The diheme cytochrome c peroxidase from Shewanella oneidensis requires reductive activation

Control of spin coupling through a redox-active bridge in a dinickel(II) porphyrin dimer: step-wise oxidations enable isolations of a chlorin-porphyrin heterodimer and a dication diradical with a singlet ground state

A dinickel(II)porphyrin dimer has been used here in which the redox-active pyrrole-moiety, similar to the tryptophan residue in diheme enzymes such as MauG and bCcP, has been placed between two Ni(II)porphyrin centers connected via a flexible, but unconjugated methylene bridge. This arrangement provides a large physical separation between the two metal centers and thus displays almost no communication between them through the bridge. Upon treatment with DDQ as an oxidant, the dinickel(II) porphyrin dimer slowly gets converted into an indolizinium-fused chlorin-porphyrin heterodimer. However, oxidations of the dinickel(II) porphyrin dimer up to two oxidizing equivalents using oxidants such as AgSbF₆ and FeCl₃ resulted in the formation of a dication diradical complex. Interestingly, in order to stabilize such a highly oxidized dication diradical, two non-conjugated methylene spacers undergo facile 2e^-/-2H⁺ oxidation to make the bridge fully π-conjugated for promoting through-bond communication. Through the oxidized and conjugated bridge, two porphyrin π-cation radicals display considerable communications leading to an efficient intramolecular spin coupling to form a singlet state. Interestingly, the redox-active nature of the bridge controls the electronic communication just by simple oxidation or reduction, and thereby, acts as a molecular switch for efficient magnetic relay.

The Roles of DmsEFAB and MtrCAB in Extracellular Reduction of Iodate by Shewanella oneidensis MR-1 with Lactate as the Sole Electron Donor

To investigate their roles in extracellular reduction of iodate (IO₃ ^- ) with lactate as an electron donor, the gene clusters of dmsEFAB, mtrCAB, mtrDEF, and so4360-4357 in Shewanella oneidensis MR-1were systematically deleted. Deletions of dmsEFAB and/or mtrCAB gene clusters diminished the bacterial ability to reduce IO₃ ^- . Furthermore, DmsEFAB and MtrCAB worked collaboratively to reduce IO₃ ^- of which DmsEFAB played a more dominant role than MtrCAB. MtrCAB was involved in detoxifying the reaction intermediate hydrogen peroxide (H₂ O₂ ). The reaction intermediate hypoiodous acid (HIO) was also found to inhibit microbial IO₃ ^- reduction. SO4360-4357 and MtrDEF, however, were not involved in IO₃ ^- reduction. Collectively, these results suggest a novel mechanism of extracellular reduction of IO₃ ^- at molecular level, in which DmsEFAB reduces IO₃ ^- to HIO and H₂ O₂ . The latter is further reduced to H₂ O by MtrCAB to facilitate the DmsEFAB-mediated IO₃ ^- reduction. The extracellular electron transfer pathway of S. oneidensis MR-1is believed to mediate electron transfer from bacterial cytoplasmic membrane, across the cell envelope to the DmsEFAB and MtrCAB on the bacterial outer membrane.

Highly Oxidized Cobalt Porphyrin Dimer: Control of Spin Coupling via a Bridge

A cobalt porphyrin dimer is constructed in which two Co(II)porphyrins are connected covalently through a redox-active diethylpyrrole moiety via a flexible but "nonconjugated" methylene bridge. Upon oxidation with even a mild oxidant such as iodine, each cobalt(II) center and porphyrin ring undergo 1e^- oxidation, leading to the formation of a 4e^--oxidized cobalt(III)porphyrin dication diradical complex. Other oxidants such as Cl₂ and Br₂ also produce similar results. To stabilize such highly oxidized dication diradicals, the "nonconjugated" methylene spacer undergoes a facile and spontaneous oxidation to form a methine group with a drastic structural change, thereby making the bridge fully π-conjugated and enabling through-bond communication. This results in a strong spin coupling between two π-cation radicals which stabilizes the singlet state. The experimental observations are also strongly supported by extensive density functional theory calculations. The present study highlights the crucial role played by the nature of the bridge in the long-range electronic communication.

