Infrared and Raman spectra of metalloporphyrins

Protonation of the Cysteine Axial Ligand Investigated in His/Cys c-Type Cytochrome by UV-Vis and Mid- and Far-IR Spectroscopy

His/Cys coordination was recently found in several c-type cytochromes, which could act as sensors, in electron transport or in regulation. Toward a better understanding of Cys function and reactivity in these cytochromes, we compare cytochrome c6 (c6wt) from the cyanobacterium Nostoc PCC 7120 with its Met58Cys mutant. We probe the axial ligands and heme properties by combining visible and mid- to far-FTIR difference spectroscopies. Cys58 determines the strong negative redox potential and pH dependence of M58C (E_mM58C = -375 mV, versus E_mc6wt = +339 mV). Mid-IR (notably Cys ν(SH), His ν(C₅N₁), heme δ(CmH)) and far-IR (ν(Fe(II)-His), ν(His-Fe(III)-Cys)) markers of the heme and ligands show that Cys58 remains a strong thiolate ligand of reduced Met58Cys at alkaline pH, while it is protonated at pH 7.5, is stabilized by a strong hydrogen bonding interaction, and weakly interacts with Fe(II). These data provide a benchmark for further analysis of c-type cytochromes with natural His/Cys coordination.

Ultrafast electronic and vibrational dynamics in brominated aluminum corroles: Energy relaxation and triplet formation

We combined femtosecond (fs) VIS pump-IR probe spectroscopy with fs VIS pump-supercontinuum probe spectroscopy to characterize the photoreaction of the hexacoordinated Al(tpfc-Br8)(py)2 in a comprehensive way. Upon fs excitation at ∼400 nm in the Soret band, the excitation energy relaxes with a time constant of (250 ± 80) fs to the S2 and S1 electronic excited states. This is evident from the rise time of the stimulated emission signal in the visible spectral range. On the same time scale, narrowing of broad infrared signals in the C=C stretching region around 1500 cm(-1) is observed. Energy redistribution processes are visible in the vibrational and electronic dynamics with time constants between ∼2 ps and ∼20 ps. Triplet formation is detected with a time constant of (95 ± 3) ps. This is tracked by the complete loss of stimulated emission. Electronic transition of the emerging triplet absorption band overlaps considerably with the singlet excited state absorption. In contrast, two well separated vibrational marker bands for triplet formation were identified at 1477 cm(-1) and at 1508 cm(-1). These marker bands allow a precise identification of triplet dynamics in corrole systems.

Surface-enhanced resonance Raman scattering of hemoproteins and those in complicated biological systems

The SERRS spectra of heme are influenced by structural changes, orientation, and selective adsorption on the Ag surface.

Peroxidase activity and involvement in the oxidative stress response of roseobacter denitrificans truncated hemoglobin

Roseobacter denitrificans is a member of the widespread marine Roseobacter genus. We report the first characterization of a truncated hemoglobin from R. denitrificans (Rd. trHb) that was purified in the heme-bound form from heterologous expression of the protein in Escherichia coli. Rd. trHb exhibits predominantly alpha-helical secondary structure and absorbs light at 412, 538 and 572 nm. The phylogenetic classification suggests that Rd. trHb falls into group II trHbs, whereas sequence alignments indicate that it shares certain important heme pocket residues with group I trHbs in addition to those of group II trHbs. The resonance Raman spectra indicate that the isolated Rd. trHb contains a ferric heme that is mostly 6-coordinate low-spin and that the heme of the ferrous form displays a mixture of 5- and 6-coordinate states. Two Fe-His stretching modes were detected, notably one at 248 cm^-1, which has been reported in peroxidases and some flavohemoglobins that contain an Fe-His-Asp (or Glu) catalytic triad, but was never reported before in a trHb. We show that Rd. trHb exhibits a significant peroxidase activity with a (k_cat/K_m) value three orders of magnitude higher than that of bovine Hb and only one order lower than that of horseradish peroxidase. This enzymatic activity is pH-dependent with a pK_a value ~6.8. Homology modeling suggests that residues known to be important for interactions with heme-bound ligands in group II trHbs from Mycobacterium tuberculosis and Bacillus subtilis are pointing toward to heme in Rd. trHb. Genomic organization and gene expression profiles imply possible functions for detoxification of reactive oxygen and nitrogen species in vivo. Altogether, Rd. trHb exhibits some distinctive features and appears equipped to help the bacterium to cope with reactive oxygen/nitrogen species and/or to operate redox biochemistry.

