Molecular and structural basis of electron transfer in tetra- and octa-heme cytochromes

Synthesis and characterization of six-coordinate iron(II/III) 5,10,15,20-tetrakis(pentafluorophenyl) porphyrinato complexes with non-hindered imidazole ligands

Four bis-imidazole iron(II/III) 5,10,15,20-tetrakis(pentafluorophenyl)porphyrinato (TFPP) complexes, [Fe(TFPP)(1-MeIm)[Formula: see text]], [Fe(TFPP)(1-VinylIm)[Formula: see text]], [Fe(TFPP)(4-MeHIm)[Formula: see text]]Cl and [Fe(TFPP)(1-EtIm)[Formula: see text]]BF[Formula: see text] (1-MeIm [Formula: see text] 1-methylimidazole, 1-VinylIm [Formula: see text] 1-vinylimidazole, 4-MeHIm [Formula: see text] 4-methylimidazole and 1-EtIm [Formula: see text] 1-ethylimidazole) were synthesized and characterized by single-crystal X-ray and UV-vis spectroscopy. A negative correlation is found between the absolute imidazole orientation ([Formula: see text] and the Fe–N[Formula: see text] distance for the [Fe(II)(Porph)(Im)[Formula: see text]] (Im [Formula: see text] 1-MeIm or 4-MeHIm) complexes where the smaller [Formula: see text] angle corresponds to a longer axial distance. Hydrogen bonding, which might affect the orientations of the axial imidazoles is found for Fe(TFPP)(4-MeHIm)[Formula: see text]]Cl (A and B). The autoreduction of [Fe(III)(TFPP)]Cl to [Fe(II)(TFPP)(1-MeIm)[Formula: see text]] with 1-methylimidazole has been monitored by UV-vis spectroscopic titration.

Relative axial ligand orientation in bis(imidazole)iron(II) porphyrinates: are "picket fence" derivatives different?

The synthesis of three new bis(imidazole)-ligated iron(II) picket fence porphyrin derivatives, [Fe(TpivPP)(1-RIm) 2] 1-RIm = 1-methyl-, 1-ethyl-, or 1-vinylimidazole) are reported. X-ray structure determinations reveal that the steric requirements of the four alpha,alpha,alpha,alpha-o-pivalamidophenyl groups lead to very restricted rotation of the imidazole ligand on the picket side of the porphyrin plane; the crowding leads to an imidazole plane orientation eclipsing an iron-porphyrin nitrogen bond. An unusual feature for these diamagnetic iron(II) species is that all three derivatives have the two axial ligands with a relative perpendicular orientation; the dihedral angles between the two imidazole planes are 77.2 degrees , 62.4 degrees , and 78.5 degrees . All three derivatives have nearly planar porphyrin cores. Mössbauer spectroscopic characterization shows that all three derivatives have quadrupole splitting constants around 1.00 mm/s at 100K.

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

Tyrosine 43 is positioned parallel to the fifth heme axial ligand, His34, of heme 1 in the tetraheme cytochrome c(3). The replacement of tyrosine with leucine increased the redox potential of heme 1 by 44 and 35 mV at the first and last reduction steps, respectively; its effects on the other hemes are small. In contrast, the Y43F mutation hardly changed the potentials. It shows that the aromatic ring at this position contributes to lowering the redox potential of heme 1 locally, although this cannot be the major contribution to the extremely low redox potentials of cytochrome c(3). Furthermore, temperature-dependent line-width broadening in partially reduced samples established that the aromatic ring at position 43 participates in the control of the kinetics of intramolecular electron transfer. The rate of reduction of Y43L cytochrome c(3) by 5-deazariboflavin semiquinone under partially reduced conditions was significantly different from that of the wild type in the last stage of the reduction, supporting the involvement of Tyr43 in regulation of reduction kinetics. The mutation of Y43L, however, did not induce a significant change in the crystal structure.

