, there is no further protection. Bicarbonate ion also protects, but larger amounts are required. These data suggest that there is significant oxidation of the enzyme even in the presence of the small anions and therefore the formation of the bound oxidant cannot be sustained in a true catalytic process.

Antioxidant enzymes and human diseases

OBJECTIVES

To describe the importance of the antioxidant enzymes superoxide dismutase, glutathione peroxidase, and catalase working together in human cells against toxic reactive oxygen species, their relationship with several pathophysiologic processes and their possible therapeutic implications.

CONCLUSIONS

Reactive oxygen species (ROS) are involved in the cell growth, differentiation, progression, and death. Low concentrations of ROS may be beneficial or even indispensable in processes such as intracellular signaling and defense against micro-organisms. Nevertheless, higher amounts of ROS play a role in the aging process as well as in a number of human disease states, including cancer, ischemia, and failures in immunity and endocrine functions. As a safeguard against the accumulation of ROS, several nonenzymatic and enzymatic antioxidant activities exist. Therefore, when oxidative stress arises as a consequence of a pathologic event, a defense system promotes the regulation and expression of these enzymes.

Fourier-transform infrared studies on azide-binding to the binuclear center of the Escherichia coli bo-type ubiquinol oxidase

Azide-binding to the heme-copper binuclear center of bo-type ubiquinol oxidase from Escherichia coli was investigated with Fourier-transform infrared spectroscopy. Deconvolution analyses of infrared spectra of the azide (14N3)-inhibited air-oxidized form showed a major infrared azide antisymmetric stretching band at 2041 cm(-1). An additional band developed at 2062.5 cm(-1) during a longer incubation. Isotope substitutions with terminally 15N-labelled azides did not show a splitting of the major band, indicating that the geometry of the bound azide is mainly in a bridging configuration between high-spin heme o and CuB. The band at 2062.5 cm(-1) showed clear splittings upon substitution with the terminally 15N-labelled azides, indicating the Cu(2+)B-N=N=N structure. Partial reduction of the oxidase with beta-NADH in the presence of azide caused an appearance of new infrared bands at 2038.5 (major) and 2009 (minor) cm(-1). The former band also showed clear splittings in the presence of the terminally 15N-labelled azides, indicating that reduction of low-spin heme b alters the structure of the binuclear center leading to the Fe(3+)o-N=N=N configuration.