Immobilized cytochrome c bound to cardiolipin exhibits peculiar oxidation state-dependent axial heme ligation and catalytically reduces dioxygen

Mitochondrial cytochrome c (cytc) plays an important role in programmed cell death upon binding to cardiolipin (CL), a negatively charged phospholipid of the inner mitochondrial membrane (IMM). Although this binding has been thoroughly investigated in solution, little is known on the nature and reactivity of the adduct (cytc-CL) immobilized at IMM. In this work, we have studied electrochemically cytc-CL immobilized on a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol. This construct would reproduce the motional restriction and the nonpolar environment experienced by cytc-CL at IMM. Surface-enhanced resonance Raman (SERR) studies allowed the axial heme iron ligands to be identified, which were found to be oxidation state dependent and differ from those of cytc-CL in solution. In particular, immobilized cytc-CL experiences an equilibrium between a low-spin (LS) 6c His/His and a high-spin (HS) 5c His/- coordination states. The former prevails in the oxidized and the latter in the reduced form. Axial coordination of the ferric heme thus differs from the (LS) 6c His/Lys and (LS) 6c His/OH(-) states observed in solution. Moreover, a relevant finding is that the immobilized ferrous cytc-CL is able to catalytically reduce dioxygen, likely to superoxide ion. These findings indicate that restriction of motional freedom due to interaction with the membrane is an additional factor playing in the mechanism of cytc unfolding and cytc-mediated peroxidation functional to the apoptosis cascade.

Investigating the thermostability of succinate: quinone oxidoreductase enzymes by direct electrochemistry at SWNTs-modified electrodes and FTIR spectroscopy

Succinate: quinone reductases (SQRs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. Herein, we compare the temperature-dependent activity and structural stability of two SQRs, the first from the mesophilic bacterium Escherichia coli and the second from the thermophilic bacterium Thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. Direct electron transfer was achieved with full membrane protein complexes at single-walled carbon nanotube (SWNT)-modified electrodes. The possible structural factors that contribute to the temperature-dependent activity of the enzymes and, in particular, to the thermostability of the Thermus thermophilus SQR are discussed.

Axial iron coordination and spin state change in a heme c upon electrostatic protein-SAM interaction

A bacterial di-heme cytochrome c binds electrostatically to a gold electrode surface coated with a negatively charged COOH-terminated SAM adopting a sort of 'perpendicular' orientation. Cyclic voltammetry, Resonance Raman and SERRS spectroscopies indicate that the high-potential C-terminal heme center proximal to the SAM's surface undergoes an adsorption-induced swapping of one axial His ligand with a water molecule, which is probably lost in the reduced form, and a low- to high-spin transition. This coordination change for a bis-His ligated heme center upon an electrostatically-driven molecular recognition is as yet unprecedented, as well as the resulting increase in reduction potential. We discuss it in comparison with the known methionine ligand lability in monoheme cytochromes c occurring upon interaction with charged molecular patches. One possible implication of this finding in biological ET is that mobile redox partners do not behave as rigid and invariant bodies, but in the ET complex are subjected to molecular changes and structural fluctuations that affect in a complex way the thermodynamics and the kinetics of the process.

Sensitive marker bands for the detection of spin states of heme in surface-enhanced resonance Raman scattering spectra of metmyoglobin

The SERRS intensity ratio of the peak at 1560 cm⁻¹to that at 1620 cm⁻¹was applied to detect the spin states of heme in metmyoglobin sensitively.

The rate-limiting step in O(2) reduction by cytochrome ba(3) from Thermus thermophilus

Cytochrome ba(3) (ba(3)) of Thermus thermophilus (T. thermophilus) is a member of the heme-copper oxidase family, which has a binuclear catalytic center comprised of a heme (heme a(3)) and a copper (Cu(B)). The heme-copper oxidases generally catalyze the four electron reduction of molecular oxygen in a sequence involving several intermediates. We have investigated the reaction of the fully reduced ba(3) with O(2) using stopped-flow techniques. Transient visible absorption spectra indicated that a fraction of the enzyme decayed to the oxidized state within the dead time (~1ms) of the stopped-flow instrument, while the remaining amount was in a reduced state that decayed slowly (k=400s(-1)) to the oxidized state without accumulation of detectable intermediates. Furthermore, no accumulation of intermediate species at 1ms was detected in time resolved resonance Raman measurements of the reaction. These findings suggest that O(2) binds rapidly to heme a(3) in one fraction of the enzyme and progresses to the oxidized state. In the other fraction of the enzyme, O(2) binds transiently to a trap, likely Cu(B), prior to its migration to heme a(3) for the oxidative reaction, highlighting the critical role of Cu(B) in regulating the oxygen reaction kinetics in the oxidase superfamily.

