Magnetic spectroscopic (EPR, ESEEM, Mössbauer, MCD and NMR) studies of low-spin ferriheme centers and their corresponding heme proteins

NMR and DFT investigation of heme ruffling: functional implications for cytochrome c

Out-of-plane (OOP) deformations of the heme cofactor are found in numerous heme-containing proteins and the type of deformation tends to be conserved within functionally related classes of heme proteins. We demonstrate correlations between the heme ruffling OOP deformation and the (13)C and (1)H nuclear magnetic resonance (NMR) hyperfine shifts of heme aided by density functional theory (DFT) calculations. The degree of ruffling in the heme cofactor of Hydrogenobacter thermophilus cytochrome c(552) has been modified by a single amino acid mutation in the second coordination sphere of the cofactor. The (13)C and (1)H resonances of the cofactor have been assigned using one- and two-dimensional NMR spectroscopy aided by selective (13)C-enrichment of the heme. DFT has been used to predict the NMR hyperfine shifts and electron paramagnetic resonance (EPR) g-tensor at several points along the ruffling deformation coordinate. The DFT-predicted NMR and EPR parameters agree with the experimental observations, confirming that an accurate theoretical model of the electronic structure and its response to ruffling has been established. As the degree of ruffling increases, the heme methyl (1)H resonances move upfield while the heme methyl and meso (13)C resonances move downfield. These changes are a consequence of altered overlap of the Fe 3d and porphyrin pi orbitals, which destabilizes all three occupied Fe 3d-based molecular orbitals and decreases the positive and negative spin density on the beta-pyrrole and meso carbons, respectively. Consequently, the heme ruffling deformation decreases the electronic coupling of the cofactor with external redox partners and lowers the reduction potential of heme.

Spectroscopic properties of rubber oxygenase RoxA from Xanthomonas sp., a new type of dihaem dioxygenase

Natural rubber [poly-(cis-1,4-isoprene)] is cleaved to 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) by rubber oxygenase A (RoxA) isolated from Xanthomonas sp. RoxA has two c-type haem centres that show two distinct alpha-bands at 549 and 553 nm in the dithionite-reduced state. A well-resolved midpoint potential (E(0)') of -65 mV was determined for one haem by spectrophotometric titrations in the absence of dioxygen with dithionite and ferricyanide as reductant and oxidant, respectively. The midpoint potential of the second haem was not resolvable (E(0)' about -130 to -160 mV). One of the two haems was reduced by NADH (549 nm alpha-band), similar to bacterial dihaem peroxidases. Evidence for an electron transfer between the two haems was provided by slow reduction of the second haem (553 nm alpha-band) upon incubation of the partially reduced enzyme at room temperature. Addition of imidazole or related compounds to RoxA led to UV/vis spectral features similar to those observed for partially reduced RoxA. Notably, reduction of RoxA with dithionite or NADH, or binding of compounds such as imidazole, resulted in a reversible inactivation of the enzyme, unlike dihaem peroxidases. In line with this result, RoxA did not show any peroxidase activity. EPR spectra of RoxA as isolated showed two low-spin Fe(III) haem centres, with apparent g-values of 3.39, 3.09, 2.23, 1.92 and 1.50. A weak signal in the g=6 region resulting from a high-spin Fe(III) haem was also observed with a preparation-dependent intensity that disappeared in the presence of imidazole. Attempts to provide spectroscopic evidence for binding of the natural substrate (polyisoprene latex) to RoxA failed. However, experimental data are presented that RoxA is able to subtract redox equivalents from its substrate or from model compounds. In conclusion, RoxA is a novel type of dihaem dioxygenase with features clearly different from classical cytochrome c peroxidases.

Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a

The electronic structures of heme a of cytochrome c oxidase in the redox states were studied, using hybrid density functional theory with a polarizable continuum model and a point charge model. We found that the most stable electronic configurations of the d electrons of the Fe ion are determined by the orbital interactions of the d orbitals of the Fe ion with the pi orbitals of the porphyrin ring and the His residues. The redox reaction of the Fe ion influences the charge density on the formyl group through the pi conjugation of the porphyrin ring. In addition, we found the charge transfer from the Fe ion to the propionate group of heme a in the redox change despite the lack of the pi-conjugation. We elucidated that the charge propagation originates from the heme a structure itself and that the origin of the charge delocalization to the heme propionate is the orbital interactions between the d orbital of the Fe ion and the p orbitals of the carboxylate part of the heme propionate via the pi conjugation of the porphyrin ring and the sigma* orbital of the C-C bond of the propionate group. The electrostatic effect by surrounding proteins enhances the charge transfer from the Fe ion to the propionate group. These results indicate that heme propionate groups serve electron mediators in electron transfer as well as electrostatic anchors, and that proteins surrounding the active site reinforce the congenital abilities of the cofactors.

Investigations of low-frequency vibrational dynamics and ligand binding kinetics of cystathionine beta-synthase

Vibrational coherence spectroscopy is used to study the low frequency dynamics of the truncated dimer of human cystathionine beta-synthase (CBS). CBS is a pyridoxal-5'-phosphate-dependent heme enzyme with cysteine and histidine axial ligands that catalyzes the condensation of serine and homocysteine to form cystathionine. A strong correlation between the "detuned" coherence spectrum (which probes higher frequencies) and the Raman spectrum is demonstrated, and a rich pattern of modes below 200 cm(-1) is revealed. Normal coordinate structural decomposition (NSD) of the ferric CBS crystal structure predicts the enhancement of normal modes with significant heme "doming", "ruffling", and "saddling" content, and they are observed in the coherence spectra near approximately 40, approximately 60, and approximately 90 cm(-1). When pH is varied, the relative intensities and frequencies of the low frequency heme modes indicate the presence of a unique protein-induced heme structural perturbation near pH 7 that differs from what is observed at higher or lower pH. For ferric CBS, we observe a new mode near approximately 25 cm(-1), possibly involving the response of the protein, which exhibits a phase jump of approximately pi for excitation on the blue and red side of the Soret band maximum. The low frequency vibrational coherence spectrum of ferrous CBS is also presented, along with our efforts to probe its NO-bound complex. The CO geminate rebinding kinetics of CBS are similar to the CO-bound form of the gene activator protein CooA, but with the appearance of a significant additional kinetic inhomogeneity. Analysis of this inhomogeneity suggests that it arises from the two subunits of CBS and leads to a factor of approximately 20 for the ratio of the average CO geminate rebinding rates of the two subunits.