Ferromagnetic Coupling in Oxidovanadium(IV)-Porphyrin Radical Dimers

Three different oxidovanadium(IV) porphyrin dimers with anti, cis, and trans arrangements of the two rings have been synthesized by changing the bridge between the porphyrin macrocycles. This provides a unique opportunity to investigate the role of the bridge and spatial arrangement between the two V^IVO centers for their electronic communication and magnetic coupling. They were characterized by the combined application of XRD analysis, UV-vis and electron paramagnetic resonance (EPR) spectroscopy, cyclic voltammetry, magnetic susceptibility, and DFT calculations. One- and two-electron oxidations produce mono- and dication diradical species, respectively, which display an unusual ferromagnetic interaction between the unpaired spins of vanadium(IV) and porphyrin π-cation radical, in contrast to other metalloporphyrin dimers. The oxidized species show a dissimilar behavior between cis and trans isomers. The ferromagnetic coupling occurs between the porphyrin π-cation radical and the unpaired electron of the V^IVO ion on the d_xy orbital, orthogonal to the porphyrin-based molecular orbitals a_1u and a_2u.

The redox potential of a heme cofactor in Nitrosomonas europaea cytochrome c peroxidase: a polarizable QM/MM study

Redox reactions are crucial to biological processes that protect organisms against oxidative stress. Metalloenzymes, such as peroxidases which reduce excess reactive oxygen species into water, play a key role in detoxification mechanisms. Here we present the results of a polarizable QM/MM study of the reduction potential of the electron transfer heme in the cytochrome c peroxidase of Nitrosomonas europaea. We have found that environment polarization does not substantially affect the computed value of the redox potential. Particular attention has been given to analyzing the role of electrostatic interactions within the protein environment and the solvent on tuning the redox potential of the heme co-factor. We have found that the electrostatic interactions predominantly explain the fluctuations of the vertical ionization/attachment energies of the heme for the sampled configurations, and that the long range electrostatic interactions (up to 40 Å) contribute substantially to the absolute values of the vertical energy gaps.

Through Bridge Spin Coupling in Homo- and Heterobimetallic Porphyrin Dimers upon Stepwise Oxidations: A Spectroscopic and Theoretical Investigation

We have described copper(II)-iron(III) and copper(II)-manganese(III) heterobimetallic porphyrin dimers and compared them with the corresponding homobimetallic analogs. UV-visible spectra are very distinct in the heterometallic species while electrochemical studies demonstrate that these species, as compared to the homobimetallic analog, are much easier to oxidize. Combined Mössbauer, EPR, NMR, magnetic and UV-visible spectroscopic studies show that upon 2e-oxidation of the heterobimetallic complexes only ring-centered oxidation occurs. The energy differences between HOMO and LUMO are linearly dependent with the low-energy NIR band obtained for the 2e-oxidized complexes. Also, strong electronic communication between two porphyrin rings through the bridge facilitates coupling between various unpaired spins present while the coupling model depends on the nature of metal ions used. While unpaired spins of Fe(III) and the porphyrin π-cation radical are strongly antiferromagnetically coupled, such coupling is rather weak between Mn(III) and a porphyrin π-cation radical. Moreover, the coupling between two π-cation radicals are much stronger in the 2e-oxidized complexes of dimanganese(III) and copper(II)-manganese(III) porphyrin dimers as compared to their diiron(III) and copper(II)-iron(III) analogs. Furthermore, coupling between the unpaired spins of a π-cation radical and copper(II) is much stronger in the 2e-oxidized complex of copper(II)-iron(III) porphyrin dimer as compared to its copper(II)-manganese(III) analog. The Mulliken spin density distributions in 2e-oxidized homo- and heterobimetallic complexes show symmetric and asymmetric spread between the two macrocycles, respectively. In both the 2e-oxidized heterobimetallic complexes, the Cu(II) porphyrin center acts as a charge donor while Fe(III)/Mn(III) porphyrin center act as a charge acceptor. The experimental observations are also strongly supported by DFT calculations.

A Stable Ferryl Porphyrin at the Active Site of Y463M BthA

BthA is a diheme enzyme that is a member of the bacterial cytochrome c peroxidase superfamily, capable of generating a highly unusual Fe(IV)Fe(IV)═O oxidation state, known to be responsible for long-range oxidative chemistry in the enzyme MauG. Here, we show that installing a canonical Met ligand in lieu of the Tyr found at the heme of MauG associated with electron transfer, results in a construct that yields an unusually stable Fe(IV)═O porphyrin at the peroxidatic heme. This state is spontaneously formed at ambient conditions using either molecular O₂ or H₂O₂. The resulting data illustrate how a ferryl iron, with unforeseen stability, may be achieved in biology.