Differential effects of glutamate-286 mutations in the aa(3)-type cytochrome c oxidase from Rhodobacter sphaeroides and the cytochrome bo(3) ubiquinol oxidase from Escherichia coli

Both the aa(3)-type cytochrome c oxidase from Rhodobacter sphaeroides (RsCcO(aa3)) and the closely related bo(3)-type ubiquinol oxidase from Escherichia coli (EcQO(bo3)) possess a proton-conducting D-channel that terminates at a glutamic acid, E286, which is critical for controlling proton transfer to the active site for oxygen chemistry and to a proton loading site for proton pumping. E286 mutations in each enzyme block proton flux and, therefore, inhibit oxidase function. In the current work, resonance Raman spectroscopy was used to show that the E286A and E286C mutations in RsCcO(aa3) result in long range conformational changes that influence the protein interactions with both heme a and heme a(3). Therefore, the severe reduction of the steady-state activity of the E286 mutants in RsCcO(aa3) to ~0.05% is not simply a result of the direct blockage of the D-channel, but it is also a consequence of the conformational changes induced by the mutations to heme a and to the heme a(3)-Cu(B) active site. In contrast, the E286C mutation of EcQO(bo3) exhibits no evidence of conformational changes at the two heme sites, indicating that its reduced activity (3%) is exclusively a result of the inhibition of proton transfer from the D-channel. We propose that in RsCcO(aa3), the E286 mutations severely perturb the active site through a close interaction with F282, which lies between E286 and the heme-copper active site. The local structure around E286 in EcQO(bo3) is different, providing a rationale for the very different effects of E286 mutations in the two enzymes. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.

Communication between R481 and Cu(B) in cytochrome bo(3) ubiquinol oxidase from Escherichia coli

The R481 residue of cytochrome bo(3) ubiquinol oxidase from E. coli is highly conserved in the heme-copper oxidase superfamily. It has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. Along these lines, proton pumping efficiency has been demonstrated to be abolished in many R481 mutants. However, R481Q in bo(3) from E. coli has been shown to be fully functional, implying that the positive charge of the arginine is not required for proton translocation [ Puustinen , A. and Wikstrom , M. ( 1999 ) Proc. Natl. Acad. Sci. U.S.A. 96 , 35 - 37 ]. In an effort to delineate the structural role of R481 in the bo(3) oxidase, we used resonance Raman spectroscopy to compare the nonfunctional R481L mutant and the functional R481Q mutant, to the wild type protein. Resonance Raman data of the oxidized and reduced forms of the R481L mutant indicate that the mutation introduces changes to the heme o(3) coordination state, reflecting a change in position and/or coordination of the Cu(B) located on the distal side of heme o(3), although it is approximately 10 A away from R481. In the reduced-CO adduct of R481L, the frequencies of the Fe-CO and C-O stretching modes indicate that, unlike the wild type protein, the Cu(B) is no longer close to the heme-bound CO. In contrast, resonance Raman data obtained from the various oxidation and ligation states of the R481Q mutant are similar to those of the wild type protein, except that the mutation causes an enhancement of the relative intensity of the beta conformer of the CO-adduct, indicating a shift in the equilibrium between the alpha and beta conformers. The current findings, together with crystallographic structural data of heme-copper oxidases, indicate that R481 plays a keystone role in stabilizing the functional structure of the Cu(B) site through a hydrogen bonding network involving ordered water molecules. The implications of these data on the proton translocation mechanism are considered.