Redox effects on the coordination geometry and heme conformation of bis(N-methylimidazole) complexes of superstructured Fe-porphyrins. A spectroscopic study

Electronic absorption, electron paramagnetic resonance (EPR), and Soret-excited resonance Raman (RR) spectra are reported for bis(N-alkylimidazole) complexes of various iron(III)-"basket-handle" (Fe(III)BHP(+)) and "picket-fence" (Fe(III)PFP(+)) porphyrins in methylene chloride. The Fe(III)BHP(+) derivatives consist of four cross-trans (CT) and two adjacent-cis (AC) -linked in which the composition and the length of the handles are variable (CT Fe(III)[(C(11)Im)(2)(+)], CT and AC Fe(III)[((C(4))(2)phi)(2)](+), CT Fe(III)[((C(3))(2)phi)(C(12))](+), CT and AC Fe(III)[((C(3))(2)phi)(2)](+)). The meso-alphaalpha betabeta and meso-alphabeta alphabeta atropisomers of Fe(III)-tetrakis(o-pivalamidophenyl)-porphyrins represents the Fe(III)PFP(+) derivatives (Fe(III)alphaalpha betabeta-T(piv)PP(+) and Fe(III)alphabeta alphabeta-T(piv)PP(+), respectively). The absorption and RR data obtained for these ferric compounds were compared to those previously published for the homologous ferrous complexes (Picaud, T., Le Moigne, C., Loock, B., Momenteau, M. and Desbois, A. J. Am. Chem. Soc. 2003, 125, 11616 and Le Moigne, C., Picaud, T., Boussac, A., Loock, B., Momenteau, M. and Desbois, A. Inorg. Chem. 2003, 42, 6081). The Soret band position of the eight investigated ferric compounds is observed between 417 and 424 nm, indicating that none of the complexes possesses a planar heme. The EPR spectra show that most of the Fe(III)BHP(+) complexes and all the Fe(III)PFP(+) complexes are rhombic B-type hemichromes (g(max) = 2.86-2.96). Notable exceptions concern the bis(N-methylimidazole) complexes of two CT Fe(III)BHP(+). The Fe(III)BHP(+) with the shortest handles (Fe(III)[((C(3))(2)phi)(2)](+)) exhibits a g value at 2.80. When the handles are lengthened by two methylene units (Fe(III)[((C(3))(2)phi)(2)](+)), the EPR spectrum corresponds to a mixture of two "highly anisotropic low-spin " or "large g(max)" type I EPR signals, a major species at g = 3.17 and a minor species at g = 3.77. All these EPR data were converted in terms of dihedral angle formed by the rings of the axial ligands. The RR spectra of the Fe(III)BHP(+) and Fe(III)PFP(+) complexes exhibited variable frequencies for the structure-sensitive nu(2) and nu(8) lines (1558-1563 cm(-1) and 386-401 cm(-1), respectively). In considering the ability of the different superstructures to stabilize particular out-of-plane distortions, this vibrational information was analyzed in terms of heme structure through changes in core size and Fe-N(pyrrole) bond length, in relation to changes in coordination geometry. The bis(N-methylimidazole) complex of Fe(III)[((C(3))(2)phi)(2)](+) was found to be the most distorted with a strongly ruffled tetrapyrrole. Because of a handle asymmetry, the heme conformation of the bis(N-methylimidazole) complex of Fe(III)[((C(3))(2)phi)(C(12))](+) was deduced to be a composition of ruffled and domed structures. The heme structure of the other complexes is a mixture of ruffled and saddled or ruffled and waved conformations. Taking into account our previous data on the ferrous series, this investigation provides information about the reorganization of the heme structure upon iron oxidation. The general trend is a decrease of either the core-size, or the Fe-N(pyrrole) bond length, or both. However, we demonstrated that the heme superstructures precisely control the nature and the extent of the tetrapyrrole reshaping. These results point out similar possible effect in the heme proteins, considering both an analogy between porphyrin superstructures and amino acids forming the heme sites and the diversity of the heme environments in the proteins.

Spectral characterization of the recombinant mouse tumor suppressor 101F6 protein

Tumor suppressor protein 101F6, a gene product of the 3p21.3 (human) and 9F1 (mouse) chromosomal region, has recently been identified as a member of the cytochrome b561 (Cyt-b561) protein family by sequence homology. The His(6)-tagged recombinant mouse tumor suppressor Cyt-b561 protein (TSCytb) was recently expressed in yeast and purified, and the ascorbate reducibility was determined. TSCytb is auto-oxidizable and has two distinct heme b centers with redox potentials of approximately 40 and approximately 140 mV. Its split alpha-band in the dithionite-reduced spectrum at both 295 and 77 K is well resolved, and the separation between the two alpha-peaks is approximately 7 nm (approximately 222 cm(-1)). Singular value decomposition analysis of the split alpha-band in the ascorbate-reduced spectra revealed the presence of two major spectral components, each of them with split alpha-band but with different peak separations (6 and 8 nm). Similar minor differences in peak separation were obtained when the split alpha-bands in ascorbate-reduced difference spectra at low (<1 mM) and high (>10 mM) ascorbate concentrations were analysed. According to low-temperature electron paramagnetic resonance (EPR) spectroscopy, the two heme b centers are in the low-spin ferric state with maximum principal g values of 3.61 and 2.96, respectively. These values differ from the ones observed for other members of the Cyt-b561 family. According to resonance Raman spectroscopy, the porphyrin rings are in a relaxed state. The spectroscopic results are only partially in agreement with those obtained earlier for the native chromaffin granule Cyt-b561.

