Role of the aromatic ring of Tyr43 in tetraheme cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F

Designing one-compartment H2O2 fuel cell using electroactive phenalenyl-based [Fe2(hnmh-PLY)3] complex as the cathode material

The sustainable chemical energy of H2O2 as a fuel and an oxidant in an advantageous single-compartment fuel cell design can be converted into electric energy, which requires molecular engineering to design suitable cathodes for lowering the high overpotential associated with H2O2 reduction. The present work covers the synthesis and structural characterization of a novel cathode material, [FeIII2(hnmh-PLY)3] complex, 1, designed from a PLY-derived Schiff base ligand (E)-9-(2-((2-hydroxynaphthalen-1-yl)methylene)hydrazineyl)-1H-phenalen-1-one, hnmh-PLYH2. Complex 1, when coated on the surface of a glassy carbon electrode (GC-1) significantly catalyzed the reduction of H2O2 in an acidic medium. Therefore, a complex 1 modified glassy carbon electrode was employed in a one-compartment H2O2 fuel cell operated in 0.1 M HCl with Ni foam as the corresponding anode to produce a high open circuit potential (OCP) of 0.65 V and a peak power density (PPD) of 2.84 mW cm-2. CV studies of complex 1 revealed the crucial participation of two Fe(III) centers for initiating H2O2 reduction, and the role of coordinated redox-active PLY units is also highlighted. In the solid state, the π-conjugated network of coordinating (hnmh-PLY) ligands in complex 1 has manifested interesting face-to-face π-π stacking interactions, which have helped the reduction of the complex and facilitated the overall catalytic performance.

Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics

Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Structural basis for the oxidation of protein-bound sulfur by the sulfur cycle molybdohemo-enzyme sulfane dehydrogenase SoxCD

The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six-electron oxidation reaction within the Sox cycle. SoxCD is an α(2)β(2) heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D(1) and D(2). SoxCD(1) misses the heme-2 domain D(2) and is catalytically as active as SoxCD. The crystal structure of SoxCD(1) was solved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys-110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD(1) substrate funnel toward the molybdopterin is narrow and partially shielded by side-chain residues of SoxD(1). For access of the sulfane-sulfur of SoxY-Cys-110 persulfide we propose that (i) the blockage by SoxD-Arg-98 is opened via interaction with the C terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine-bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom that is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Because SoxYZ, SoxXA, and SoxB are already structurally characterized, with SoxCD(1) the structures of all key enzymes of the Sox cycle are known with atomic resolution.

Geometric constraints for porphyrin binding in helical protein binding sites

Helical bundles which bind heme and porphyrin cofactors have been popular targets for cofactor-containing de novo protein design. By analyzing a highly nonredundant subset of the protein databank we have determined a rotamer distribution for helical histidines bound to heme cofactors. Analysis of the entire nonredundant database for helical sequence preferences near the ligand histidine demonstrated little preference for amino acid side chain identity, size, or charge. Analysis of the database subdivided by ligand histidine rotamer, however, reveals strong preferences in each case, and computational modeling illuminates the structural basis for some of these findings. The majority of the rotamer distribution matches that predicted by molecular simulation of a single porphyrin-bound histidine residue placed in the center of an all-alanine helix, and the deviations explain two prominent features of natural heme protein binding sites: heme distortion in the case of the cytochromes C in the m166 histidine rotamer, and a highly prevalent glycine residue in the t73 histidine rotamer. These preferences permit derivation of helical consensus sequence templates which predict optimal side chain-cofactor packing interactions for each rotamer. These findings thus promise to guide future design endeavors not only in the creation of higher affinity heme and porphyrin binding sites, but also in the direction of bound cofactor geometry.

Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment

A general method has been developed to characterize the hydrophobicity or hydrophilicity of the microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating a quantitative property descriptor (QPD) based on the relative (to water) hydrophobicity of the MENV. Values of the QPD were calculated for a test set of 733 proteins to analyze the modulating effects on amino acid residue properties by the MENV in which they are imbedded. The QPD values and solvent accessibility were used to derive a partitioning of residues based on the MENV hydrophobicities. From this partitioning, a new hydrophobicity scale was developed, entirely in the context of protein structure, where amino acid residues are immersed in one or more "MENVpockets." Thus, the partitioning is based on the residues "sampling" a large number of "solvents" (MENVs) that represent a very large range of hydrophobicity values. It was found that the hydrophobicity of around 80% of amino acid side chains and their MENV are complementary to each other, but for about 20%, the MENV and their imbedded residue can be considered as mismatched. Many of these mismatches could be rationalized in terms of the structural stability of the protein and/or the involvement of the imbedded residue in function. The analysis also indicated a remarkable conservation of local environments around highly conserved active site residues that have similar functions across protein families, but where members have relatively low sequence homology. Thus, quantitative evaluation of this QPD is suggested, here, as a tool for structure-function prediction, analysis, and parameter development for the calculation of properties in proteins.

Strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3

Tetraheme cytochrome c 3 (cyt c 3) exhibits extremely low reduction potentials and unique properties. Since axial ligands should be the most important factors for this protein, every axial histidine of Desulfovibrio vulgaris Miyazaki F cyt c 3 was replaced with methionine, one by one. On mutation at the fifth ligand, the relevant heme could not be linked to the polypeptide, revealing the essential role of the fifth histidine in heme linking. The fifth histidine is the key residue in the structure formation and redox regulation of a c-type cytochrome. A crystal structure has been obtained for only H25M cyt c 3. The overall structure was not affected by the mutation except for the sixth methionine coordination at heme 3. NMR spectra revealed that each mutated methionine is coordinated to the sixth site of the relevant heme in the reduced state, while ligand conversion takes place at hemes 1 and 4 during oxidation at pH 7. The replacement of the sixth ligand with methionine caused an increase in the reduction potential of the mutated heme of 222-244 mV. The midpoint potential of a triheme H52M cyt c 3 is higher than that of the wild type by approximately 50 mV, suggesting a contribution of the tetraheme architecture to the lowering of the reduction potentials. The hydrogen bonding of Thr24 with an axial ligand induces a decrease in reduction potential of approximately 50 mV. In conclusion, the bis-histidine coordination is strategically essential for the structure formation and the extremely low reduction potential of cyt c 3.

Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3

The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.

Functional roles of the heme architecture and its environment in tetraheme cytochrome c

Cytochromes are involved in a wide variety of redox reactions in living systems. Some of them contain multiple hemes such as Desulfovibrio cytochrome c3 and Shewanella small tetraheme cytochrome c. The significance of c-type tetraheme architectures was discussed. A cyclic heme architecture and its environment regulate the extremely low redox potentials of cytochrome c3 in addition to bis-imidazole coordination and heme exposure. Each heme in cytochrome c3 plays a different role in the electron transport to/from [NiFe] hydrogenase and the specific CO-binding. In contrast, the chain-like heme architecture in Shewanella small tetraheme cytochrome c and soluble fumarate reductase provides a pathway for directional electron transfer. Thus, the tetraheme architectures do not comprise simple heme assemblies but sophisticated devices.

Role of positive charge of lysine residue on cytochrome c3for electrostatic interaction with hydrogenase

Cytochrome c3from Desulfovibrio vulgaris (Miyazaki) is an electron transfer protein containing four hemes per molecule. Its physiological electron transfer partner is the hydrogenase which catalyzes reversible oxidation of hydrogen. The complex formation between cytochrome c3and hydrogenase is caused by electrostatic interaction, because cytochrome c3is a basic protein and hydrogenase is an acidic protein. As cytochrome c3has 20 lysine residues among 108 amino acids, the positive charges of some lysine residues may play an important role in the interaction with hydrogenase. To clarify the role of positive charge of lysine residue, the positive charge was changed to neutral or negative charge using chemical modification and site-directed mutagenesis. When the positive charges around heme IV were changed, the hydrogen evolution rate with hydrogenase decreased. The affinity between hydrogenase and mutated cytochrome c3(K57Q, K57E, K72Q, K94Q, K94E) were not affected. On the other hand, the affinity of K72E cytochrome c3for hydrogenase was very low. These results suggest that the positive charge around heme IV plays an important role in the electrostatic interaction with hydrogenase in hydrogen evolution.