Solvent effects on the absorption, circular dichroism and Raman spectroscopy of meso-tetrakis [3-methoxy-4-(N-carbazyl)n-hexyloxyphenyl] porphyrin in water-THF solution

Solutions of meso-tetrakis [3-methoxy-4-(N-carbazyl)n-hexyloxyphenyl] porphyrin (4C6-TPP) in a water-organic mixture (tetrahydrofuran, THF) generate aggregates with absorption spectra characterized by broader red shifts of the Soret band relative to the monomeric porphyrin band. For the aggregated form several phenyl modes enhance and some modes weaken, the nu(2), nu(3) and nu(11) bands in the Raman spectra are slightly downshifted compared with the monomeric form. These data suggest that the phenyl groups of 4C6-TPP in the aggregate rotate to an orientation more coplanar with the porphyrin core. The increased conjugation of the meso-phenyl rings with the porphyrin core brings about the red shift of the Soret band. The circular dichroism (CD) band of the aggregate undergoes some changes with time, as indicated by the transition from a negative band to no signal resulted from the rotation of phenyl groups. All of the results imply that the location of the phenyl groups plays a key role in the determination of the morphology of the aggregate.

Zinc phthalocyanine thin film and chemical analyte interaction studies by density functional theory and vibrational techniques

Thin films of zinc phthalocyanine have been deposited on KBr and glass substrates by the thermal evaporation method and characterized by the x-ray diffraction, optical, infrared and Raman techniques. The observed x-ray diffraction and infrared absorption spectra of as-deposited thin films suggest the presence of an α crystalline phase. Infrared and Raman spectra of thin films after exposure to vapours of ammonia and methanol have also been recorded. Shifts in the position of some IR and Raman bands in the spectra of exposed films have been observed. Some bands also show changes in their intensity on exposure. Increased charge on the phthalocyanine ring and out-of-plane distortion of the core due to interaction between zinc phthalocyanine and vapour molecules involving the fifth coordination site of the central metal ion may be responsible for the band shifts. Changes in the intensity of bands are interpreted in terms of the lowering of molecular symmetry from D(4h) to C(4v) due to doming of the core. Molecular parameters and Mulliken atomic charges of zinc phthalocyanine and its complexes with methanol and ammonia have been calculated from density functional theory. The binding energy of the complexes have also been calculated. Calculated values of the energy for different complexes suggest that axially coordinated vapour molecules form the most stable complex. Calculated Mulliken atomic charges show net charge transfer from vapour molecules to the phthalocyanine ring for the most stable complex.

Critical structural role of R481 in cytochrome c oxidase from Rhodobacter sphaeroides

The R481 residue in cytochrome c oxidase from Rhodobacter sphaeroides forms hydrogen bonds with the propionate groups of both heme a and heme a(3). It has been postulated that R481 is the proton loading site in the proton exit pathway essential for proton translocation. A recent functional study showed that the mutations of R481 to His, Leu and Gln cause the reduction of the activity to approximately 5-18% of the native level, and the absence of proton pumping in R481Q but retention of approximately 40% efficiency in R481H and R481L (H.J. Lee, L. Ojemyr, A. Vakkasoglu, P. Brzezinski and R. B. Gennis, manuscript submitted). To decipher the molecular mechanism underlying the perturbed functionalities, we have used resonance Raman spectroscopy to examine the structural properties of the three mutants. The data show that the frequencies of the formyl CO stretching modes of both the heme a and a(3) in the mutants are characteristic of formyl groups exposed to an aqueous environment, indicating that the mutations disrupt the native H-bonding interaction between the formyl group of heme a and R52, as well as the hydrophobic environment surrounding the formyl group of heme a(3). In addition to the change in the environments of heme a and a(3), the Raman data show that the mutations induce a partial conversion of the heme a(3) from a high-spin to a low-spin state, suggesting that the mutations are associated with the rearrangement of the Cu(B)-heme a(3) binuclear center. The Raman results reported here demonstrate that R481 plays a critical role in supporting efficient proton pumping, by holding the heme groups in a proper environment.

Vibration and Fluorescence Spectra of Porphyrin-Cored 2,2-Bis(methylol)-propionic Acid Dendrimers

