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Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450. [ABSTRACT FROM AUTHOR]

In alkaline media (pH 12) a catalytic peroxidase activity of cytochrome b 5 was found associated to a different conformational state. Upon incubation at this pH, cytochrome b 5 electronic absorption spectrum was altered, with disappearance of characteristic bands of cytochrome b 5 at pH 7.0. The appearance of new electronic absorption bands and EPR measurements support the formation of a cytochrome b 5 class B hemichrome with an acquired ability to bind polar ligands. This hemichrome is characterized by a negative formal redox potential and the same folding properties than cytochrome b 5 at pH 7. The acquired peroxidase-like activity of cytochrome b 5 found at pH 12, driven by a hemichrome formation, suggests a role of this protein in peroxidation products propagation. [ABSTRACT FROM AUTHOR]

Chromosome replication in Escherichia coli is initiated by DnaA. DnaA binds ATP which is essential for formation of a DnaA-oriC nucleoprotein complex that promotes strand opening, helicase loading and replisome assembly. Following initiation, DnaAATP is converted to DnaAADP primarily by the Regulatory Inactivation of DnaA process (RIDA). In RIDA deficient cells, DnaAATP accumulates leading to uncontrolled initiation of replication and cell death by accumulation of DNA strand breaks. Mutations that suppress RIDA deficiency either dampen overinitiation or permit growth despite overinitiation. We characterize mutations of the last group that have in common that distinct metabolic routes are rewired resulting in the redirection of electron flow towards the cytochrome bd-1. We propose a model where cytochrome bd-1 lowers the formation of reactive oxygen species and hence oxidative damage to the DNA in general. This increases the processivity of replication forks generated by overinitiation to a level that sustains viability. [ABSTRACT FROM AUTHOR]

The oleaginous yeast Debaryomyces hansenii is a good model to understand molecular mechanisms involved in halotolerance because of its impressive ability to survive under a wide range of salt concentrations. Several cellular adaptations are implicated in this response, including the presence of a cyanide-insensitive ubiquinol oxidase (Aox). This protein, which is present in several taxonomical orders, has been related to different stress responses. However, little is known about its role in mitochondria during transitions from low to high saline environments. In this report, we analyze the effects of Aox in shifts from low to high salt concentrations in the culture media. At early stages of a salt insult, we observed that this protein prevents the overflow of electrons on the mitochondrial respiratory chain, thus, decreasing the production of reactive oxygen species. Interestingly, in the presence of high osmolite concentrations, Aox activity is able to sustain a stable membrane potential when coupled to complex I, despite a compromised cytochrome pathway. Taken together, our results suggest that under high osmolarity conditions Aox plays a critical role regulating mitochondrial physiology. [ABSTRACT FROM AUTHOR]

Hydrogen (H2) consumption and methane (CH4) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 μM added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH4 production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH4 formation rate in the cytochrome-containing Methanosarcina barkeri grown on H2 and CO2. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H2 partial pressure (pH2) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH2 values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH2 threshold recorded to date in pure methanogen culture, which suggests that M.bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H2 concentrations. Our study has implications for research on the H2-driven deep subsurface biosphere and biogas reactor performance. [ABSTRACT FROM AUTHOR]

The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance. [ABSTRACT FROM AUTHOR]

The catalytic activity of cytochrome c (cyt c) to peroxidize cardiolipin to its oxidized form is required for the release of pro-apoptotic factors from mitochondria, and for execution of the subsequent apoptotic steps. However, the structural basis for this peroxidation reaction remains unclear. In this paper, we determined the three-dimensional NMR solution structure of yeast cyt c Y67H variant with high peroxidase activity, which is almost similar to that of its native form. The structure reveals that the hydrogen bond between Met80 and residue 67 is disrupted. This change destabilizes the sixth coordination bond between heme Fe3+ ion and Met80 sulfur atom in the Y67H variant, and further makes it more easily be broken at low pH conditions. The steady-state studies indicate that the Y67H variant has the highest peroxidase activities when pH condition is between 4.0 and 5.2. Finally, a mechanism is suggested for the peroxidation of cardiolipin catalyzed by the Y67H variant, where the residue His67 acts as a distal histidine, its protonation facilitates O-O bond cleavage of H2O2 by functioning as an acidic catalyst. [ABSTRACT FROM AUTHOR]