Redox-coupled conformational alternations in cytochrome c(3) from D. vulgaris Miyazaki F on the basis of its reduced solution structure

Heteronuclear NMR spectroscopy was performed to determine the solution structure of (15)N-labeled ferrocytochrome c(3) from Desulfovibrio vulgaris Miyazaki F (DvMF). Although the folding of the reduced cytochrome c(3) in solution was similar to that of the oxidized one in the crystal structure, the region involving hemes 1 and 2 was different. The redox-coupled conformational change is consistent with the reported solution structure of D. vulgaris Hildenborough ferrocytochrome c(3), but is different from those of other cytochromes c(3). The former is homologous with DvMF cytochrome c(3) in amino acid sequence. Small displacements of hemes 1 and 2 relative to hemes 3 and 4 were observed. This observation is consistent with the unusual behavior of the 2(1)CH(3) signal of heme 3 reported previously. As shown by the (15)N relaxation parameters of the backbone, a region between hemes 1 and 2 has more flexibility than the other regions. The results of this work strongly suggest that the cooperative reduction of hemes 1 and 2 is based on the conformational changes of the C-13 propionate of heme 1 and the aromatic ring of Tyr43, and the interaction between His34 and His 35 through covalent and coordination bonds.

Crystal structure of the oxidised and reduced acidic cytochrome c3from Desulfovibrio africanus

Unique among sulphate-reducing bacteria, Desulfovibrio africanus has two periplasmic tetraheme cytochromes c3, one with an acidic isoelectric point which exhibits an unusually low reactivity towards hydrogenase, and another with a basic isoelectric point which shows the usual cytochrome c3reactivity. The crystal structure of the oxidised acidic cytochrome c3of Desulfovibrio africanus (Dva.a) was solved by the multiple anomalous diffraction (MAD) method and refined to 1.6 A resolution. Its structure clearly belongs to the same family as the other known cytochromes c3, but with weak parentage with those of the Desulfovibrio genus and slightly closer to the cytochromes c3of Desulfomicrobium norvegicum. In Dva.a, one edge of heme I is completely exposed to the solvent and surrounded by a negatively charged protein surface. Heme I thus seems to play an important role in electron exchange, in addition to heme III or heme IV which are the electron exchange ports in the other cytochromes c3. The function of Dva.a and the nature of its redox partners in the cell are thus very likely different. By alignment of the seven known 3D structures including Dva.a, it is shown that the structure which is most conserved in all cytochromes c3is the four-heme cluster itself. There is no conserved continuous protein structure which could explain the remarkable invariance of the four-heme cluster. On the contrary, the proximity of the heme edges is such that they interact directly by hydrophobic and van der Waals contacts. This direct interaction, which always involves a pyrrole CA-CB side-chain and its bound protein cysteine Sgammaatom, is probably the main origin of the four-heme cluster stability. The same kind of interaction is found in the chaining of the hemes in other multihemic redox proteins.The crystal structure of reduced Dva. a was solved at 1.9 A resolution. The comparison of the oxidised and reduced structures reveals changes in the positions of water molecules and polar residues which probably result from changes in the protonation state of amino acids and heme propionates. Water molecules are found closer to the hemes and to the iron atoms in the reduced than in the oxidised state. A global movement of a chain fragment in the vicinity of hemes III and IV is observed which result very likely from the electrostatic reorganization of the polypeptide chain induced by reduction.

Further characterization of the two tetraheme cytochromes c3 from Desulfovibiro africanus: nucleotide sequences, EPR spectroscopy and biological activity