Bis-MPA dendron-coated free-base tetraphenylporphyrin and zinc-tetraphenyl-porphyrin (TPPH(2) and TPPZn) were studied in comparison with simple porphyrins (H(2)P, ZnP) by theoretical simulation of their infrared, Raman and electronic absorption spectra, as well as fluorescense emission. Infrared and fluorescence spectra of the dendrimers were measured and interpreted along with time-resolved measurements of the fluorescence. The 0-1 emission band of the dendron substituted TPPZn was found to experience a "heavy substitution"-effect. The 0-1 vibronic emission signal is associated with a longer decay time (approx. 7 - 8 ns) than the 0-0 emission (approx. 1 - 1.5 ns). The former contributed with more relative emission yield for larger dendron substituents, in agreement with the appearance of steady-state emission spectra showing increased contribution from the 0-1 vibronic fluorescence band at 650 nm. No such substitution effect was observed in the electronic or vibrational spectra of the substituted free-base variant, TPPH(2). Vibration spectra of the parent porphyrins (H(2)P, ZnP, TPPH(2) and TPPZn) were calculated by density functional theory (DFT) using the B3LYP/6-31G** approximation and a detailed analysis of the most active vibration modes was made based on both literature and our own experimental data. Based on the results of theoretical calculations the wide vibronic bands in the visible region were assigned. The vibronic structure also gave a qualitative interpretation of bands in the electronic absorption spectra as well as in fluorescence emission depending on the size of dendrimer substitution. From the results of time-dependent DFT calculations it is suggested that the TPPZn-cored dendrimers indicate strong vibronic interaction and increased Jahn-Teller distortion of the prophyrin core for larger dendrimer generations. Specifically, this leads to the entirely different behaviour of the emission spectra upon substitution of the TPPH(2) and TPPZn variants, which was also experimentally observed. Since TPPH(2) is originally of lower symmetry the specific distortion upon dendron substitution is not expected to the same extent, which also was in agreement with the experimental findings.

Substrate-protein interaction in human tryptophan dioxygenase: the critical role of H76

The initial and rate-limiting step of the kynurenine pathway in humans involves the oxidation of tryptophan to N-formyl kynurenine catalyzed by two hemeproteins, tryptophan 2,3-dioxygenase (hTDO) and indoleamine 2,3-dioxygenase (hIDO). In hTDO, the conserved H76 residue is believed to act as an active site base to deprotonate the indole NH group of Trp, the initial step of the Trp oxidation reaction. In hIDO, this histidine is replaced by a serine. To investigate the role of the H76, we have studied the H76S and H76A mutants of hTDO. Activity assays show that the mutations cause a decrease in k(cat) and an increase in K(M) for both mutants. The decrease in the k(cat) is accounted for by the replacement of the active site base catalyst, H76, with a weaker base, possibly a water, whereas the increase in K(M) is attributed to the loss of the specific interactions between the H76 and the substrate as well as the protein matrix. Resonance Raman studies with various Trp analogs indicate that the substrate is positioned in the active site by the ammonium, carboxylate, and indole groups, via intricate H-bonding and hydrophobic interactions. This scenario is consistent with the observation that l-Trp binding significantly perturbs the electronic properties of the O(2)-adduct of hTDO. The important structural and functional roles of H76 in hTDO is underscored by the observation that the electronic configuration of the active ternary complex, l-Trp-O(2)-hTDO, is sensitive to the H76 mutations.

Resonance Raman study of free-base tetraphenylporphine and its dication

Resonance Raman spectra of free-base tetraphenylporphine and its dication obtained with 441.6, 476.5, 488.0 and 514.5 nm excitation lines in the frequency region 100-1625 cm(-1) are reported. Some bands due to in-plane and out-of-plane vibrational modes, which are symmetry forbidden under ideal D(2h), are also seen in the Raman spectra of these molecules. These bands arise due to dynamic and/or static coupling of out-of-plane modes with the allowed in-plane modes. Dynamic coupling may be facilitated by the proton tunneling, while static coupling is due to out-of-plane distortion in the geometrical structure of the molecule. Shift in the positions for certain bands in the Raman spectra of dication are interpreted on the basis of electronic changes due to sharing of electrons of the B(1u) orbital by the two added protons.

Heme carbonyls: environmental effects on nu(C-O) and Fe-C/C-O bond length correlations

The synthesis and characterization of four low-spin (carbonyl)iron(II) tetraphenylporphyrinates, [Fe(TPP)(CO)(L)], where L = 1-methylimidazole, 2-methylimidazole, 1,2-dimethylimidazole (unsolvated), and 1,2-dimethylimidazole (toluene solvate) are reported. The complexes show nearly the same value of nu(C-O) in toluene solution (1969-72 cm(-1)) but a large range of CO stretching frequencies in the solid-state (1926-1968 cm(-1)). The large solid-state variation results from CO interactions in the solid state, as shown by an examination of the crystal structures of the four complexes. The high precision of the four structures obtained allows us to make a number of structural and spectroscopic correlations that describe the Fe-C-O and N(Im)-Fe-CO units. The values of nu(C-O) and the Fe-C and C-O bond distances are strongly correlated and provide a structural, as well as a spectroscopic, correlation of the pi back-bonding model. The interactions of CO described are closely related to the large range of CO stretching frequencies observed in heme proteins and specific interactions observed in carbonylmyoglobin (MbCO).