Significant change in electronic structures of heme upon reduction by strong Coulomb repulsion between Fe d electrons

We report total-energy electronic-structure calculations based on the density functional theory performed on a low-spin heme. We have found that the high-lying occupied and low-lying unoccupied states having Fe d and/or porphyrin pi orbital character are significantly rearranged upon the reduction of the heme. An analysis of these states shows that the remarkable elevation of the Fe d levels takes place due to the strong Coulombic repulsion between accommodated d electrons. Due to a peculiarity of the heme, this elevation could be controlled by lower-lying empty porphyrin pi states, leading to electron transfer from Fe d orbitals to the porphyrin pi ones in order to reduce the Coulomb-energy cost. This self-limiting mechanism provides a natural explanation not only for the present calculated results, but also for general electron delocalization appearing under various physiological conditions, regardless of the types of the hemes.

Unusual flexibility of distal and proximal histidine residues in the haem pocket of Drosophila melanogaster haemoglobin

Several pH-dependent low-spin ferric haem forms are identified in a frozen solution of the ferric ¹²¹Cys→Ser mutant of Drosophila melanogaster haemoglobin (DmHb1*) using electron paramagnetic resonance (EPR) techniques. Different forms with EPR parameters typical of bis-histidine coordinated haem iron centers were observed. Strong pH-dependent changes in the EPR signatures were observed related to changes in the haem pocket. The pulsed EPR data indicate that both the distal and proximal histidine exhibit a large libration around the Fe-N(His) axis. The resonance Raman spectra of the CO-ligated ferrous form of Drosophila melanogaster haemoglobin are typical of an open conformation, with little stabilization of the CO ligand by the surrounding amino-acid residues. The EPR data of the cyanide-ligated ferric DmHb1* indicates a close similarity with cyanide-ligated ferric myoglobin. The structural characteristics of DmHb1* are found to clearly differ from those of other bis-histidine-coordinated globins.

Hyperfine correlation spectroscopy and electron spin echo envelope modulation spectroscopy study of the two coexisting forms of the hemeprotein cytochrome c6 from Anabaena Pcc7119

Oxidized cytochrome c(6) from Anabaena PCC 7119 was studied by electron spin echo envelope modulation spectroscopy. Hyperfine couplings of the unpaired electron with several nuclei were detected, in particular those of the nitrogens bound to the iron atom. Combining the experimental information here presented and previous continuous wave-electron paramagnetic resonance and electron nuclear double resonance results, some details on the electronic structure of the heme center in the protein are obtained. These results are discussed on the basis of a molecular model that considers one unpaired electron localized mainly in the iron d orbitals and propagation of the spin density within the heme center via spin polarization of the nitrogen sigma-orbitals. The coexistence of two heme forms at physiological pH values in this c-type cytochrome is also discussed taking into account the experimental evidence.

Modulation of the ligand-field anisotropy in a series of ferric low-spin cytochrome c mutants derived from Pseudomonas aeruginosa cytochrome c-551 and Nitrosomonas europaea cytochrome c-552: a nuclear magnetic resonance and electron paramagnetic resonance study

Cytochromes of the c type with histidine-methionine (His-Met) heme axial ligation play important roles in electron-transfer reactions and in enzymes. In this work, two series of cytochrome c mutants derived from Pseudomonas aeruginosa (Pa c-551) and from the ammonia-oxidizing bacterium Nitrosomonas europaea (Ne c-552) were engineered and overexpressed. In these proteins, point mutations were induced in a key residue (Asn64) near the Met axial ligand; these mutations have a considerable impact both on heme ligand-field strength and on the Met orientation and dynamics (fluxionality), as judged by low-temperature electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectra. Ne c-552 has a ferric low-spin (S = 1/2) EPR signal characterized by large g anisotropy with g(max) resonance at 3.34; a similar large g(max) value EPR signal is found in the mitochondrial complex III cytochrome c1. In Ne c-552, deletion of Asn64 (NeN64Delta) changes the heme ligand field from more axial to rhombic (small g anisotropy and g(max) at 3.13) and furthermore hinders the Met fluxionality present in the wild-type protein. In Pa c-551 (g(max) at 3.20), replacement of Asn64 with valine (PaN64V) induces a decrease in the axial strain (g(max) at 3.05) and changes the Met configuration. Another set of mutants prepared by insertion (ins) and/or deletion (Delta) of a valine residue adjacent to Asn64, resulting in modifications in the length of the axial Met-donating loop (NeV65Delta, NeG50N/V65Delta, PaN50G/V65ins), did not result in appreciable alterations of the originally weak (Ne c-552) or very weak (Pa c-551) axial field but had an impact on Met orientation, fluxionality, and relaxation dynamics. Comparison of the electronic fingerprints in the overexpressed proteins and their mutants reveals a linear relationship between axial strain and average paramagnetic heme methyl shifts, irrespective of Met orientation or dynamics. Thus, for these His-Met axially coordinated Fe(III), the large g(max) value EPR signal does not represent a special case as is observed for bis-His axially coordinated Fe(III) with the two His planes perpendicular to each other.