The genes encoding the basic and acidic tetraheme cytochromes c3 from Desulfovibrio africanus have been sequenced. The corresponding amino acid sequences of the basic and acidic cytochromes c3 indicate that the mature proteins consist of a single polypeptide chain of 117 and 103 residues, respectively. Their molecular masses, 15102 and 13742 Da, respectively, determined by mass spectrometry, are in perfect agreement with those calculated from their amino acid sequences. Both D. africanus cytochromes c3 are synthesized as precursor proteins with signal peptides of 23 and 24 residues for the basic and acidic cytochromes, respectively. These cytochromes c3 exhibit the main structural features of the cytochrome c3 family and contain the 16 strictly conserved cysteine + histidine residues directly involved in the heme binding sites. The D. africanus acidic cytochrome c3 differs from all the other homologous cytochromes by its low content of basic residues and its distribution of charged residues in the amino acid sequence. The presence of four hemes per molecule was confirmed by EPR spectroscopy in both cytochromes c3. The g-value analysis suggests that in both cytochromes, the angle between imidazole planes of the axial histidine ligands is close to 90 degrees for one heme and much lower for the three others. Moreover, an unusually high exchange interaction (approximately 10[-2] cm[-1]) was evidenced between the highest potential heme (-90 mV) and one of the low potential hemes in the basic cytochrome c3. The reactivity of D. africanus cytochromes c3 with heterologous [NiFe] and [Fe] hydrogenases was investigated. Only the basic one interacts with the two types of hydrogenase to achieve efficient electron transfer, whereas the acidic cytochrome c3 exchanges electrons specifically with the basic cytochrome c3. The difference in the specificity of the two D. africanus cytochromes c3 has been correlated with their highly different content of basic and acidic residues.

A single mutation in the heme 4 environment of Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000) greatly affects the molecule reactivity

The gene encoding Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000), a dimeric octaheme cytochrome belonging to the polyheme cytochrome c3 superfamily, has been cloned and successfully expressed in another sulfate reducing bacteria, D. desulfuricans G201. The gene, named cycD, is monocistronic and encodes a cytochrome precursor of 135 amino acids with an extension at the NH2 terminus of 24 amino acids. This extension acts as a signal sequence which allows export across the cytoplasmic membrane into the periplasmic space. Tyrosine 73, which is in a close contact with the histidine sixth axial ligand to the heme 4 iron atom, has been replaced by a glutamate residue using site-directed mutagenesis. The cytochrome mutant when expressed in D. desulfuricans G201, is correctly folded and matured. A global increase of the oxidoreduction potentials of about 50 mV is measured for the Y73E cytochrome. The mutation also has a strong influence on the interaction of the cytochrome with its redox partner, the hydrogenase. This suggests, like the tetraheme cytochrome c3 (Mr 13, 000), heme 4 is the interactive heme in the cytochrome-hydrogenase complex and that alteration of the heme 4 environment can greatly affect the electron transfer reaction with its redox partner.

The cytochrome c3 superfamily: amino acid sequence of a dimeric octahaem cytochrome c3 (M(r) 26,000) isolated from Desulfovibrio gigas

Cytochrome c3 (M(r) 26000) isolated from Desulfovibrio gigas is a dimeric cytochrome consisting of two identical subunits of 109 amino acids, each of which contains four haem groups. On the basis of its amino acid sequence, this cytochrome clearly belongs to the cytochrome c3 superfamily, and will be classified in class III of the c-type cytochromes as defined by Ambler [(1980) in From Cyclotrons to Cytochromes (Robinson, A. B. and Kaplan, N. O., eds.), pp. 263-279, Academic Press, London]. It contains ten cysteine and nine histidine residues in each subunit, and eight cysteines and eight histidines linked to the four haem groups were found to be invariant on alignment of all known cytochrome c3 sequences. Two intermolecular disulphide bridges have been determined between cysteine residues 5 and 46 of the two monomers. Cytochrome c3 (M(r) 26,000) from D gigas is clearly different from cytochrome c3 (M(r) 13,000) from the same strain, with which it shows only 27% sequence identity. Compared with cytochrome c3 (M(r) 26,000) from D. desulfuricans Norway, the three-dimensional structure of which has been determined, 26.95% of the residues have been conserved. In the enzyme from D. desulfuricans Norway, hydrophobic interactions have been described across the dimer interface. Residues involved in similar interactions seem to be well conserved in the equivalent D. gigas cytochrome. This sequence provides structural data to allow specification of this new subclass of polyhaem cytochromes. Furthermore, D. gigas cytochrome c3 (M(r) 26,000) is the first polyhaem cytochrome shown to contain two disulphide bridges linking two identical subunits, which could induce more rigid folding. The folding and the evolution of this family of polyhaem cytochromes are discussed.

