Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies

Modularity of membrane-bound charge-translocating protein complexes

Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δμ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.

The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes

Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.

Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.

A brief survey of the "cytochromome"

Multihaem cytochromes c are widespread in nature where they perform numerous roles in diverse anaerobic metabolic pathways. This is achieved in two ways: multihaem cytochromes c display a remarkable diversity of ways to organize multiple hemes within the protein frame; and the hemes possess an intrinsic reactive versatility derived from diverse spin, redox and coordination states. Here we provide a brief survey of multihaem cytochromes c that have been characterized in the context of their metabolic role. The contribution of multihaem cytochromes c to dissimilatory pathways handling metallic minerals, nitrogen compounds, sulfur compounds, organic compounds and phototrophism are described. This aims to set the stage for the further exploration of the vast unknown "cytochromome" that can be anticipated from genomic databases.

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.

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.

Pivotal role of the strictly conserved aromatic residue F15 in the cytochrome c7 family

Cytochromes c(7) are periplasmic triheme proteins that have been reported exclusively in δ-proteobacteria. The structures of five triheme cytochromes identified in Geobacter sulfurreducens and one in Desulfuromonas acetoxidans have been determined. In addition to the hemes and axial histidines, a single aromatic residue is conserved in all these proteins-phenylalanine 15 (F15). PpcA is a member of the G. sulfurreducens cytochrome c(7) family that performs electron/proton energy transduction in addition to electron transfer that leads to the reduction of extracellular electron acceptors. For the first time we probed the role of the F15 residue in the PpcA functional mechanism, by replacing this residue with the aliphatic leucine by site-directed mutagenesis. The analysis of NMR spectra of both oxidized and reduced forms showed that the heme core and the overall fold of the mutated protein were not affected. However, the analysis of (1)H-(15)N heteronuclear single quantum coherence NMR spectra evidenced local rearrangements in the α-helix placed between hemes I and III that lead to structural readjustments in the orientation of heme axial ligands. The detailed thermodynamic characterization of F15L mutant revealed that the reduction potentials are more negative and the redox-Bohr effect is decreased. The redox potential of heme III is most affected. It is of interest that the mutation in F15, located between hemes I and III in PpcA, changes the characteristics of the two hemes differently. Altogether, these modifications disrupt the balance of the global network of cooperativities, preventing the F15L mutant protein from performing a concerted electron/proton transfer.

Direct monitoring of pollutants based on an electrochemical biosensor with novel peroxidase (POX1B)

A biosensor for the monitoring of phenolic compounds based on a new protein named POX(1B) purified from garlic which demonstrates similar biochemical properties to peroxidase is investigated. The enzyme was immobilized into chitosan microspheres with covalent link. The properties of the biosensor were analyzed with Fourier transform-infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) and cyclic voltammetry (CV). FT-IR demonstrates the covalent attachment of POX(1B) into chitosan and SEM shows high dispersion of the POX(1B) into the chitosan microspheres. The redox potential of POX(1B) in chitosan is 147 mV vs. SCE, which is much higher than reported works using HRP, demonstrating excellent direct electrochemical behaviour of the POX(1B). The electrocatalytic activity of the obtained biosensor towards chlorophenols derivatives in a large range from 10 pM to 10 microM was demonstrated. The mediator free POX(1B)-based biosensor exhibited high sensitivity towards 2,6-dichlorophenol, 4-chlorophenol and pentachlorophenol. A detection limit of 1 pM in the case of 4-chlorophenol was demonstrated with kinetic constant K(m,app) of 0.42 microM with high rapidity of electrochemical response of the biosensor of 1 s.

Redox-linked structural changes associated with the formation of a catalytically competent form of the diheme cytochrome c peroxidase from Pseudomonas aeruginosa

A recombinant form of the prototypic diheme bacterial cytochrome c peroxidase (BCCP) from Pseudomonas aeruginosa (PsaCCP) has been expressed in Escherichia coli and purified to homogeneity. This material was used to carry out the first integrated biochemical, spectroscopic and structural investigation of the factors leading to reductive activation of this class of enzymes. A single, tightly bound, Ca2+ ion (K = 3 x 10(10) M-1) found at the domain interface of both the fully oxidized and mixed-valence forms of the enzyme is absolutely required for catalytic activity. Reduction of the electron-transferring (high-potential) heme in the presence of Ca2+ ions triggers substantial structural rearrangements around the active-site (low-potential) heme to allow substrate binding and catalysis. The enzyme also forms a mixed-valence state in the absence of Ca2+ ions, but a combination of electronic absorption, and EPR spectroscopies suggests that under these circumstances the low potential heme remains six-coordinate, unable to bind substrate and therefore catalytically inactive. Our observations strongly suggest that the two mixed-valence forms of native PsaCCP reported previously by Foote and colleagues (Foote, N., Peterson, J., Gadsby, P., Greenwood, C., and Thomson, A. (1985) Biochem. J. 230, 227-237) correspond to the Ca2+-loaded and -depleted forms of the enzyme.