Axial ligand coordination in sterically strained vanadyl porphyrins: synthesis, structure, and properties

A hitherto unknown family of six-coordinate vanadyl porphyrins of the sterically crowded, nonplanar 2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetranitroporphyrin incorporating axial ligand L [where L is pyridine, tetrahydrofuran (THF), or methanol (MeOH)] has been isolated as VO(tn-OEP)(L) in the solid phase for the first time and also structurally characterized. The presence of four electron-withdrawing, bulky nitro groups at the meso positions of vanadyl octaethylporphyrins severely distorts the porphyrin macrocycles and significantly enhances the affinity for the axial ligands, where even weak sigma-donating ligands, such as MeOH, bind strongly enough to be isolable in the solid phase and that too under the offset effects of the macrocyclic distortions. Thus, the axial ligand affinity is influenced by both the electronic and conformational effect, which cannot be separated completely in this series. The solid-state magnetic measurements and their typical electron paramagnetic resonance (EPR) spectrum show the presence of a single, unpaired electron, consistent with V(IV) formulation. The VO stretching frequency for VO(tn-OEP) occurs as a sharp, strong peak at 1008 cm(-1), which is consistent with five-coordinate vanadyl porphyrins, while VO(tn-OEP)(L) displays a strong band at lower wavenumbers. The downshift in nu(VO) upon axial coordination increases with increasing donor strength of the axial ligands; for pyridine, the downshift is 30 cm(-1), while for THF and MeOH, the downshifts are nearly 18 cm(-1). X-ray structure determinations authenticate axial coordination in a purely saddle-distorted porphyrin macrocycle for all of the complexes reported here in which V-Np distances are significantly shorter, while the porphyrin cores have been expanded on axial ligand coordination. As a result, vanadium atoms are more inplane than in a five-coordinate species. The binding of L does not change the spin or metal oxidation states (V(IV), d(1)-system) of the complexes; therefore, the changes observed are truly the reflections of axial ligand coordination. Electrochemical data obtained from cyclic voltammetric studies reveal that the complexes are much easier to reduce (by approximately 1200 mV) but more difficult to oxidize (by approximately 500 mV) as compared to nearly planar VO(OEP). The complexes undergo two one-electron oxidations due to pi-cation radical and dication formation and three one-electron reductions. The first two reductions are because of pi-anion radical and dianion formation, while the third quasi-reversible reduction is assigned to a metal-centered process (V(IV) --> V(III)). These results can be useful for identifying the interaction of the vanadyl porphyrins with the biological targets in their reported involvement in potent insulinomimetic activity and in anti-HIV agents.

The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex?

Recent progress in understanding the Q-cycle mechanism of the bc(1) complex is reviewed. The data strongly support a mechanism in which the Q(o)-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron-sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe-2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q(o)-site, and the reduced iron-sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c(1) and liberate the H(+). When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O(2) is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b(L) to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b(L) to enhance the rate constant. The acceptor reactions at the Q(i)-site are still controversial, but likely involve a "two-electron gate" in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b(150) phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed. The mechanism discussed is applicable to a monomeric bc(1) complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b(L) hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.

Membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing nitrosomonas europaea: a ubiquinone reductase

Cytochrome c(m552) (cyt c(m552)) from the ammonia-oxidizing Nitrosomonas europaea is encoded by the cycB gene, which is preceded in a gene cluster by three genes encoding proteins involved in the oxidation of hydroxylamine: hao, hydroxylamine oxidoreductase; orf2, a putative membrane protein; cycA, cyt c(554). By amino acid sequence alignment of the core tetraheme domain, cyt c(m552) belongs to the NapC/TorC family of tetra- or pentaheme cytochrome c species involved in electron transport from membrane quinols to a variety of periplasmic electron shuttles leading to terminal reductases. However, cyt c(m552) is thought to reduce quinone with electrons originating from HAO. In this work, the tetrahemic 27 kDa cyt c(m552) from N. europaea was purified after extraction from membranes using Triton X-100 with subsequent exchange into n-dodecyl beta-d-maltoside. The cytochrome had a propensity to form strong SDS-resistant dimers likely mediated by a conserved GXXXG motif present in the putative transmembrane segment. Optical spectra of the ferric protein contained a broad ligand-metal charge transfer band at approximately 625 nm indicative of a high-spin heme. Mossbauer spectroscopy of the reduced (57)Fe-enriched protein revealed the presence of high-spin and low-spin hemes in a 1:3 ratio. Multimode EPR spectroscopy of the native state showed signals from an electronically interacting high-spin/low-spin pair of hemes. Upon partial reduction, a typical high-spin heme EPR signal was observed. No EPR signals were observed from the other two low-spin hemes, indicating an electronic interaction between these hemes as well. UV-vis absorption data indicate that CO (ferrous enzyme) or CN(-) (ferric or ferrous enzyme) bound to more than one and possibly all hemes. Other anionic ligands did not bind. The four ferrous hemes of the cytochrome were rapidly oxidized in the presence of oxygen. Comparative modeling, based on the crystal structure and conserved residues of the homologous NrfH protein from Desulfovibrio of cyt c(m552), predicted some structural elements, including a Met-ligated high-spin heme in a quinone-binding pocket, and likely axial ligands to all four hemes.