When Geobacter sulfurreducens utilizes an electrode as its electron acceptor, cells embed themselves in a conductive biofilm tens of microns thick. While environmental conditions such as pH or redox potential have been shown to change close to the electrode, less is known about the response of G. sulfurreducens to growth in this biofilm environment. To investigate whether respiratory protein abundance varies with distance from the electrode, antibodies against an outer membrane multiheme cytochrome (OmcB) and cytoplasmic acetate kinase (AckA) were used to determine protein localization in slices spanning ∼25 µm-thick G. sulfurreducens biofilms growing on polished electrodes poised at +0.24 V (vs. Standard Hydrogen Electrode). Slices were immunogold labeled post-fixing, imaged via transmission electron microscopy, and digitally reassembled to create continuous images allowing subcellular location and abundance per cell to be quantified across an entire biofilm. OmcB was predominantly localized on cell membranes, and 3.6-fold more OmcB was detected on cells 10–20 µm distant from the electrode surface compared to inner layers (0–10 µm). In contrast, acetate kinase remained constant throughout the biofilm, and was always associated with the cell interior. This method for detecting proteins in intact conductive biofilms supports a model where the utilization of redox proteins changes with depth. [ABSTRACT FROM AUTHOR]

Confocal Resonance Raman Microscopy (CRRM) was used to probe variations of redox state of c-type cytochromes embedded in living mixed-culture electroactive biofilms exposed to different electrode polarizations, under potentiostatic and potentiodynamic conditions. In the absence of the metabolic substrate acetate, the redox state of cytochromes followed the application of reducing and oxidizing electrode potentials. Real-time monitoring of the redox state of cytochromes during cyclic voltammetry (CV) in a potential window where cytochromes reduction occurs, evidenced a measurable time delay between the oxidation of redox cofactors probed by CV at the electrode interface, and oxidation of distal cytochromes probed by CRRM. This delay was used to tentatively estimate the diffusivity of electrons through the biofilm. In the presence of acetate, the resonance Raman spectra of young (10 days, j = 208±49 µA cm−2) and mature (57 days, j = 267±73 µA cm−2) biofilms show that cytochromes remained oxidized homogeneously even at layers as far as 70 µm from the electrode, implying the existence of slow metabolic kinetics that do not result in the formation of a redox gradient inside the biofilm during anode respiration. However, old biofilms (80 days, j = 190±37 µA cm−2) with thickness above 100 µm were characterized by reduced catalytic activity compared to the previous developing stages. The cytochromes in these biofilm were mainly in the reduced redox state, showing that only aged mixed-culture biofilms accumulate electrons during anode respiration. These results differ substantially from recent observations in pure Geobacter sulfurreducens electroactive biofilms, in which accumulation of reduced cytochromes is already observed in thinner biofilms, thus suggesting different bottlenecks in current production for mixed-culture and G. sulfurreducens biofilms. [ABSTRACT FROM AUTHOR]