Stacks of Metalloporphyrins: Comparison of Experimental and Computational Results

Numerous metalloporphyrin stacks have been synthesized and studied. Electronic interactions between constituent metalloporphyrins are able to determine the structures and properties of porphyrin arrays. In 2016, Co(II)-, Cu(II)-, Pt(II)-, and Zn(II)-porphyrins were shown to pack to form dimers as well as trimers. Porphyrin rings were found to strongly overlap with lateral shifts between ring centers. However, no binding energies and electronic structures of these stacks have been reported. We have performed first computational study of the dimers of Co(II)-, Cu(II)-, and Zn(II)-porphyrins, both in vacuum and in two implicit solvents. For all three stacks the configurations with strong overlap of the metalloporphyrin rings with lateral shifts between ring centers were found to be the global minimum structures, ¹A for [ZnP]₂ and ³A for [CuP]₂ and [CoP]₂. Also, open-shell singlets with the same energy or close-lying in energy were found for [CuP]₂ and [CoP]₂. The binding energies were calculated to be significant, from ca. -13 to -39 kcal/mol (gas phase, depending on the computational approach). The computational results showed quite good agreement with the experimental data. The dimers were found to be bound by strong bonding combinations of the monomer MOs which explained significant binding energies computed for the dimers. The shifted dimer configurations could be explained by the way how the monomer MOs preferably overlap.

MbnH is a diheme MauG-like protein associated with microbial copper homeostasis

Methanobactins (Mbns) are ribosomally-produced, post-translationally modified peptidic copper-binding natural products produced under conditions of copper limitation. Genes encoding Mbn biosynthetic and transport proteins have been identified in a wide variety of bacteria, indicating a broader role for Mbns in bacterial metal homeostasis. Many of the genes in the Mbn operons have been assigned functions, but two genes usually present, mbnP and mbnH, encode uncharacterized proteins predicted to reside in the periplasm. MbnH belongs to the bacterial diheme cytochrome c peroxidase (bCcP)/MauG protein family, and MbnP contains no domains of known function. Here, we performed a detailed bioinformatic analysis of both proteins and have biochemically characterized MbnH from Methylosinus (Ms.) trichosporium OB3b. We note that the mbnH and mbnP genes typically co-occur and are located proximal to genes associated with microbial copper homeostasis. Our bioinformatics analysis also revealed that the bCcP/MauG family is significantly more diverse than originally appreciated, and that MbnH is most closely related to the MauG subfamily. A 2.6 Å resolution structure of Ms. trichosporium OB3b MbnH combined with spectroscopic data and peroxidase activity assays provided evidence that MbnH indeed more closely resembles MauG than bCcPs, although its redox properties are significantly different from those of MauG. The overall similarity of MbnH to MauG suggests that MbnH could post-translationally modify a macromolecule, such as internalized CuMbn or its uncharacterized partner protein, MbnP. Our results indicate that MbnH is a MauG-like diheme protein that is likely involved in microbial copper homeostasis and represents a new family within the bCcP/MauG superfamily.

Reduction of hydrogen peroxide in gram-negative bacteria - bacterial peroxidases

Bacteria display an array of enzymes to detoxify reactive oxygen species that cause damage to DNA and to other biomolecules leading to cell death. Hydrogen peroxide is one of these species, with endogenous and exogenous sources, such as lactic acid bacteria, oxidative burst of the immune system or chemical reactions at oxic-anoxic interfaces. The enzymes that detoxify hydrogen peroxide will be the focus of this review, with special emphasis on bacterial peroxidases that reduce hydrogen peroxide to water. Bacterial peroxidases are periplasmic cytochromes with either two or three c-type haems, which have been classified as classical and non-classical bacterial peroxidases, respectively. Most of the studies have been focus on the classical bacterial peroxidases, showing the presence of a reductive activation in the presence of calcium ions. Mutagenesis studies have clarified the catalytic mechanism of this enzyme and were used to propose an intramolecular electron transfer pathway, with far less being known about the intermolecular electron transfer that occurs between reduced electron donors and the enzyme. The physiological function of these enzymes was not very clear until it was shown, for the non-classical bacterial peroxidase, that this enzyme is required for the bacteria to use hydrogen peroxide as terminal electron acceptor under anoxic conditions. These non-classical bacterial peroxidases are quinol peroxidases that do not require reductive activation but need calcium ions to attain maximum activity and share similar catalytic intermediates with the classical bacterial peroxidases.