Spectroscopic investigation of isonitrile complexes of ferric and ferrous microperoxidase 8

Microperoxidase 8 (MP8) is able to react with alkyl- and aryl-isonitriles (RNC) both in its reduced and oxidized states, to form MP8Fe(II)- and MP8Fe(III)-CNR complexes. The coordination and spin states of these complexes have been fully characterized by UV-visible and resonance Raman spectroscopies. Both MP8Fe(II)- and MP8Fe(III)-CNR complexes are hexacoordinate low-spin complexes, which bear a single RNC ligand on the distal face of the heme and keep the His 18 ligand on its proximal face, trans to the RNC ligand. A comparison of these characteristics with those of the Fe-CNR complexes of other hemoproteins suggests that both MP8Fe(II)- and MP8Fe(III)-CNR complexes present a Fe-C-N linear arrangement. This may be due to the lack of any interactions of the RNC ligand with the octapeptide of MP8 that is mainly located over the opposite face of the heme. Finally the formation of hexacoordinate low-spin MP8Fe(II)- and MP8Fe(III)-CNR complexes constitutes a new example of the reactivity of MP8 with a new class of weak sigma-donating and strong pi-accepting ligands, which adds to its already very rich coordination chemistry.

Spectroscopic studies of rhodamine 6G dispersed in polymethylcyanoacrylate

We report here electronic absorption, fluorescence and resonance Raman studies of rhodamine 6G laser dye dispersed in the polymethylcyanoacrylate matrix. In the electronic absorption and fluorescence spectra of dispersed rhodamine 6G, band maxima are red shifted compared to solution. Raman spectra show some new bands. These spectral changes arise due to matrix effect and interaction between rhodamine 6G and the host material involving amine group of rhodamine.

Interactions of soluble guanylate cyclase with diatomics as probed by resonance Raman spectroscopy

Soluble guanylate cyclase (sGC, EC 4.6.1.2) acts as a sensor for nitric oxide (NO), but is also activated by carbon monoxide in the presence of an allosteric modulator. Resonance Raman studies on the structure-function relations of sGC are reviewed with a focus on the CO-adduct in the presence and absence of allosteric modulator, YC-1, and substrate analogues. It is demonstrated that the sGC isolated from bovine lung contains one species with a five-coordinate (5c) ferrous high-spin heme with the Fe-His stretching mode at 204 cm(-1), but its CO adduct yields two species with different conformations about the heme pocket with the Fe-CO stretching (nuFe-CO) mode at 473 and 489 cm(-1), both of which are His- and CO-coordinated 6c ferrous adducts. Addition of YC-1 to it changes their population and further addition of GTP yields one kind of 6c (nuFe-CO=489 cm(-1)) in addition to 5c CO-adduct (nuFe-CO=521 cm(-1)). Under this condition the enzymatic activity becomes nearly the same level as that of NO adduct. Addition of gamma-S-GTP yields the same effect as GTP does but cGMP and GDP gives much less effects. Unexpectedly, ATP cancels the effects of GTP. The structural meaning of these spectroscopic observations is discussed in detail.

Expression, purification and spectroscopic characterization of the cytochrome P450 CYP121 from Mycobacterium tuberculosis

The CYP121 gene from the pathogenic bacterium Mycobacterium tuberculosis has been cloned and expressed in Escherichia coli, and the protein purified to homogeneity by ion exchange and hydrophobic interaction chromatography. The CYP121 gene encodes a cytochrome P450 enzyme (CYP121) that displays typical electronic absorption features for a member of this superfamily of hemoproteins (major Soret absorption band at 416.5 nm with alpha and beta bands at 565 and 538 nm, respectively, in the oxidized form) and which binds carbon monoxide to give the characteristic Soret band shift to 448 nm. Resonance Raman, EPR and MCD spectra show the protein to be predominantly low-spin and to have a typical cysteinate- and water-ligated b-type heme iron. CD spectra in the far UV region describe a mainly alpha helical conformation, but the visible CD spectrum shows a band of positive sign in the Soret region, distinct from spectra for other P450s recognized thus far. CYP121 binds very tightly to a range of azole antifungal drugs (e.g. clotrimazole, miconazole), suggesting that it may represent a novel target for these antibiotics in the M. tuberculosis pathogen.