Process of Maturation of Tetraheme Cytochrome c3 in a Shewanella Expression System

The process of maturation of multiheme proteins is not yet well known, while that of monoheme ones has been relatively well investigated. Two kinds of partly unfolded tetraheme cytochrome c3 were obtained on overexpression in Shewanella oneidensis TSP-C. These proteins were characterized by circular dichroism and nuclear magnetic resonance spectroscopy. It turned out that the tetraheme architecture, and the fifth and sixth ligand coordination are almost mature, while some parts of the polypeptide are unfolded. The unfolded residues are mainly located in the helix-rich region including heme attachment and axial ligand sites. This suggests that the formation of the heme architecture, coordination of axial ligands and helix formation should be coupled with each other. While the former two can take place automatically, the helix formation would need help by a chaperone-like function in the cytochrome c maturation (Ccm) machinery. It must be working in sulphate-reducing bacteria. The Ccm machinery in S. oneidensis is likely insufficient to help the maturation of proteins with cyclic heme architectures. This is the first report providing an insight into the process of maturation of tetraheme cytochrome c3.

Roles of charged residues in pH-dependent redox properties of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

Complicated pH-properties of the tetraheme cytochrome c3 (cyt c3) from Desulfovibrio vulgaris Miyazaki F (DvMF) were examined by the pH titrations of 1H-15N HSQC spectra in the ferric and ferrous states. The redox-linked pKa shift for the propionate group at C13 of heme 1 was observed as the changes of the NH signals around it. This pKa shift is consistent with the redox-linked conformational alteration responsible for the cooperative reduction between hemes 1 and 2. On the other hand, large chemical shift changes caused by the protonation/deprotonation of Glu41 and/or Asp42, and His67 were redox-independent. Nevertheless, these charged residues affect the redox properties of the four hemes. Furthermore, one of interesting charged residues, Glu41, was studied by site-directed mutagenesis. E41K mutation increased the microscopic redox potentials of heme 1 by 46 and 34 mV, and heme 2 by 35 and 30 mV at the first and last reduction steps, respectively. Although global folding in the crystal structure of E41K cyt c3 is similar to that of wild type, local change was observed in 1H NMR spectrum. Glu41 is important to keep the stable conformation in the region between hemes 1 and 2, controlling the redox properties of DvMF cyt c3. In contrast, the kinetic parameters for electron transfer from DvMF [NiFe] hydrogenase were not influenced by E41K mutation. This suggests that the region between hemes 1 and 2 is not involved in the interaction with [NiFe] hydrogenase, and it supports the idea that heme 4 is the exclusive entrance gate to accept the electron in the initial reduction stage.

Desulfovibrio desulfuricans G20 Tetraheme Cytochrome Structure at 1.5Å and Cytochrome Interaction with Metal Complexes

The structure of the type I tetraheme cytochrome c(3) from Desulfovibrio desulfuricans G20 was determined to 1.5 Angstrom by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated by circular dichroism studies. Again, only small changes in protein structure were documented. The location of the molybdate ion near heme IV in the crystal structure suggested heme IV as the site of electron exit from the reduced cytochrome and implicated Lys14 and Lys56 in binding. Analysis of structurally conserved water molecules in type I cytochrome c(3) crystal structures identified interactions predicted to be important for protein stability and possibly for intramolecular electron transfer among heme molecules.

Specific Binding of CO to Tetraheme Cytochrome c3

Carbon monoxide (CO) has been identified as another bioactive molecule like NO. Binding of CO to a tetraheme cytochrome c(3) (cyt c(3)) was investigated using visible absorption spectroscopy, circular dichroism (CD), and NMR. CO was found to bind to the four hemes in different manners. CD spectra, however, indicated that only single-site CO binding can keep the protein intact. The K(d) for the single-site binding was 8.0 microM, which is a typical value for a CO sensor protein. Furthermore, NMR spectra of uniformly (15)N-labeled and specifically [(15)N]His-labeled proteins have provided evidence that CO specifically binds to the sixth coordination site of heme 2 via single-site binding. The CO-bound cyt c(3) could conduct redox reactions. In light of triheme cytochrome c(7), the CO-bound cyt c(3) may work as an electron transporter. It was reported for sulfate-reducing bacteria that CO can be used as an energy source and CO cycling is operating like H(2) cycling. Therefore, the CO-bound cyt c(3) may play a role in maintaining electron transport pathways on accumulation of toxic CO for its utilization.