A widely distributed diheme enzyme from Burkholderia that displays an atypically stable bis-Fe(IV) state

Bacterial diheme peroxidases represent a diverse enzyme family with functions that range from hydrogen peroxide (H2O2) reduction to post-translational modifications. By implementing a sequence similarity network (SSN) of the bCCP_MauG superfamily, we present the discovery of a unique diheme peroxidase BthA conserved in all Burkholderia. Using a combination of magnetic resonance, near-IR and Mössbauer spectroscopies and electrochemical methods, we report that BthA is capable of generating a bis-Fe(IV) species previously thought to be a unique feature of the diheme enzyme MauG. However, BthA is not MauG-like in that it catalytically converts H2O2 to water, and a 1.54-Å resolution crystal structure reveals striking differences between BthA and other superfamily members, including the essential residues for both bis-Fe(IV) formation and H2O2 turnover. Taken together, we find that BthA represents a previously undiscovered class of diheme enzymes, one that stabilizes a bis-Fe(IV) state and catalyzes H2O2 turnover in a mechanistically distinct manner.

Oxidized OxyR Up-Regulates ahpCF Expression to Suppress Plating Defects of oxyR- and Catalase-Deficient Strains

It is well established that in bacteria, such as Escherichia coli, OxyR is a transcriptional regulator that mediates the response to H₂O₂ by activating the OxyR regulon, which consists of many genes that play vital roles in oxidative stress resistance. In Shewanella, OxyR regulates, however, in both reduced and oxidized states, the production of H₂O₂ scavengers, including major catalase KatB and NADH peroxidase AhpCF. Here we showed that the oxyR mutant carried a plating defect manifested as division arresting, a phenotype that can be completely suppressed by an OxyR variant constitutively existing in oxidized form (OxyR^L197P). This effect of OxyR^L197P could not be solely attributed to the increment in KatB production, since the suppression was also observed in the absence of KatB. Although expression of peroxidase CcpA was greatly activated by OxyR^L197P, the contribution of the protein in alleviating plating defect was negligible. We eventually identified AhpCF as the critical factor, when produced at substantially elevated levels by OxyR^L197P, to protect the cell from H₂O₂ attack. Our data indicate that AhpCF is a particularly important peroxidase in oxidative stress resistance in Shewanella, not only playing a compensatory role for catalase, but also by itself providing sufficient protection from killing of H₂O₂ generated abiotically.

A dimanganese(iii) porphyrin dication diradical and its transformation to a μ-hydroxo porphyrin–oxophlorin heterodimer

Spin coupling models are different between iron and manganese in their dication diradical complexes, which is reflected in their reactivity as shown.

Stepwise oxidations of a nickel(ii)–iron(iii) heterobimetallic porphyrin dimer: structure, spectroscopic and theoretical investigation

A novel nickel(ii)–iron(iii) heterobimetallic ethene-bridged porphyrin dimer has been synthesized which upon two-electron oxidation produces a nickel(ii)–iron(iii) dication diradical complex where radicals undergo extensive conjugation through the bridge for all possible interactions.

Resonance Raman, Electron Paramagnetic Resonance, and Magnetic Circular Dichroism Spectroscopic Investigation of Diheme Cytochrome c Peroxidases from Nitrosomonas europaea and Shewanella oneidensis

Cytochrome c peroxidases (bCcPs) are diheme enzymes required for the reduction of H₂O₂ to water in bacteria. There are two classes of bCcPs: one is active in the diferric form (constitutively active), and the other requires the reduction of the high-potential heme (H-heme) before catalysis commences (reductively activated) at the low-potential heme (L-heme). To improve our understanding of the mechanisms and heme electronic structures of these different bCcPs, a constitutively active bCcP from Nitrosomonas europaea ( NeCcP) and a reductively activated bCcP from Shewanella oneidensis ( SoCcP) were characterized in both the diferric and semireduced states by electron paramagnetic resonance (EPR), resonance Raman (rRaman), and magnetic circular dichroism (MCD) spectroscopy. In contrast to some previous crystallographic studies, EPR and rRaman spectra do not indicate the presence of significant amounts of a five-coordinate, high-spin ferric heme in NeCcP or SoCcP in either the diferric or semireduced state in solution. This observation points toward a mechanism of activation in which the active site L-heme is not in a static, five-coordinate state but where the activation is more subtle and likely involves formation of a six-coordinate hydroxo complex, which could then react with hydrogen peroxide in an acid-base-type reaction to create Compound 0, the ferric hydroperoxo complex. This mechanism lies in stark contrast to the diheme enzyme MauG that exhibits a static, five-coordinate open heme site at the peroxidatic heme and that forms a more stable Fe^IV═O intermediate.