Structural changes in cytochrome c oxidase induced by cytochrome c binding. A resonance raman study

Electrostatically stabilized complexes of fully oxidized cytochrome c oxidase from Paracoccus denitrificans and horse heart cytochrome c were studied by resonance Raman spectroscopy. The experiments were carried out with the wild-type oxidase and a variant in which a negatively charged amino acid in the binding domain (D257) is replaced by an asparagine. It is shown that cytochrome c induces structural changes at heme a and heme a(3) which are reminiscent to those found in mammalian cytochrome c oxidase-cytochrome c complex. The spectral changes are attributed to subtle changes in the heme-protein interactions implying that there is a structural communication from the binding domain even to the remote catalytic center. Only for the heme a modes minor spectral differences were found in the response of the wild-type and the D257N variant oxidase upon cytochrome c binding indicating that electrostatic interactions of aspartate 257 are not crucial for the perturbation of the catalytic site structure in the complex. On the other hand, in none of the complexes, structural changes were detected in the bound cytochrome c. These findings are in contrast to previous results obtained with beef heart cytochrome c oxidase which triggers the formation of a new conformational state of cytochrome c assumed to be involved in the biological electron transfer process.

Nitration of internal tyrosine of cytochrome c probed by resonance Raman scattering

Tyrosines can be selectively nitrated in a protein and the resultant chromophore can be used as an in situ probe of the tyrosine environment. Resonance Raman scattering could have specific advantages as a detection method because of the inherent selectivity of the technique and because shifts in the intensity and frequency of the nitro stretch can be detected and related to the form and environment of the nitrotyrosine. To evaluate this possibility the internal residue Tyr67 of cytochrome c was nitrated and resonance Raman scattering was recorded. With 413.1-nm excitation the resonance scattering from the heme protein dominates, but with 457.9-nm excitation intense bands due to nitrostretching vibrations are readily observed. The frequency of the internal Tyr67 indicates an aqueous environment that suggests that on nitration this residue becomes exposed on the protein surface or that water enters the active pocket. pH dependent measurements can be used to follow the protonation of the residue. A pK(a) of approximately 7 also indicates an aqueous environment. This initial study indicates that resonance Raman scattering does have unique advantages as an in situ probe of the local structure of nitrated tyrosine residues.

The structural and functional role of lysine residues in the binding domain of cytochrome c in the electron transfer to cytochrome c oxidase

The interactions of yeast iso-1 cytochrome c with bovine cytochrome c oxidase were studied using cytochrome c variants in which lysines of the binding domain were substituted by alanines. Resonance Raman spectra of the fully oxidized complexes of both proteins reveal structural changes of both the heme c and the hemes a and a3. The structural changes in cytochrome c are the same as those observed upon binding to phospholipid vesicles where the bound protein exists in two conformers, B1 and B2. Whereas the structure of B1 is the same as that of the unbound cytochrome c, the formation of B2 is associated with substantial alterations of the heme pocket. In cytochrome c oxidase, the structural changes in both hemes refer to more subtle perturbations of the immediate protein environment and may be a result of a conformational equilibrium involving two states. These changes are qualitatively different to those observed for cytochrome c oxidase upon poly-l-lysine binding. The resonance Raman spectra of the various cytochrome c/cytochrome c oxidase complexes were analyzed quantitatively. The spectroscopic studies were paralleled by steady-state kinetic measurements of the same protein combinations. The results of the spectra analysis and the kinetic studies were used to determine the stability of the complexes and the conformational equilibria B2/B1 for all cytochrome c variants. The complex stability decreases in the order: wild-type WT > J72K > K79A > K73A > K87A > J72A > K86A > K73A/K79A (where J is the natural trimethyl lysine). This order is not exhibited by the conformational equilibria. The electrostatic control of state B2 formation does not depend on individual intermolecular salt bridges, but on the charge distribution in a specific region of the front surface of cytochrome c that is defined by the lysyl residues at positions 72, 73 and 79. On the other hand, the conformational changes in cytochrome c oxidase were found to be independent of the identity of the bound cytochrome c variant. The maximum rate constants determined from steady-state kinetic measurements could be related to the conformational equilibria of the bound cytochrome c using a simple model that assumes that the conformational transitions are faster than product formation. Within this model, the data analysis leads to the conclusion that the interprotein electron transfer rate constant is around two times higher in state B2 than in B1. These results can be interpreted in terms of an increase of the driving force in state B2 as a result of the large negative shift of the reduction potential.