Crystal structure of a dimeric octaheme cytochrome c3 (M(r) 26,000) from Desulfovibrio desulfuricans Norway

BACKGROUND

The octaheme cytochrome C3 (M(r) 26,000; cc3) from Desulfovibrio desulfuricans Norway is a dimeric cytochrome made up of two identical subunits, each containing four heme groups. It is involved in the redox transfer chain of sulfate-reducing bacteria, which links the periplasmic oxidation of hydrogen to the cytoplasmic reduction of sulfate. The amino-acid sequence of cc3 shows similarities to that of the tetraheme cytochrome c3 (M(r) 13,000; c3) from the same bacteria. Structural analysis of cc3 forms a basis for understanding the precise roles of the multiheme-containing redox proteins and the reason for the presence of several different multiheme cytochromes in one bacterial strain.

RESULTS

The crystal structure of cytochrome cc3 has been determined at 2.16 A resolution. The subunits display the c3 structural fold with significant amino-acid substitutions, relative to the tetraheme cytochromes c3, in the regions of the dimer interface. The identical subunits are related by a crystallographic twofold axis, with one heme of each subunit in close contact. The overall structure and the environments of the different heme groups are compared with those of the tetraheme cytochromes c3.

CONCLUSIONS

A common scheme for interactions between these types of cytochrome and their redox partners involves the interaction of a heme crevice, surrounded by positively charged lysine residues, with acidic residues surrounding the redox partner's functional group. Despite the relatively acidic character of cytochrome cc3, the crevice of one heme is surrounded by a high number of positively charged residues, in the same manner as has been reported for cytochromes c3. The environment of this heme is formed by four flexible surface loops which are variable in length and orientation in the different c3-type cytochromes although the overall structural folds are very similar. It has been proposed that this region, adapted in topology and charge, is the interaction site for physiological partners and is also most likely to be the interaction site in the dimeric cytochrome cc3.

Thermal stability of the polyheme cytochrome c3 superfamily

The cytochrome c3 superfamily includes Desulfovibrio polyheme cytochromes c. We report the characteristic thermal stability parameters of the Desulfovibrio desulfuricans Norway (D.d.N.) cytochromes c3 (M(r) 13,000 and M(r) 26,000) and the Desulfovibrio vulgaris Hildenborough (D.v.H.) cytochrome c3 (M(r) 13,000) and high molecular mass cytochrome c (Hmc), as obtained with the help of electronic spectroscopy, voltammetric techniques and differential scanning calorimetry. The polyheme cytochromes are denatured over a wide range of temperatures: the D.v.H. cytochrome c3 is highly thermostable (Td = 121 degrees C) contrary to the D.d.N. protein (Td = 73 degrees C). The thermostability of the polyheme cytochromes is redox state dependent. The results are discussed in the light of the structural and functional relationships within the cytochrome c3 superfamily.

Principles of protein-protein recognition from structure to thermodynamics

Specific recognition is illustrated by X-ray structures of protease-inhibitor, antigen-antibody and other high affinity complexes including five electron transfer complexes. We attempt to give a physical definition to affinity and specificity on the basis of these data. In a protein-protein complex, specific recognition results from the assembly of complementary surfaces into well-packed interfaces that cover about 1500 A2 and contain about ten hydrogen bonds. These interfaces are larger than between molecules in protein crystals, and smaller than between subunits in oligomeric proteins. We relate the size and chemical nature of interfaces in complexes to the thermodynamical parameters that characterize affinity: the heat capacity and free enthalpy (Gibbs energy) of dissociation at equilibrium, the activation free enthalpy for the dissociation reaction. The same structural and thermodynamical parameters are inadequate for representing the specificity of recognition. We propose instead to describe specificity with the help of statistical physics, and we illustrate the application of the random energy model to antigen-antibody recognition by analyzing results of computer simulations by docking.