SoxAX cytochromes, a new type of heme copper protein involved in bacterial energy generation from sulfur compounds

SoxAX cytochromes are essential for the function of the only confirmed pathway for bacterial thiosulfate oxidation, the so-called "Sox pathway," in which they catalyze the initial formation of a S-S bond between thiosulfate and the SoxYZ carrier protein. Our work using the Starkeya novella diheme SoxAX protein reveals for the first time that in addition to two active site heme groups, SoxAX contains a mononuclear Cu(II) center with a distorted tetragonal geometry and three to four nitrogen ligands, one of which is a histidine. The Cu(II) center enhanced SoxAX activity in a newly developed, glutathione-based assay system that mimics the natural reaction of SoxAX with SoxYZ. EPR spectroscopy confirmed that the SoxAX Cu(II) center is reduced by glutathione. At pH 7 a K(m) (app) of 0.19+/-0.028 mm and a k(cat) (app) of 5.7+/-0.25s(-1) were determined for glutathione. We propose that SoxAX cytochromes are a new type of heme-copper proteins, with SoxAX-mediated S-S bond formation involving both the copper and heme centers.

Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins

Early investigation of the electron paramagnetic resonance spectra of bis-histidine-coordinated membrane-bound ferriheme proteins led to the description of a spectral signal that had only one resolved feature. These became known as "highly anisotropic low-spin" or "large g(max)" ferriheme centers. Extensive work with small-molecule model heme complexes showed that this spectroscopic signature occurs in bis-imidazole ferrihemes in which the planes of the imidazole ligands are nearly perpendicular, deltaphi = 57-90 degrees. In the last decade protein crystallographic studies have revealed the atomic structures of a number of examples of bis-histidine heme proteins. A frequent characteristic of these large g(max) ferrihemes in membrane-bound proteins is the occurrence of the heme within a four-helix bundle with a left-handed twist. The histidine ligands occur at the same level on two diametrically opposed helices of the bundle. These ligands have the same side-chain conformation and ligate heme iron on the bundle axis, resulting in a quasi-twofold symmetric structure. The two non-ligand-bearing helices also obey this symmetry, and have a conserved small residue, usually glycine, where the edge of the heme ring makes contact with the helix backbones. In many cases this small residue is preceded by a threonine or serine residue whose side-chain hydroxyl oxygen acts as a hydrogen-bond acceptor from the N(delta1) atom of the heme-ligating histidine. The deltaphi angle is thus determined by the common histidine side-chain conformation and the crossing angle of the ligand-bearing helices, in some cases constrained by hydrogen bonds to the serine/threonine residues on the non-ligand-bearing helices.

Detailed assignment of the magnetic circular dichroism and UV-vis spectra of five-coordinate high-spin ferric [Fe(TPP)(Cl)]

High-spin (hs) ferric heme centers occur in the catalytic or redox cycles of many metalloproteins and exhibit very complicated magnetic circular dichroism (MCD) and UV-vis absorption spectra. Therefore, detailed assignments of the MCD spectra of these species are missing. In this study, the electronic spectra (MCD and UV-vis) of the five-coordinate hs ferric model complex [Fe(TPP)(Cl)] are analyzed and assigned for the first time. A correlated fit of the absorption and low-temperature MCD spectra of [Fe(TPP)(Cl)] lead to the identification of at least 20 different electronic transitions. The assignments of these spectra are based on the following: (a) variable temperature and variable field saturation data, (b) time-dependent density functional theory calculations, (c) MCD pseudo A-terms, and (d) correlation to resonance Raman (rRaman) data to validate the assignments. From these results, a number of puzzling questions about the electronic spectra of [Fe(TPP)(Cl)] are answered. The Soret band in [Fe(TPP)(Cl)] is split into three components because one of its components is mixed with the porphyrin A2u72-->Eg82/83 (pi-->pi*) transition. The broad, intense absorption feature at higher energy from the Soret band is due to one of the Soret components and a mixed sigma and pi chloro to iron CT transition. The high-temperature MCD data allow for the identification of the Q v band at 20 202 cm(-1), which corresponds to the C-term feature at 20 150 cm(-1). Q is not observed but can be localized by correlation to rRaman data published before. Finally, the low energy absorption band around 650 nm is assigned to two P-->Fe charge transfer transitions, one being the long sought after A1u(HOMO)-->d pi transition.

Photodynamic Therapy: Porphyrins and Phthalocyanines as Photosensitizers

The present work is focussed on the principles of photodynamic therapy (PDT), emphasizing the photochemical mechanisms of reactive oxygen species formation and the consequent biochemical processes generated by the action of reactive oxygen species on various biological macromolecules and organelles. This paper also presents some of the most used photosensitizers, including Photofrin, and the new prototypes of photosensitizers, analysing their physicochemical and spectroscopic properties. At this point, the review discusses the therapeutic window of absorption of specific wavelengths involving first- and second-generation photosensitizers, as well as the principal light sources used in PDT. Additionally, the aggregation process, which consists in a phenomenon common to several photosensitizers, is studied. J-aggregates and H-aggregates are discussed, along with their spectroscopic effects. Most photosensitizers have a significant hydrophobic character; thus, the study of the types of aggregation in aqueous solvent is very relevant. Important aspects of the coordination chemistry of metalloporphyrins and metallophthalocyanines used as photosensitizers are also discussed. The state-of-the-art in PDT is evaluated, discussing recent articles in this area. Furthermore, macrocyclic photosensitizers, such as porphyrins and phthalocyanines, are specifically described. The present review is an important contribution, because PDT is one of the most auspicious advances in the therapy against cancer and other non-malignant diseases.