Our previous studies showed that an extract from Camellia sinenesis (green tea), which contains several polyphenols, attenuates nephrotoxicity caused by cyclosporine A (CsA). Since polyphenols are stimulators of mitochondrial biogenesis (MB), this study investigated whether stimulation of MB plays a role in green tea polyphenol protection against CsA renal toxicity. Rats were fed a powdered diet containing green tea polyphenolic extract (0.1%) starting 3 days prior to CsA treatment (25 mg/kg, i.g. daily for 3 weeks). CsA alone decreased renal nuclear DNA-encoded oxidative phosphorylation (OXPHOS) protein ATP synthase-β (AS-β) by 42%, mitochondrial DNA (mtDNA)-encoded OXPHOS protein NADH dehydrogenase-3 (ND3) by 87% and their associated mRNAs. Mitochondrial DNA copy number was also decreased by 78% by CsA. Immunohistochemical analysis showed decreased cytochrome c oxidase subunit IV (COX-IV), an OXPHOS protein, in tubular cells. Peroxisome proliferator-activated receptor-γ coactivator (PGC)-1α, the master regulator of MB, and mitochondrial transcription factor-A (Tfam), the transcription factor that regulates mtDNA replication and transcription, were 42% and 90% lower, respectively, in the kidneys of CsA-treated than in untreated rats. These results indicate suppression of MB by chronic CsA treatment. Green tea polyphenols alone and following CsA increased AS-β, ND3, COX-IV, mtDNA copy number, PGC-1α mRNA and protein, decreased acetylated PGC-1α, and increased Tfam mRNA and protein. In association with suppressed MB, CsA increased serum creatinine, caused loss of brush border and dilatation of proximal tubules, tubular atrophy, vacuolization, apoptosis, calcification, and increased neutrophil gelatinase-associated lipocalin expression, leukocyte infiltration, and renal fibrosis. Green tea polyphenols markedly attenuated CsA-induced renal injury and improved renal function. Together, these results demonstrate that green tea polyphenols attenuate CsA-induced kidney injury, at least in part, through the stimulation of MB. [ABSTRACT FROM AUTHOR]

A novel biosensor was developed by entrapping cytochrome c (Cyt c) in thin films of the room temperature ionic liquid (RTIL) containing nanocomposites of poly(diallyldimethylammonium chloride)-graphene nanosheets-gold nanoparticles (PDDA-Gp-AuNPs) at a 11-mercaptoundecanoic acid-6-mercapto-1-hexanol modified gold electrode. The synthesized PDDA-Gp-AuNPs hybrid nanocomposites were characterized by UV-vis spectroscopy, Raman spectroscopy, scanning electron microscopy and atomic force microscopy. The PDDA-Gp-AuNPs nanocomposites could increase the effective surface of the electrode, enhance the fixed amount of Cyt c on the electrode surface, promote the electron transfer and facilitate the catalytic activity of Cyt c. The RTIL could provide a biocompatible microenvironment to keep Cyt c biological activities, act as an effective mediator to immobilize a large number of Cyt c on the electrode and have good conductivity to improve electron transfer. Therefore, the resultant electrode exhibited good electrochemical performance and electrocatalytic activity. It could be used for electrochemical detection of H2O2 with rapid response, high sensitivity, wide linear range and low detection limit, as well as good stability, repeatability and selectivity. The sensor might be promising for practical application. [ABSTRACT FROM AUTHOR]

Age-related diseases are associated with increased production of reactive oxygen and carbonyl species such as methylglyoxal. Aminoacetone, a putative threonine catabolite, is reportedly known to undergo metal-catalyzed oxidation to methylglyoxal, NH4+ ion, and H2O2 coupled with (i) permeabilization of rat liver mitochondria, and (ii) apoptosis of insulin-producing cells. Oxidation of aminoacetone to methylglyoxal is now shown to be accelerated by ferricytochrome c, a reaction initiated by one-electron reduction of ferricytochrome c by aminoacetone without amino acid modifications. The participation of O2•− and HO• radical intermediates is demonstrated by the inhibitory effect of added superoxide dismutase and Electron Paramagnetic Resonance spin-trapping experiments with 5,5′-dimethyl-1-pyrroline-N-oxide. We hypothesize that two consecutive one-electron transfers from aminoacetone (E0 values = −0.51 and −1.0 V) to ferricytochrome c (E0 = 0.26 V) may lead to aminoacetone enoyl radical and, subsequently, imine aminoacetone, whose hydrolysis yields methylglyoxal and NH4+ ion. In the presence of oxygen, aminoacetone enoyl and O2•− radicals propagate aminoacetone oxidation to methylglyoxal and H2O2. These data endorse the hypothesis that aminoacetone, putatively accumulated in diabetes, may directly reduce ferricyt c yielding methylglyoxal and free radicals, thereby triggering redox imbalance and adverse mitochondrial responses. [ABSTRACT FROM AUTHOR]