Cooperative interaction of high-potential hemes in the cytochrome subunit of the photosynthetic reaction center of bacterium Ectothiorhodospira shaposhnikovii

Cooperative interaction of the high-potential hemes (C(h)) in the cytochrome subunit of the photosynthesizing bacterium Ectothiorhodospira shaposhnikovii was studied by comparing redox titration curves of the hemes under the conditions of pulse photoactivation inducing single turnover of electron-transport chain and steady-state photoactivation, as well as by analysis of the kinetics of laser-induced oxidation of cytochromes by reaction center (RC). A mathematical model of the processes of electron transfer in cytochrome-containing RC was considered. Theoretical analysis revealed that the reduction of one heme C(h) facilitated the reduction of the other heme, which was equivalent to a 60 mV positive shift of the midpoint potential. In addition, reduction of the second heme C(h) caused a three- to four-fold acceleration of the electron transfer from the cytochrome subunit to RC.

Crystal structure of the 16 heme cytochrome from Desulfovibrio gigas: a glycosylated protein in a sulphate-reducing bacterium

Sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. HmcA is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. We report the crystal structure of HmcA isolated from the periplasm of Desulfovibrio gigas. Crystals were grown using polyethylene glycol 8K and zinc acetate, and diffracted beyond 2.1 A resolution. A multiple-wavelength anomalous dispersion experiment at the iron absorption edge enabled us to obtain good-quality phases for structure solution and model building. DgHmcA has a V-shape architecture, already observed in HmcA isolated from Desulfovibrio vulgaris Hildenborough. The presence of an oligosaccharide molecule covalently bound to an Asn residue was observed in the electron density maps of DgHmcA and confirmed by mass spectrometry. Three modified monosaccharides appear at the highly hydrophobic vertex, possibly acting as an anchor of the protein to the cytoplasmic membrane.

Resonance Raman fingerprinting of multiheme cytochromes from the cytochrome c 3 family

Resonance Raman (RR) spectroscopy was used to investigate conformational characteristics of the hemes of several ferricytochromes of the cytochrome c3 family, electron transfer proteins isolated from the periplasm and membranes of sulfate-reducing bacteria. Our analysis concentrated on the low-frequency region of the RR spectra, a fingerprint region that includes vibrations for heme-protein C-S bonds [nu(C(a)S)]. It has been proposed that these bonds are directly involved in the electron transfer process. The three groups of tetraheme cytochrome c3 analyzed, namely Type I cytochrome c (3) (TpIc (3)s), Type II cytochrome c (3) (TpIIc (3)s) and Desulfomicrobium cytochromes c3, display different frequency separations for the two nu(C(a)S) lines that are similar among members of each group. These spectral differences correlate with differences in protein structure observed among the three groups of cytochromes c3. Two larger cytochromes of the cytochrome c3 family display RR spectral characteristics for the nu(C(a)S) lines that are closer to TpIIc3 than to TpIc3. Two other multiheme cytochromes from Desulfovibrio that do not belong to the cytochrome c3 family display nu(C(a)S) lines with reverse relative areas in comparison with the latter family. This RR study shows that the small differences in protein structure observed among these cytochrome c3 correlate to differences on the heme-protein bonds, which are likely to have an impact upon the protein function, making RR spectroscopy a sensitive and useful tool for characterizing these cytochromes.

Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview

Sulphate-reducing organisms are widespread in anaerobic enviroments, including the gastrointestinal tract of man and other animals. The study of these bacteria has attracted much attention over the years, due also to the fact that they can have important implications in industry (in biocorrosion and souring of oil and gas deposits), health (in inflamatory bowel diseases) and the environment (bioremediation). The characterization of the various components of the electron transport chain associated with the hydrogen metabolism in Desulfovibrio has generated a large and comprehensive list of studies. This review summarizes the more relevant aspects of the current information available on the structural data of various molecules associated with hydrogen metabolism, namely hydrogenases and cytochromes. The transmembrane redox complexes known to date are also described and discussed. Redox-Bohr and cooperativity effects, observed in a few cytochromes, and believed to be important for their functional role, are discussed. Kinetic studies performed with these redox proteins, showing clues to their functional inter-relationship, are also addressed. These provide the groundwork for the application of a variety of molecular modelling approaches to understanding electron transfer and protein interactions among redox partners, leading to the characterization of several transient periplasmic complexes. In contrast to the detailed understanding of the periplasmic hydrogen oxidation process, very little is known about the cytoplasmic side of the respiratory electron transfer chain, in terms of molecular components (with exception of the terminal reductases), their structure and the protein-protein interactions involved in sulphate reduction. Therefore, a thorough understanding of the sulphate respiratory chain in Desulfovibrio remains a challenging task.