Catalytically self-sufficient P450 CYP102 (cytochrome P450 BM-3): resonance Raman spectral characterization of the heme domain and of the holoenzyme

The resonance Raman spectra of CYP102 holoenzyme and of the CYP102 heme domain in the reduced state have been obtained for the first time. Spectra of the oxidized heme domain have also been measured. Whereas the spectra of the isolated heme domain are similar to those obtained for other hexacoordinated low-spin P450s, the holoenzyme spectra exhibited unexpected features. The most plausible explanation is that they reflect an electron transfer to the heme from photoreduced flavins. The results obtained for both the oxidized and reduced heme domain bring additional support to the use of CYP102 as a model for microsomal mammalian P450 enzymes, showing that the heme moiety in CYP102 has similar properties to the hemes in microsomal P450s.

Differential characterization of neutrophil cytochrome p30 and cytochrome b-558 by low-temperature absorption and resonance Raman spectroscopies

Cytochrome p30, a novel hemoprotein isolated from rabbit peritoneal neutrophils [Escriou, V., Laporte, F., Garin, J., Brandolin, G. & Vignais, P. V. (1994) J. Biol. Chem. 269, 14007-14014] has been characterized by low-temperature (77 K) absorption and resonance Raman spectroscopies. The spectral data have been compared with those obtained with neutrophil cytochrome b-558. At room temperature, the absorption difference spectra (reduced minus oxidized) of cytochrome p30 and cytochrome b-558 could not been distinguished from each other. However, at 77 K, significant differences were observed. In particular, the alpha band of cytochrome p30 was split whereas that of cytochrome b-558 was symmetrical, but particularly broad. The resonance Raman spectra of cytochrome p30 provided evidence for the presence of two hemes both in the ferric and ferrous states. One of them was a six-coordinated low-spin heme either oxidized or reduced whereas the other one was a high-spin heme, five-coordinated in the reduced state and six-coordinated in the oxidized state. It is probable that two histidine residues constitute the axial ligands of the six-coordinated low-spin heme of cytochrome p30. The resonance Raman spectra of cytochrome b-558 allowed the detection of a six-coordinated low-spin heme, similar to that found in cytochrome p30. The component typical of the high-spin heme of cytochrome p30 was however absent in the spectra of oxidized and reduced cytochrome b-558.

Study of the coordination chemistry of prostaglandin G/H synthase by resonance Raman spectroscopy

Resonance Raman spectra of prostaglandin G/H synthase (PGHS) in its ferric and ferrous states have been obtained by Soret excitation. In native PGHS, which contained only 0.25 heme/monomeric apoprotein, the ferric heme was in a high-spin hexacoordinated state. The presence of a vibration at 289 cm-1 that was responsive to H(2)16O -> H(2)18O replacement was taken as evidence for the presence of a H-bonded H2O molecule as the sixth ligand of the Fe. A study, by CD and resonance Raman spectroscopy, of heme incorporation into the apoprotein showed that, for heme/protein ratios lower than 0.5, the heme was in the same ferric high-spin hexacoordinated state as in the native enzyme. For heme/protein ratios higher than 0.5, the concomitant formation of two minor species was observed: a low-spin hexacoordinated species which could be due to the axial coordination of a distal histidine to the Fe trans to its proximal histidine ligand; and a high-spin pentacoordinated species that corresponded to non-specific binding of the heme to the apoprotein. In the reduced state, the heme of PGHS contained a high-spin pentacoordinated Fe(II) with a histidine as the proximal ligand. However, this species shifted spontaneously towards a low-spin hexacoordinated Fe(II) species in which the iron was probably coordinated by a distal histidine as the sixth axial ligand. The PGHS Fe(II).CO derivative displayed an Fe-CO stretching mode at 529 cm-1, which is in the range observed for peroxidases. Such a high frequency could be due to H-bonding between the oxygen atom of the CO ligand and the distal histidine, His207. Since this histidine plays an important role, by coordination of Fe(II) or Fe(III) of PGHS and stabilization of the ligands of the Fe, H2O or CO by H-bonding, it is suggested that this histidine could also play a key role in the cleavage of the O-O bond of peroxides by peroxidases.