Atp6p is an essential subunit of the ATP synthase proton translocating domain, which is encoded by the mitochondrial DNA (mtDNA) in yeast. We have replaced the coding sequence of Atp6p gene with the non-respiratory genetic marker ARG8m. Due to the presence of ARG8m, accumulation of ρ-/ρ0 petites issued from large deletions in mtDNA could be restricted to 20–30% by growing the atp6 mutant in media lacking arginine. This moderate mtDNA instability created favorable conditions to investigate the consequences of a specific lack in Atp6p. Interestingly, in addition to the expected loss of ATP synthase activity, the cytochrome c oxidase respiratory enzyme steady-state level was found to be extremely low (<5%) in the atp6 mutant. We show that the cytochrome c oxidase-poor accumulation was caused by a failure in the synthesis of one of its mtDNA-encoded subunits, Cox1p, indicating that, in yeast mitochondria, Cox1p synthesis is a key target for cytochrome c oxidase abundance regulation in relation to the ATP synthase activity. We provide direct evidence showing that in the absence of Atp6p the remaining subunits of the ATP synthase can still assemble. Mitochondrial cristae were detected in the atp6 mutant, showing that neither Atp6p nor the ATP synthase activity is critical for their formation. However, the atp6 mutant exhibited unusual mitochondrial structure and distribution anomalies, presumably caused by a strong delay in inner membrane fusion. [ABSTRACT FROM AUTHOR]

Using a combination of Mössbauer spectroscopy and density functional calculations, we have determined that the ferryl forms of P450BM3 and P450cam are protonated at physiological pH. Density functional calculations were performed on large active-site models of these enzymes to determine the theoretical Mössbauer parameters for the ferryl and protonated ferryl (FeIVOH) species. These calculations revealed a significant enlargement of the quadrupole splitting parameter upon protonation of the ferryl unit. The calculated quadrupole splittings for the protonated and unprotonated ferryl forms of P450BM3 are ΔEQ = 2.17 mm/s and ΔEQ = 1.05 mm/s, respectively. For P450cam, they are ΔEQ = 1.84 mm/s and ΔEQ = 0.66 mm/s, respectively. The experimentally determined quadrupole splittings (P450BM3, ΔEQ = 2.16 mm/s; P450cam, ΔEQ = 2.06 mm/s) are in good agreement with the values calculated for the protonated forms of the enzymes. Our results suggest that basic ferryls are a natural consequence of thiolate-ligated hemes. [ABSTRACT FROM AUTHOR]

Electrospray ionization in combination with Fourier transform ion cyclotron resonance spectrometry is used to prepare and characterize at a molecular level high-valent oxoiron intermediates formed in the reaction of [(TPFPP)FeIII]Cl (TPFPP= meso-tetrakis(pentafluorophenyl)porphinato dianion) (1-Cl) with H2O2 in methanol. The intrinsic reactivity in the gas phase of the iron(IV) oxo porphyrin cation radical complex, [(TPFPP)·+FeIV=O]+, has been probed toward selected substrates (S), chosen among naturally occurring and model compounds. Whereas CO and cyclohexane proved to be unreactive, olefins, sulfides, amines, and phosphites all undergo oxygen atom transfer in the gas phase yielding the reduction product 1 and/or an adduct ion ([1-S]+). The reaction efficiencies show a qualitative correlation with the oxophilic character of the active site of S. A notable exception is nitric oxide, which displays a remarkably high reactivity, in line with the important role of NO reactions with iron porphyrin complexes. Furthermore, subsidiary information on the neat association reaction of 1 with selected ligands (L) has been obtained by a kinetic study showing that both the efficiency and the extent of ligation toward the naked ion 1 depend on the electron-donating ability of L. [ABSTRACT FROM AUTHOR]

Focuses on the theoretical perspective on the structure and mechanism by cytochrome P450 enzymes. Description of cytochrome P450 enzymes; Advantage of the advances in density functional theory; Presentation of the coverage, sources of computational results, and models of the enzyme.

Studies the structure and chemistry of cytochrome P450. Emphasis on the role of cytochrome P450 in biology; Presence of the cytochrome P450 in all branches of the tree of life that catalogs the diversity of life forms; Discussion on the formation of the peroxol/hydroperoxo complex.