YhjA - An Escherichia coli trihemic enzyme with quinol peroxidase activity

The trihemic bacterial cytochrome c peroxidase from Escherichia coli, YhjA, is a membrane-anchored protein with a C-terminal domain homologous to the classical bacterial peroxidases and an additional N-terminal (NT) heme binding domain. Recombinant YhjA is a 50 kDa monomer in solution with three c-type hemes covalently bound. Here is reported the first biochemical and spectroscopic characterization of YhjA and of the NT domain demonstrating that NT heme is His63/Met125 coordinated. The reduction potentials of P (active site), NT and E hemes were established to be -170 mV, +133 mV and +210 mV, respectively, at pH 7.5. YhjA has quinol peroxidase activity in vitro with optimum activity at pH 7.0 and millimolar range K_M values using hydroquinone and menadiol (a menaquinol analogue) as electron donors (K_M = 0.6 ± 0.2 and 1.8 ± 0.5 mM H₂O₂, respectively), with similar turnover numbers (k_cat = 19 ± 2 and 13 ± 2 s^-1, respectively). YhjA does not require reductive activation for maximum activity, in opposition to classical bacterial peroxidases, as P heme is always high-spin 6-coordinated with a water-derived molecule as distal axial ligand but shares the need for the presence of calcium ions in the kinetic assays. Formation of a ferryl Fe(IV) = O species was observed upon incubation of fully oxidized YhjA with H₂O₂. The data reported improve our understanding of the biochemical properties and catalytic mechanism of YhjA, a three-heme peroxidase that uses the quinol pool to defend the cells against hydrogen peroxide during transient exposure to oxygenated environments.

Multiheme proteins: effect of heme–heme interactions

This Frontier illustrates a brief personal account on the effect of heme–heme interactions in dihemes which thereby discloses some of the evolutionary design principles involved in multiheme proteins for their diverse structures and functions.

Biochemical characterization of the bacterial peroxidase from the human pathogen Neisseria gonorrhoeae

Neisseria gonorrhoeae is an obligate human pathogen that expresses an array of molecular systems to detoxify reactive oxygen species as defense mechanisms during colonization and infection. One of these is the bacterial peroxidase that reduces H₂O₂ to water in its periplasm. The soluble form of this enzyme was heterologously expressed in E. coli in the holo-form binding two c-types hemes, a high-potential E heme and a low-potential P heme, with redox potentials of (+310mV) and (-190mV/-300mV), respectively in the presence of calcium ions, at pH7.5. Visible and EPR spectroscopic analysis together with activity assays indicate the presence of a calcium dependent reductive activation mechanism in thgonorrhoeaeNeisseria gonorrhoeae bacterial peroxidase, in which P heme is bis-His coordinated low-spin in the fully oxidized state of the enzyme, and becomes penta-coordinated high-spin upon reduction of E heme in the presence of calcium ions. The activated enzyme has a high affinity for H₂O₂ (K_M of 4±1μM), with maximum activity being attained at pH7.0 and 37°C, with the rate-limiting step in the catalytic cycle being the electron transfer between the two hemes. In this enzyme, dimer formation is not promoted at high ionic strength, thus differing from the classical bacterial peroxidases. These results contribute to the understanding of the involvement of Neisseria gonorrhoeae bacterial peroxidase has a first line defense mechanism against exogenously produced hydrogen peroxide in the host environment.