Redox Interaction of Cytochrome c3 with [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F

Cytochrome c3 isolated from a sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki F, is a tetraheme protein. Its physiological partner, [NiFe] hydrogenase, catalyzes the reversible oxidoreduction of molecular hydrogen. To elucidate the mechanism of electron transfer between cytochrome c3 and [NiFe] hydrogenase, the transient complex formation by these proteins was investigated by means of NMR. All NH signals of uniformly 15N-labeled ferric cytochrome c3 except N-terminus, Pro, and Gly73 were assigned. 1H-15N HSQC spectra were recorded for 15N-labeled ferric and ferrous cytochrome c3, in the absence and presence of hydrogenase. Chemical shift perturbations were observed in the region around heme 4 in both oxidation states. Additionally, the region between hemes 1 and 3 in ferrous cytochrome c3 was affected in the presence of hydrogenase, suggesting that the mode of interaction is different in each redox state. Heme 3 is probably the electron gate for ferrous cytochrome c3. To investigate the transient complex of cytochrome c3 and hydrogenase in detail, modeling of the complex was performed for the oxidized proteins using a docking program, ZDOCK 2.3, and NMR data. Furthermore, the roles of lysine residues of cytochrome c3 in the interaction with hydrogenase were investigated by site-directed mutagenesis. When the lysine residues around heme 4 were replaced by an uncharged residue, methionine, one by one, the Km of the electron-transfer kinetics increased. The results showed that the positive charges of Lys60, Lys72, Lys95, and Lys101 around heme 4 are important for formation of the transient complex with [NiFe] hydrogenase in the initial stage of the cytochrome c3 reduction. This finding is consistent with the most possible structure of the transient complex obtained by modeling.

Phospholipid-dependent regulation of cytochrome c3-mediated electron transport across membranes

Cytochrome c3 (cyt c3) can mediate electron transport across phosphatidylcholine (PC)/cardiolipin (CL) and PC/phosphatidylglycerol (PG) membranes. A two-molecule process is involved in the electron transport across PC/CL membranes in the liquid-crystalline state. In contrast, a single-molecule process dominates the electron transport across PC/CL membranes in the gel state and PC/PG membranes in the liquid-crystalline and gel states. Namely, the electron transport mechanism differs with the phospholipid composition and membrane fluidity. The rate-limiting step of the two-molecule process was lateral diffusion of cyt c3 in membranes. The rate constants for the three single-molecule process cases were similar to each other. To elucidate these reaction processes, interactions between cyt c3 and phosphate groups and between cyt c3 and the glycerol backbones of phospholipid bilayers were investigated by means of 31P and 2H solid-state NMR, respectively, for CL and PC/CL membranes. The results showed that the polar headgroups of both phosphatidylcholine and CL are involved in the binding of cyt c3. Also, cyt c3 penetrates into membranes, which would induce distortion of the lipid bilayer. The molecular mechanisms underlying the single- and two-molecule processes are discussed in terms of membrane structure.

Roles of Noncoordinated Aromatic Residues in Redox Regulation of Cytochrome c3 from Desulfovibrio vulgaris Miyazaki F

The roles of aromatic residues in redox regulation of cytochrome c(3) were investigated by site-directed mutagenesis at every aromatic residue except for axial ligands (Phe20, Tyr43, Tyr65, Tyr66, His67, and Phe76). The mutations at Phe20 induced large chemical shift changes in the NMR signals for hemes 1 and 3, and large changes in the microscopic redox potentials of hemes 1 and 3. The NMR signals of the axial ligands of hemes 1 and 3 were also affected. Analysis of the nature of the mutations revealed that a hydrophobic environment and aromaticity are important for the reduction of the redox potentials of hemes 1 and 3, respectively. There was also a global effect. The replacement of Tyr66 with leucine induced chemical shift changes for heme 4, and changes in the microscopic redox potentials of heme 4. The mutations of Tyr65 induced changes in the chemical shifts and microscopic redox potentials for every heme, suggesting that Tyr65 stabilizes the global conformation, thereby reducing the redox potentials. In contrast, although the mutations of His67 and Phe76 caused chemical shift changes for heme 2, they did not affect its redox potentials, showing these residues are not important. All noncoordinated aromatic residues conserved in the cytochrome c(3) subfamily with heme binding motifs CXXCH, CXXXXCH, CXXCH, and CXXXXCH (Phe20, Tyr43, and Tyr66) are involved in the pi-pi interaction, which causes a decrease in the redox potential of the interacting heme. The global effect can be attributed to either direct or indirect interactions among the four hemes in the cyclic architecture.