Recent spectroscopic, kinetics, and structural studies on cytochrome c oxidases (CcOs) suggest that the histidine-tyrosine cross-link at the heme a3—CuB binuclear active site plays a key role in the reductive O2-cleavage process. In this report, we describe dioxygen reactivity of copper and heme/Cu assemblies in which the imidazole—phenol moieties are employed as a part of copper ligand LN4OH (2-&lcub;4-[2-(bis-pyridin-2-ylmethyl-amino)-ethyl]-imidazol-1-yl&rcub;-4,6-di -tert-butyl-phenol). Stopped-flow kinetic studies reveal that low-temperature oxygenation of [Cul(LN4OH)]+ (1) leads to rapid formation of a copper-superoxo species [Cull(LN4OH)(O2-)]+ (1a), which further reacts with 1 to form the 2:1 Cu:O2 adduct, peroxo complex [&lcub;Cull(LN4OH)&rcub;2(O22-)]22+ (1b). Complex 1b is also short-lived, and a dimer Cu(II)-phenolate complex [CuII(LN4O-)]22+ (1c) eventually forms as a final product in the later stage of the oxygenation reaction. Dioxygen reactivities of 1 and its anisole analogue [CuI(LN4OMe)]+ (2) in the presence of a heme complex (F8)FeII (3) (F8 = tetrakis(2,6,-difluorotetraphenyl)-porphyrinate) are also described. Spectroscopic investigations including UV-vis, 1H and 2H NMR, EPR, and resonance Raman spectroscopies along with spectrophotometric titration reveal that low-temperature oxygenation of 1/3 leads to formation of a heme-peroxo-copper species [(F8)FeIII-(O22 )-CuII(LN4OH)]+ (4), v(o-o) = 813 cm-1 Complex 4 is an S = 2 spin system with strong antiferromagnetic coupling between high-spin iron(III) and copper(II) through a bridging peroxide ligand. A very similar complex [(F8)FeIII-(O22- )-CuII(LN4OMe)]+ (5) (v(o-o) = 815 cm-1) can be generated by utilizing the anisole compound 2, which indicates that the cross-linked phenol moiety in 4 does not interact with the bridging peroxo group between heme and copper. This investigation thus reveals that a stable heme-peroxo-copper species can be generated even in the presence of an imidazole-phenol group (i.e., possible electron/proton donor source) in close proximity. Future studies are needed to probe key factors that can trigger the reductive O-O cleavage in CcO model compounds. [ABSTRACT FROM AUTHOR]

Abstract: Models capable of predicting the possible involvement of cytochromes P450 in the metabolism of drugs or drug candidates are important tools in drug discovery and development. Ideally, functional information would be obtained from crystal structures of all the cytochromes P450 of interest. Initially, only crystal structures of distantly related bacterial cytochromes P450 were available—comparative modeling techniques were used to bridge the gap and produce structural models of human cytochromes P450, and thereby obtain some useful functional information. A significant step forward in the reliability of these models came four years ago with the first crystal structure of a mammalian cytochrome P450, rabbit CYP2C5, followed by the structures of two human enzymes, CYP2C8 and CYP2C9, and a second rabbit enzyme, CYP2B4. The evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism, is presented as a case study. [Copyright &y& Elsevier]

Abstract: The coordination chemistry of the one-electron reduced form of nitric oxide, termed a nitroxyl or nitrosyl hydride (NO− or HNO), is described with special focus on its interaction with hemes and heme model complexes. Nitroxyl intermediates have been proposed in the catalytic cycles of several heme-based nitrite and nitric oxide reductases; in fungal cytochrome P450nor, a short-lived nitroxyl-adduct has been observed during catalytic turnover. Ferrous-nitroxyl adducts were first identified in electrochemical reductions of nitrosyl porphyrins and heme proteins, but only recently have these species been characterized in solution. Small molecule HNO complexes of transition metals are rare, and the several reported species are presented with descriptions of their synthesis, and a comparison of available spectroscopic data. Special emphasis is given to the long-lived HNO adduct of myoglobin, including its synthesis by various routes and characterization by 1H NMR, resonance Raman and X-ray absorption spectroscopy. HNO is isoelectronic with 1O2, and as with oxymyoglobin, there are several possible descriptions for its bonding with a ferrous heme; an analogy to the π-bonding interactions of a Fischer carbene is presented. A survey of the reactivity associated with the characterizable HNO complexes is made, including redox and protonation equilibrium, reactivity with small molecules, and dissociation or displacement reactions. [Copyright &y& Elsevier]