Characterization of Shewanella oneidensis MtrC: a cell-surface decaheme cytochrome involved in respiratory electron transport to extracellular electron acceptors

MtrC is a decaheme c-type cytochrome associated with the outer cell membrane of Fe(III)-respiring species of the Shewanella genus. It is proposed to play a role in anaerobic respiration by mediating electron transfer to extracellular mineral oxides that can serve as terminal electron acceptors. The present work presents the first spectropotentiometric and voltammetric characterization of MtrC, using protein purified from Shewanella oneidensis MR-1. Potentiometric titrations, monitored by UV-vis absorption and electron paramagnetic resonance (EPR) spectroscopy, reveal that the hemes within MtrC titrate over a broad potential range spanning between approximately +100 and approximately -500 mV (vs. the standard hydrogen electrode). Across this potential window the UV-vis absorption spectra are characteristic of low-spin c-type hemes and the EPR spectra reveal broad, complex features that suggest the presence of magnetically spin-coupled low-spin c-hemes. Non-catalytic protein film voltammetry of MtrC demonstrates reversible electrochemistry over a potential window similar to that disclosed spectroscopically. The voltammetry also allows definition of kinetic properties of MtrC in direct electron exchange with a solid electrode surface and during reduction of a model Fe(III) substrate. Taken together, the data provide quantitative information on the potential domain in which MtrC can operate.

The crystal structure of the pentahaem c-type cytochrome NrfB and characterization of its solution-state interaction with the pentahaem nitrite reductase NrfA

NrfB is a small pentahaem electron-transfer protein widely involved in the respiratory reduction of nitrite or nitric oxide to ammonia, processes that provide energy for anaerobic metabolism in many enteric bacteria and also serve to detoxify these reactive nitrogen species. The X-ray crystal structure of Escherichia coli NrfB is presented at 1.74 A (1 A=0.1 nm) resolution. The architecture of the protein is that of a 40 A 'nanowire' in which the five haems are positioned within 6 A of each other along a polypeptide scaffold. During nitrite reduction, the physiological role of NrfB is to mediate electron transfer to another pentahaem protein, NrfA, the enzyme that catalyses periplasmic nitrite or nitric oxide reduction. Protein-protein interaction studies suggest NrfA and NrfB can form a 20-haem NrfA2-NrfB2 heterotetrameric complex.

Low-temperature EPR and Mössbauer spectroscopy of two cytochromes with His-Met axial coordination exhibiting HALS signals

C-type cytochromes with histidine-methionine (His-Met) iron coordination play important roles in electron-transfer reactions and in enzymes. Low-temperature electron paramagnetic resonance (EPR) spectra of low-spin ferric cytochromes c can be divided into two groups, depending on the spread of g values: the normal rhombic ones with small g anisotropy and g(max) below 3.2, and those featuring large g anisotropy with g(max) between 3.3 and 3.8, also denoted as highly axial low spin (HALS) species. Herein we present the detailed magnetic properties of cytochrome c(553) from Bacillus pasteurii (g(max) 3.36) and cytochrome c(552) from Nitrosomonas europaea (g(max) 3.34) over the pH range 6.2 to 8.2. Besides being structurally very similar, cytochrome c(553) shows the presence of a minor rhombic species at pH 6.2 (6 %), whereas cytochrome c(552) has about 25 % rhombic species over pH 7.5. The detailed Mössbauer analysis of cytochrome c(552) confirms the presence of these two low-spin ferric species (HALS and rhombic) together with an 8 % ferrous form with parameters comparable to the horse cytochrome c. Both EPR and Mössbauer data of axial cytochromes c with His-Met iron coordination are consistent with an electronic (d(xy))(2) (d(xz))(2) (d(yz))(1) ground state, which is typical for Type I model hemes.

Activation of the cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. Reaction of oxidized enzyme with substrate drives a ligand switch at heme c

Cytochromes cd(1) are dimeric bacterial nitrite reductases, which contain two hemes per monomer. On reduction of both hemes, the distal ligand of heme d(1) dissociates, creating a vacant coordination site accessible to substrate. Heme c, which transfers electrons from donor proteins into the active site, has histidine/methionine ligands except in the oxidized enzyme from Paracoccus pantotrophus where both ligands are histidine. During reduction of this enzyme, Tyr(25) dissociates from the distal side of heme d(1), and one heme c ligand is replaced by methionine. Activity is associated with histidine/methionine coordination at heme c, and it is believed that P. pantotrophus cytochrome cd(1) is unreactive toward substrate without reductive activation. However, we report here that the oxidized enzyme will react with nitrite to yield a novel species in which heme d(1) is EPR-silent. Magnetic circular dichroism studies indicate that heme d(1) is low-spin Fe(III) but EPR-silent as a result of spin coupling to a radical species formed during the reaction with nitrite. This reaction drives the switch to histidine/methionine ligation at Fe(III) heme c. Thus the enzyme is activated by exposure to its physiological substrate without the necessity of passing through the reduced state. This reactivity toward nitrite is also observed for oxidized cytochrome cd(1) from Pseudomonas stutzeri suggesting a more general involvement of the EPR-silent Fe(III) heme d(1) species in nitrite reduction.