Functionally Distinct Bacterial Cytochrome c Peroxidases Proceed through a Common (Electro)catalytic Intermediate

The diheme cytochrome c peroxidase from Shewanella oneidensis (So CcP) requires a single electron reduction to convert the oxidized, as-isolated enzyme to an active conformation. We employ protein film voltammetry to investigate the mechanism of hydrogen peroxide turnover by So CcP. When the enzyme is poised in the active state by incubation with sodium l-ascorbate, the graphite electrode specifically captures a highly active state that turns over peroxide in a high potential regime. This is the first example of an on-pathway catalytic intermediate observed for a bacterial diheme cytochrome c peroxidase that requires reductive activation, consistent with the observed voltammetric response from the diheme cytochrome c peroxidase from Nitrosomonas europaea (Ne), which is constitutively active and does not require the same one electron activation. Mutational analysis at the active site of So CcP confirms that the rate-limiting step involves a proton-coupled single electron reduction of a high valent iron species centered on the low-potential heme, consistent with the same mutation in Ne CcP. The pH dependence of catalysis for wild-type So CcP suggests that reduction shifts the pK(a)'s of at least two amino acids. Mutation of His81 in "loop 1", a surface exposed loop thought to shift conformation during the reductive activation process, eliminated one of the pH dependent features, confirming that the loop 1 shifts, changing the environment of His81 during the rate-limiting step. The observed catalytic intermediate has the same electron stoichiometry and similar pH dependence to that previously reported for Ne CcP, which is constitutively active and therefore hypothesized to follow a different catalytic mechanism. The prominent similarities between the rate-limiting steps of differing mechanistic classes of bCcPs suggest unexpected similarities in the intermediates formed.

Oxidation triggers extensive conjugation and unusual stabilization of two di-heme dication diradical intermediates: role of bridging group for electronic communication

Synthetic analogs of diheme enzyme MauG have been reported. Unlike the bis-Fe(iv) state in MauG, the 2e-oxidation stabilizes two ferric hemes, each coupled with a porphyrin π-cation radical.

MauG is a diheme enzyme that utilizes two covalently bound c-type hemes to catalyse the biosynthesis of the protein-derived cofactor tryptophan tryptophylquinone. The two hemes are physically separated by 14.5 Å and a hole-hopping mechanism is proposed in which a tryptophan residue located between the hemes undergoes reversible oxidation and reduction to increase the effective electronic coupling element and enhance the rate of reversible electron transfer between the hemes in bis-Fe(iv) MauG. The present work describes the structure and spectroscopic investigation of 2e-oxidations of the synthetic diheme analogs in which two heme centers are covalently connected through a conjugated ethylene bridge that leads to the stabilization of two unusual trans conformations (U and P′ forms) with different and distinct spectroscopic and geometric features. Unlike in MauG, where the two oxidizing equivalents are distributed within the diheme system giving rise to the bis-Fe(iv) redox state, the synthetic analog stabilizes two ferric hemes, each coupled with a porphyrin cation radical, a scenario resembling the binuclear dication diradical complex. Interestingly, charge resonance-transition phenomena are observed here both in 1e and 2e-oxidised species from the same system, which are also clearly distinguishable by their relative position and intensity. Detailed UV-vis-NIR, X-ray, Mössbauer, EPR and ¹H NMR spectroscopic investigations as well as variable temperature magnetic studies have unraveled strong electronic communications between two porphyrin π-cation radicals through the bridging ethylene group. The extensive π-conjugation also allows antiferromagnetic coupling between iron(iii) centers and porphyrin radical spins of both rings. DFT calculations revealed extended π-conjugation and H-bonding interaction as the major factors in controlling the stability of the conformers.

Enzymatic exploration of catalase from a nanoparticle producing and biodecolorizing algae Shewanella xiamenensis BC01

Shewanella xiamenensis (SXM) was found to produce nanoparticles (NPs) under aerobic condition. The oxidoreductase enzymatic activities including of catalase, manganese peroxidase, laccase, NADH dehydrogenase, flavin reductase, azoreductase and Fe reductase are first investigated. Catalase showed the greatest enzymatic activity among all oxidoreductases in SXM, which with strong activities in multiple substrates of ABTS, guaiacol and 2,6-DMP. The optimum temperature, pH, concentrations of H2O2 and 2,6-DMP for this enzyme were found to be 65 °C, pH 4.0, 128.7 mM and 10 mM, respectively. Finally, from the kinetic parameters and structure simulation of catalase, implied that SXM would potentially apply in bioremediation, microbe fuel cells (MFCs) and nano-biotechnology based on its distinguished enzymatic system.

An ethane-bridged porphyrin dimer as a model of di-heme proteins: inorganic and bioinorganic perspectives and consequences of heme–heme interactions

A brief account of our recent efforts on how inter-heme interactions can possibly change the structure and functional properties of the individual heme centers in a highly flexible ethane-bridged porphyrin dimer has been presented.