New compounds were tested in vitro on aromatase activity in human placental and equine testicular microsomes. Equine aromatase, very well characterized biochemically, is used as a comparative model to understand the mechanism of aromatase inhibition. Among 15 molecules screened, 5 of them ( 11 - 15 ) strongly inhibit human and equine aromatases with IC 50 values ranging from 13-85 nM and from 23-103 nM respectively. These results were corroborated by K i / K m values. Moreover, spectral studies showed a type II spectrum with both enzymes, which is characteristic of an interaction between the nitrogen atom of the molecule and the heme of the cytochrome P450. Compound 12 , which has the lowest IC 50 and K i / K m ratio, inactivates aromatase in a dose and time-dependent manner. This might be very important for the treatment of estrogen-dependent diseases such as breast cancer. Finally, MTT assays on E293 cells revealed that the molecules were not cytotoxic. [ABSTRACT FROM AUTHOR]

In cyanobacteria, cytochrome c6 and plastocyanin are able to replace each other as redox carriers in the photosynthetic and respiratory electron transport chains with the synthesis of one or another protein being regulated by the copper concentration in the culture medium. However, the presence of a third unidentified electron carrier has been suggested. To address this point, we have constructed two deletion mutants of the cyanobacterium Synechocystis sp. PCC 6803, each variant lacking either the pete or petJ gene, which respectively codes for the copper or heme protein. The photoautotrophic and heterotrophic growth rate of the two mutants in copper-free and copper-supplemented medium as well as their photosystem I reduction kinetics in vivo were compared with those of wild-type cells. The two mutant strains grow at equivalent rates and show similar in vivo photosystem I reduction kinetics as wildtype cells when cultured in media that allow the expression of just one of the two electron donor proteins, but their ability to grow and reduce photosystem I is much lower when neither cytochrome c6 nor plastocyanin is expressed. These findings indicate that the normal functioning of the cyanobacterial photosynthetic and respiratory chains obligatorily depends on the presence of either cytochrome c6 or plastocyanin. [ABSTRACT FROM AUTHOR]

The pre-steady-state reduction of cytochrome P450 (P450) 2B4 by P450 reductase (reductase) was modeled by assuming that an equilibrium between three catalytic conformers of P450 regulates the multi-phasic reduction of the enzyme. This model was compared to a model of reduction involving a minimum number of phases. Based on several criteria, the former model seems to provide an improved fit to the reduction data. Substrates were divided into two groups based on their effects at different concentrations of reductase. Surprisingly, in the presence of some substrates (group 1) but not others (group 2), the rate of reduction was actually slower with an excess of reductase than with equimolar reductase and P450. Presumably, oxidized reductase binds differently to P450 than reduced reductase. A schematic model based on two sites of interaction between reductase and P450 2B4 is offered to explain the unusual reduction kinetics with the two different groups of substrates. [Copyright &y& Elsevier]

Presents the study on the contact shifts and magnetic tensor orientation in Rhodobacter capsulatus ferrocytochrome. Magnetic susceptibility studies of Rhodobacter capsulatus ferrocytochrome; Determination of the differences in chemical shift; Orientation and anisotropy of the paramagnetic susceptibility tensor; Paramagnetic chemical shifts of heme protons.

1H nuclear magnetic resonance (NMR) spectroscopy has been used to examine cytochrome c551.5 (c7) from the sulfur reducer, Desulfuromonas acetoxidans. This protein contains three hemes. Two stable oxidation states (the fully oxidized and the fully reduced) as well as intermediate oxidation states were studied. The axial ligands of the iron were found to be neutral histidines. The redox properties of cytochrome c7 were examined and good quantitative agreement found between the NMR results and previously reported redox potential measurements. The properties of cytochrome c7 are discussed together with those of the homologous tetraheme cytochromes c3 isolate from sulfate-reducing bacteria. [ABSTRACT FROM AUTHOR]