Synthesis and spectroscopic studies on iron(III) complexes of 1-benzotriazol-1-yl-1-[(p-X-phenyl)hydrazono]propan-2-one

A new series of iron(III) complexes are synthesized from the reaction of the polyfunctional ligands 1-benzotriazol-1-yl-1-[p-X-phenyl]hydrazono]propan-2-one (X=H, Cl, NO(2), CH(3) or OCH(3) corresponding to HL(1),HL(2), HL(3), HL(4) or HL(5), respectively, with iron(III) chloride in the presence of LiOH by the conventional and microwave induced energy methods. The conventional method led to the formation of [FeL(3)].nH(2)O but the microwave induced energy gave [FeLCl(2)], n=1-3 and L is the anion of HL(1)-HL(5). The complexes are characterized by the elemental analysis, molar conductivity, magnetic and spectral (FT-IR, UV-vis and ESR) studies. The magnetic and spectral studies showed that [FeLCl(2)] are polymeric octahedral, [Fe(L(1))(3)].H(2)O is a low spin octahedral and (d(xz),d(yz))(4) (d(xy))(1) ground state, [FeL(3)].nH(2)O, L=anion of HL(4) or HL(5) and are octahedral with intermediate spin (S=32) with ground state (d(xy))(2)(d(xz),d(yz))(3) electronic configuration while for the anions of HL(2) and HL(3), they have (t(2g))(3)(e(g))(5) admixed with (d(xy))(2)(d(xz),d(yz))(3) configurations. From the ESR data, the contribution of the high spin (S=52) and low spin (S=32) to the quantum mechanical spin intermediate (QMS), and the crystal field parameters Delta and V are calculated and related to the electronic and steric effects of the ligands. The electronic spectral data confirm that obtained from the ESR, and the different ligand field parameters as well as the pi-->t(2g), t(2g)-->e(g), e(g)-->pi*, pi-->pi* transitions are estimated and compared with that experimentally obtained.

A dedicated haem lyase is required for the maturation of a novel bacterial cytochrome c with unconventional covalent haem binding

In bacterial c-type cytochromes, the haem cofactor is covalently attached via two cysteine residues organized in a haem c-binding motif. Here, a novel octa-haem c protein, MccA, is described that contains only seven conventional haem c-binding motifs (CXXCH), in addition to several single cysteine residues and a conserved CH signature. Mass spectrometric analysis of purified MccA from Wolinella succinogenes suggests that two of the single cysteine residues are actually part of an unprecedented CX15CH sequence involved in haem c binding. Spectroscopic characterization of MccA identified an unusual high-potential haem c with a red-shifted absorption maximum, not unlike that of certain eukaryotic cytochromes c that exceptionally bind haem via only one thioether bridge. A haem lyase gene was found to be specifically required for the maturation of MccA in W. succinogenes. Equivalent haem lyase-encoding genes belonging to either the bacterial cytochrome c biogenesis system I or II are present in the vicinity of every known mccA gene suggesting a dedicated cytochrome c maturation pathway. The results necessitate reconsideration of computer-based prediction of putative haem c-binding motifs in bacterial proteomes.

Protonated Heme

The ions formally corresponding to protonated heme [Fe(II)-hemeH](+) have been obtained by collision-induced dissociation from the electrospray ionization of microperoxidase (MP11) and their gas-phase chemistry has been studied by FTICR mass spectrometry. H/D-exchange reactions, used as a tool to gain information on the protonation sites in polyfunctional molecules, show that labile hydrogens pertain to the propionyl substituents at the periphery of the protoporphyrin IX. Several conceivable isomers for protonated heme have been evaluated by density functional theory. The most stable among the species investigated is the one corresponding to protonation at the beta carbon atom of a vinyl group, yielding a proton affinity (PA) value for [Fe(II)-heme] of 1220 kJ mol(-1). This high PA is consistent with the inertness of the hydrogen atoms at the protonation site towards H/D exchange with ND(3) and CD(3)CO(2)D. Peculiar features of this [Fe(II)-hemeH](+) isomer emerge by analysis of its electronic structure, showing that the vinyl group undergoing formal protonation has gained significant radical character due to electron transfer from the metal center. As a consequence, the iron atom acquires partial iron(III) character and none of the two formal descriptions [Fe(II)-hemeH(+)] and [Fe(III)-hemeH(.)](+) alone may adequately illustrate the protonated heme ion. In agreement with this description, the reactivity of protonated heme presents dual facets, resembling iron(III) in some aspects and iron(II) in others. On the one hand, protonated heme behaves like [Fe(III)-heme](+) ions in H/D-exchange reactions. On the other, it shows markedly decreased reactivity towards the addition of ligands with the notable exception of NO, in line with the high affinity shown by iron(II) complexes towards this molecule, NO, of key biological role.

Axial coordination of heme in ferric CcmE chaperone characterized by EPR spectroscopy

In Escherichia coli cytochrome c maturation requires a set of eight proteins including the heme chaperone CcmE, which binds heme transiently, yet covalently. Several variants of CcmE were purified and analyzed by continuous-wave electron paramagnetic resonance, electron nuclear double resonance, and hyperfine sublevel correlation spectroscopy to investigate the heme axial coordination. Results reveal the presence of a number of coordination environments, two high-spin heme centers with different rhombicities, and at least one low-spin heme center. The low-spin species was shown to be an artifact induced by the presence of available histidines in the vicinity of the iron. Both of the high-spin forms are five-coordinated, and comparison of the spectra of the wild-type CcmE with those of the mutant CcmE(Y134H) proves that the higher-rhombicity form is coordinated by Tyr134. The low-rhombicity (axial) form does not have a histidine residue or a water molecule as an axial ligand. However, we identified exchangeable protons coupled to the iron ion. We propose that the axial form can be coordinated by a carboxyl group of an acidic residue in the flexible domain of the protein. The two species would represent two different conformations of the flexible alpha-helix domain surrounding the heme. This conformational flexibility confers CcmE special dynamic properties that are certainly important for its function.