Methionine ligand lability of homologous monoheme cytochromes c

Direct electrochemical analysis of adsorbed bacterial monoheme cytochromes c has revealed a phenomenological loss of the axial methionine when examined using pyrolytic "edge-plane" graphite (EPG) electrodes. While prior findings have reported that the Met-loss state may be quantitatively understood using the cytochrome c from Hydrogenobacter thermophilus as a model system, here we demonstrate that the formation of the Met-loss state upon EPG electrodes can be observed for a range of cytochrome orthologs. Through an electrochemical comparison of the wild-type proteins from organisms of varying growth temperature optima, we establish that Met-ligand losses at graphite surfaces have similar energetics to the "foldons" for known protein folding pathways. Furthermore, a downward shift in reduction potential to approximately -100 mV vs standard hydrogen electrode was observed, similar to that of the alkaline transition found in mitochondrial cytochromes c. Pourbaix diagrams for the Met-loss forms of each cytochrome, considered here in comparison to mutants where the Met-ligand has been substituted to His or Ala, suggest that the nature of the Met-loss state is distinct from either a His-/aquo- or a bis-His-ligated heme center, yet more closely matches the pKa values found for bis-His-ligated hemes., We find the propensity for adoption of the Met-loss state in bacterial monoheme cytochromes c scales with their overall thermal stability, though not with the specific stability of the Fe-Met bond.

Protection from oxidative stress relies mainly on derepression of OxyR-dependent KatB and Dps in Shewanella oneidensis

Shewanella thrives in redox-stratified environments where accumulation of H2O2 becomes inevitable because of the chemical oxidation of reduced metals, sulfur species, or organic molecules. As a research model, the representative species Shewanella oneidensis has been extensively studied for its response to various stresses. However, little progress has been made toward an understanding of the physiological and genetic responses of this bacterium to oxidative stress, which is critically relevant to its application as a dissimilatory metal-reducing bacterium. In this study, we systematically investigated the mechanism underlying the response to H2O2 at cellular, genomic, and molecular levels. Using transcriptional profiling, we found that S. oneidensis is hypersensitive to H2O2 in comparison with Escherichia coli, and well-conserved defense genes such as ahpCF, katB, katG, and dps appear to form the first line of defense, whereas iron-sulfur-protecting proteins may not play a significant role. Subsequent identification and characterization of an analogue of the E. coli oxyR gene revealed that S. oneidensis OxyR is the master regulator that mediates the bacterial response to H2O2-induced oxidative stress by directly repressing or activating the defense genes. The sensitivity of S. oneidensis to H2O2 is likely attributable to the lack of an inducible manganese import mechanism during stress. To cope with stress, major strategies that S. oneidensis adopts include rapid removal of the oxidant and restriction of intracellular iron concentrations, both of which are achieved predominantly by derepression of the katB and dps genes.

Impact of quaternary structure upon bacterial cytochrome c peroxidases: does homodimerization matter?

All known active forms of diheme bacterial cytochrome c peroxidase (bCcP) enzymes are described by a homodimeric state. Further, the majority of bCcPs reported display activity only when the high-potential electron transfer heme of the protein (Fe(H)) is reduced to the ferrous oxidation state. Reduction of Fe(H) results in a set of conformational changes allowing for the low-potential peroxidatic heme (Fe(L)) to adopt a high-spin, five-coordinate state that is capable of binding substrate. Here we examine the impact of dimerization upon the activity of the Shewanella oneidensis (So) bCcP by the preparation of single charge-reversal mutants at the dimer interface and use the resulting constructs to illustrate why dimerization is likely a requirement for activity in bCcPs. The E258K mutant is found to form a monomeric state in solution as characterized by size exclusion chromatography and analytical ultracentrifugation analyses. The resulting E258K monomer has an unfolding stability comparable to that of wild-type So bCcP and an activity that is only slightly diminished (k(cat)/K(m) = 23 × 10(6) M(-1) s(-1)). Spectroscopic and potentiometric analyses reveal that while the thermodynamic stability of the activated form of the enzyme is unchanged (characterized by the E(m) value of the Fe(H)(II)/Fe(H)(III) couple), the kinetic stability of the activated form of the enzyme has been greatly diminished upon generation of the monomer. Together, these data suggest a model in which dimerization of bCcP enzymes is required to stabilize the lifetime of the activated form of the enzyme against reoxidation of Fe(H) and deactivation of Fe(L).