Phenobarbital-induced coumarin 7-hydroxylase is high in DBA/2J and low in C57BL/6N inbred mice: this genetic difference is encoded by tide Coli locus on chromosome 7. The aim of this study was to develop art antibody specific for this cytochrome P-450 polymorphism. P-450 fractions, highly specific for phenobarbital-inducible coumarin 7-hydroxylase activity, were purified from DBA/2J and C57BL/6N mouse liver microsomes. Both proteins are 49 kDa. as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Soret peaks of the reduced cytochrome · CO complexes are 451 nm. Reconstituted DBA/2J coumarin 7-hydroxylase activity exhibits a V twice as high as, and a Km value 10-fold less than, the reconstituted C57BL/6N activity. Antibodies were raised in rabbit. By Ouchterlony immunodiffusion, both antibodies show 100% cross-reactivity with DBA/2J and C57BL/6N microsomes and purified antigens. Yet, DBA/2J but not C57BL/6N 7-hydroxylase activity is inhibited by the antibody to DBA/2J P-450. Both DBA/2J and C57BL/6N activities are blocked by the antibody to C57BL/6N P-450. Neither antibody has any effect on liver microsomal d-benzphetamine N-demethylase, ethylmorphine N-demethylase, aminopyrine N-demethylase. 7-ethoxycoumarin O-deethylase, acetanilide 4-hydroxylase, or aryl hydrocarbon (benzo[a]pyrene) hydroxylase activity. The DBA/2J protein most specific for phenobarbital-induced coumarin 7-hydroxylation is designated ‘P-450Coh’. Anti-(P-450Coh) precipitates a relatively minor 49-kDa protein from detergent-solubilized microsomes and from in vitro translation of poly(A+)-enriched total RNA of phenobarbital-treated DBA/2J mouse liver, whereas the major phenobarbital-induced P-450 proteins exhibit a molecular mass of about 51 kDa. The immunoprecipitated translation products correspond to a messenger RNA of 2100±100 nucleotides. [ABSTRACT FROM AUTHOR]

The behaviour of cytochrome b5 reductase holoenzyme and apoenzyme toward blue-dextran-Sepharose has been studied. Holoenzyme was adsorbed at low ionic strength and could be eluted with 100 μM NADH or NAD+. Flavin-free enzyme was even more strongly bound and could be eluted with 1 M NaCl, or 100 μM NADH + 10 μM FAD. Separately the cofactors were without effect. FMN was less effective than FAD. ADP and AMP eluted nothing. Cibacron blue F3GA was found to exert a mixed inhibition on NADH oxidation. Dye binding to holoenzyme elicited a characteristic red shift in its spectrum. Comparison of the difference spectrum amplitudes at 680 and 585 nm showed the presence of a second binding mode at higher dye concentrations. These results point to the existence for cytochrome b5 reductase of two binding sites with high affinity for blue-dextran-Sepharose: the NADH binding site and the flavin binding site. For the latter it is clear that the isoalloxazine pocket must play a role in dye binding. Cytochrome b5 reductase is the second flavoenzyme which has been shown to have affinity for immobilized dye at the flavin site, the first one being flavocytochrome b2, an FMN-dependent enzyme [D. Pompon and F. Lederer (1978) Eur. J. Biochern. 90, 563–569]. [ABSTRACT FROM AUTHOR]

1. The effects of perchlorate on cytochrome c have been investigated by 1H and 35Cl NMR, electron paramagnetic resonance and optical spectroscopy. 2. The pK values for the formation and disappearance of the major alkaline conformation were found to be displaced from 9.3 to 8.3 and from 10.4 to 10.9, respectively. The displacement was dependent on the ClO4- concentration below 0.1 M. 3. Competition experiments between perchlorate and chloride show that ClO4- binds both to the neutral and alkaline forms but with a higher affinity for the latter. The appearance of a new binding site in the alkaline form accounts for the markedly enhanced relaxation rate of 35ClO4- in this pH range. Complex formation between cyanide and the alkaline species results in the loss of this binding site, which probably is located close to or within the heme crevice. 4. The neutral form of ferricytochrome c also binds perchlorate strongly as evidence by the unique appearance of a high-spin signal dependent on pH and perchlorate concentration. This signal disappears with the same pK value as the neutral form. The effects of perchlorate on cytochrome c are due to specific binding of this ion. [ABSTRACT FROM AUTHOR]