Multi-heme cytochromes--new structures, new chemistry

Heme is one of the most pervasive cofactors in nature and the c-type cytochromes represent one of the largest families of heme-containing proteins. Recent progress in bacterial genomic analysis has revealed a vast range of genes encoding novel c-type cytochromes that contain multiple numbers of heme cofactors. The genome sequence of Geobacter sulfurreducens, for example, includes some one hundred genes encoding c-type cytochromes, with around seventy of these containing two, or more, heme groups and with one protein containing an astonishing twenty seven heme groups. This wealth of cytochromes is of great significance in the respiratory flexibility shown by bacteria such as Geobacter. In addition, we are now discovering that many of these multi-heme cytochromes have associated enzymatic activities and in some cases this is revealing new chemistries. The purpose of this perspective is to describe recent progress in the structural and functional analyses of these new multi-heme cytochromes. To illustrate this we have chosen to focus on three of these cytochromes which exhibit catalytic activities; nitrite reductase, hydroxylamine oxidoreductase and tetrathionate reductase. In addition we consider the multi-heme cytochromes from Geobacter and Desulfovibrio species. Finally, we consider and contrast the repeating structural modules found in these multi-heme cytochromes.

Reorganization and conformational changes in the reduction of tetraheme cytochromes

Molecular dynamics simulation (MD) constitutes an alternative to time-consuming experiments for studying conformational changes. We apply MD on a redox system where experimental information exists for the fully oxidized and fully reduced states: tetraheme cytochrome c3. Instead of doing one simulation for each state, we apply 10 4-ns replicas for both states, which provides robust statistics to characterize the redox changes. Besides these long simulations, we perform 120 short ones (50 ps), where an equilibrated oxidized state is perturbed to a reduced state. This allows the application of a nonequilibrium method, the subtraction technique, which makes it possible to characterize the different timescales of conformational changes. Reduction induces conformational changes in the N-terminus and on the loops spanning residues 36-42 and 88-93, which correlate very well with experiments, demonstrating the applicability of this methodology. We also analyze the effect of reduction on hydrogen bonds, solvent accessible surface and bound water, the changes being found to involve the hemes and propionate groups. Redox-induced protonation is also investigated, by protonating the propionates D from hemes I and IV. Although this change in the former does not have major conformational consequences, it induces in the latter conformational changes beyond the ones obtained with reduction.

Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies

The tetraheme protein cytochrome c(3) (Cyt-c(3)) from Desulfovibrio gigas, immobilized on a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid, is studied by theoretical and spectroscopic methods. Molecular dynamics simulations indicate that the protein docks to the negatively charged SAM via its lysine-rich domain around the exposed heme IV. Complex formation is associated with only little protein structural perturbations. This finding is in line with the resonance Raman and surface-enhanced resonance Raman (SERR) spectroscopic results that indicate essentially the same heme pocket structures for the protein in solution and adsorbed on SAM-coated Ag electrodes. Electron- and proton-binding equilibrium calculations reveal substantial negative shifts of the redox potentials compared to the protein in solution. The magnitude of these shifts decreases in the order heme IV (-161 mV) > heme III (-73 mV) > heme II (-57 mV) > heme I (-26 mV), resulting in a change of the order of reduction. These shifts originate from the distance-dependent electrostatic interactions between the SAM headgroups and the individual hemes, leading to a stabilization of the oxidized forms. The results of the potential-dependent SERR spectroscopic analyses are consistent with the theoretical predictions and afford redox potential shifts of -160 mV (heme IV), -90 mV (heme III), -70 mV (heme II), and +20 mV (heme I) relative to the experimental redox potentials for Cyt-c(3) in solution. SERR spectroscopic experiments reveal electric-field-induced changes of the redox potentials also for the structurally very similar Cyt-c(3) from Desulfovibrio vulgaris, although the shifts are somewhat smaller compared to Cyt-c(3) from D. gigas. This study suggests that electric-field-induced redox potential shifts may also occur upon binding to biomembranes or partner proteins and thus may affect biological electron transfer processes.

Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3)

Redox protein complexes between type I and type II tetraheme cytochromes c(3) from Desulfovibrio vulgaris Hildenborough are here analyzed using theoretical methodologies. Various complexes were generated using rigid-body docking techniques, and the two lowest energy complexes (1 and 2) were relaxed using molecular dynamics simulations with explicit solvent and subjected to further characterization. Complex 1 corresponds to an interaction between hemes I from both cytochromes c(3). Complex 2 corresponds to an interaction between the heme IV from type I and the heme I from type II cytochrome c(3). Binding free energy calculations using molecular mechanics, Poisson-Boltzmann, and surface accessibility methods show that complex 2 is more stable than complex 1. Thermodynamic calculations on complex 2 show that complex formation induces changes in the reduction potential of both cytochromes c(3), but the changes are larger in the type I cytochrome c(3) (the largest one occurring on heme IV, of approximately 80 mV). These changes are sufficient to invert the global titration curves of both cytochromes, generating directionally in electron transfer from type I to type II cytochrome c(3), a phenomenon of obvious thermodynamic origin and consequences, but also with kinetic implications. The existence of processes like this occurring at complex formation may constitute a natural design of efficient redox chains.