Phosphate group effects upon the equilibrium of iron(III) meso-tetrakis (4-N-methylpyridiniumyl) porphyrin in aqueous solution

Iron(III) meso-tetrakis (4-N-methylpyridiniumyl) porphyrin (FeTMPyP) undergoes a complex equilibrium in aqueous solution as a function of pH. Use of phosphate buffers, a common practice in biomedical applications of porphyrins, suggests the complexation of phosphate anion at the sixth coordination position to the iron, which contributes to the complexity of the equilibrium in the pH range from 1 to 4. In the absence of phosphate the equilibrium is simplified in a similar way as in the presence of high salt concentrations. Combined use of optical absorption, (1)H NMR and infrared spectroscopies, together with the literature data, suggest the formation of hexacoordinated monoaqueous-phosphate FeTMPyP complex in a limited acidic pH range. Discussion of the behavior of cationic FeTMPyP as compared to anionic iron(III) meso-tetrakis (4-sulfonatophenyl) porphyrin (FeTPPS(4)) is presented in regard to equilibrium of different species to explain the observed complex equilibrium.

Pentacoordinate and hexacoordinate ferric hemes in acid medium: EPR, UV–Vis and CD studies of the giant extracellular hemoglobin of Glossoscolex paulistus

The equilibrium complexity involving different axially coordinated hemes is peculiar to hemoglobins. The pH dependence of the spontaneous exchange of ligands in the extracellular hemoglobin from Glossoscolex paulistus was studied using UV-Vis, EPR, and CD spectroscopies. This protein has a complex oligomeric assembly with molecular weight of 3.1 MDa that presents an important cooperative effect. A complex coexistence of different species was observed in almost all pH values, except pH 7.0, where just aquomet species is present. Four new species were formed and coexist with the aquomethemoglobin upon acidification: (i) a "pure" low-spin hemichrome (Type II), also called hemichrome B, with an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (ii) a strong g(max) hemichrome (Type I), also showing an usual spin state (d(xy))(2)(d(xz),d(yz))(3); (iii) a hemichrome with unusual spin state (d(xz),d(yz))(4)(d(xy))(1) (Type III); (iv) and a high-spin pentacoordinate species. CD measurements suggest that the mechanism of species formation could be related with an initial process of acid denaturation. However, it is worth mentioning that based on EPR the aquomet species remains even at acidic pH, indicating that the transitions are not complete. The "pure" low-spin hemichrome presents a parallel orientation of the imidazole ring planes but the strong g(max) hemichrome is a HALS (highly anisotropic low-spin) species indicating a reciprocally perpendicular orientation of the imidazole ring planes. The hemichromes and pentacoordinate formation mechanisms are discussed in detail.

CW-EPR and ENDOR study of cytochrome c6 from Anabaena PCC 7119

The detailed analysis of the continuous-wave electron paramagnetic resonance and electron nuclear double resonance measurements on cytochrome c(6) from Anabaena PCC7119 reveals several electronic and structural properties of this hemeprotein. The oxidized protein shows two forms that differ in the arrangement of the residues that act as heme axial ligands. Information about the orientation of these residues is obtained for one of the forms, which turns out to differ from that found in the reduced protein from x-ray experiments. The biological significance of these results is discussed.

Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation

A method for calculating the electron-transfer matrix element V(RP) using density functional theory Kohn-Sham orbitals is presented and applied to heme dimers of varying relative orientation. The electronic coupling decays with increased iron separation according to V(RP) = V(0)(RP)exp(-beta r/2) with a distance dependence parameter beta approximately 2 A(-1) for hemes with parallel porphyrins and either 1.1 or 4.0 A(-1) when the porphyrin planes are perpendicular, depending on the alignment of the iron d(pi) orbital. These findings are used to interpret the observed orientation of the hemes in tetraheme redox proteins such as Flavocytochrome c(3) fumarate reductase (Ifc(3), PDB code 1QJD) of Shewanella frigidimarina, another flavocytochrome from the same bacterium (Fcc(3), 1E39) and a small tetraheme cytochrome of Shewanella oneidensis strain MR1 (1M1P). Our results show that shifting and rotating the hemes controls the adiabaticity of the three electron hopping steps.

Electron Distribution in Iron Octaethyloxophlorin Complexes. Importance of the Fe(III) Oxophlorin Trianion Form in the Bis-pyridine and Bis-imidazole Complexes

The apportionment of electrons between iron and the porphyrinic macrocycle in complexes of octaethyloxophlorin (H3OEPO) has been a vexing problem. In particular, for (Py)2Fe(OEPO), which is an important intermediate in heme degradation, three resonance structures involving Fe(III), Fe(II), or Fe(I), respectively, have been considered. To clarify this matter, the electronic and geometric structures of (Py)2Fe(III)(OEPO), (Im)2Fe(III)(OEPO).2THF, and (Im)2Fe(III)(OEPO).1.6CHCl3 have been examined by single-crystal X-ray diffraction, measurement of magnetic moments as a function of temperature, and EPR and NMR spectral studies. The results clearly show that both complexes exist in the Fe(III)/oxophlorin trianion form rather than the Fe(II)/oxophlorin radical form previously established for (2,6-xylylNC)(2)Fe(II)(OEPO.). In the solid state from 10 to 300 K, (Py)2Fe(III)(OEPO) exists in the high-spin (S = 5/2) state with the axial ligands in parallel planes, a planar porphyrin, and long axial Fe-N distances. However, in solution it exists predominantly in a low-spin (S = 1/2) form. In contrast, the structures of (Im)2Fe(III)(OEPO).2THF and (Im)2Fe(III)(OEPO).1.6CHCl3 consist of porphyrins with a severe ruffled distortion, axial ligands in nearly perpendicular planes, and relatively short axial Fe-N distances. The crystallographic, magnetic, EPR, and NMR results all indicate that (Im)2Fe(III)(OEPO) exists in the low-spin Fe(III) form in both the solid state and in solution.