Cytochrome-c-deficient mutants ofAzotobacter vinelandiihave been isolated following mutagenesis with N-methyl-N′-nitro-N-nitrosoguanidine. These mutants grow well under nitrogen-fixing conditions and studies of the physiology and energy conservation efficiency show no apparent differences from those of the parent strain. Under oxygen-limited growth conditions, the growth rate of the cytochrome-c-deficient mutant was slightly slower (approx. 15%) than that of the parent strain. Cytochromes of the c-type are required for the oxidation of artificial electron donors such as reduced N,N,N′,N′-tetramethyl-p-phenylenediamine [Ph(NMe2)2]. This study could not demonstrate a physiological role for the c-type cytochromes which further supports the idea that the minor Ph(NMe2)2-oxidizing pathway of the electron transport chain may be independent of the major pathway terminated by cytochrome d. [ABSTRACT FROM AUTHOR]

In the present study, we synthesized 14C-labelled 5-nitro-l.2.4-triazol-3-one (NTO) and investigated its hepatic metabolism by dexamethasone-induced murine hepatic microsomes. Under the nitrogen atmosphere. 5-amino-l.2.4-triazol-3-one was the only detected metabolite of NTO. The microsomal nitroreductase activity was dependent on NADPH, totally inhibited by carbon monoxide and partially inhibited by oxygen. In aerobic conditions, beside a low amount of amine, the major metabolite formed is the 5-hydroxy-triazolone, urazole. This compound resulted from the oxidative denitrification of NTO, which produced equivalent amount of nitrite. This reaction, like the nitroreductase activity, was dependent on NADPH and totally inhibited by carbon monoxide. Both nitroreduction and oxidative denitrification were inhibited by imidazole-related inhibitors: miconazole and methimazole, and to a less extent by N-octylamine. The microsomal denitrification was induced by the treatment of mrs with dexamethasone and phenobarbital. The microsomal reductase activity is present in untreated rat microsomes, and recovered with various inducers. The results of this study indicate the role played by cytochrome P-450 in the metabolism of NTO. supported by its transformation with reconstituted cytochrome P-450 systems. [ABSTRACT FROM AUTHOR]

Two new multiheme cytochromes were isolated from the anaerobic sulfur reducing bacterium Desulfuromonas acetoxidans. They have monomeric molecular masses of 50 and 65 kDa and contain six and eight hemes, respectively. Visible and EPR spectroscopies, in the as-isolated (oxidised) cytochromes, show the presence of only low-spin hemes in the 50-kDa cytochrome, and of high-spin and low-spin hemes in the 65-kDa cytochrome. The EPR spectra of the native 65-kDa cytochrome indicate multiple heme—heme interactions, including integer-spin systems as judged by parallel-mode EPR. The 50-kDa cytochrome has a complex redox pattern, as shown by EPR redox titrations, and contains one heine with unusual characteristics. Both cytochromes cover an extremely wide range of reduction potentials, which go from + 100 mV to - 375 mV for the 50-kDa cytochrome, and +185 mV to -235 mV for the 65-kDa cytochrome. The two cytochromes were tested for hydroxylamine oxidoreductase activity and polysulfide reductase activity, but neither displayed any activity. In contrast, it was found for the first time that the previously characterised cytochrome c551.5, from the same bacterium is very active in the reduction of polysulfide, which suggests that it acts as a terminal reductase in D. acetoxidans. [ABSTRACT FROM AUTHOR]

The evolution of CYP102A1 variants with enhanced activity and altered specificity characteristics. [ABSTRACT FROM AUTHOR]

Cites key research findings indicating a new and earlier pro-apoptotic role for cytochrome c. Role of cytochrome c release from the mitochondria as a component of the apoptotic cell-death program; Effects of the cytochrome c-catalyzed peroxidation of cardiolipin on the binding of cytochrome c to the mitochondrial inner membrane and the permeabilization of the outer membrane; Implications for chemistry and biology.