Valence-tautomerism in high-valent iron and manganese porphyrins

Iron and manganese hemes are "high-valent" when the valence state of the metal exceeds III. Redox chemistry of the high valent metal complexes involves redistribution of holes and electrons over the metal ion and the porphyrin and axial ligands, defined as valence tautomerism. Thus, catalytic pathways of heme-containing biomolecules such as peroxidases, catalases and cytochromes P450 involve valence tautomerism, as do pathways of biomimetic oxygen transfer catalysis by manganese porphyrins, robust catalysts with potential commercial value. Determinants of the site of electron abstraction are key to understanding valence tautomerism. In model systems, metal-centered oxidation is supported by hard anionic axial ligands that are also strongly pi-donating, such as oxo, aryl, bix-methoxy and bis-fluoro groups. Manganese(IV) is more stable than iron(IV) and metal-centered one-electron oxidations occur with weaker pi-donating axial ligands such as bisazido, -isocyanato, -hypochlorito and bis chloro groups. Virtually all known high-valent iron porphyrin complexes oxidized by two-electrons above the ferric state are coordinated by the strongly pi-donating oxo or nitrido ligands. In all well-characterized oxo complexes, iron is in the ferryl state and the second oxidizing equivalent resides on the porphyrin. Complexes with iron(V) have not been definitively characterized. One-electron oxidation of oxomanganese(IV) porphyrin complexes gives the oxomanganese(IV) porphyrin pi-cation redicals. In aqueous solution, oxidation of Mn(III) complexes of tetra cationic N-methylpyridiniumylporphyrin isomers by monooxygen donors yields a transient oxomanganese(V) species.     

Modeling truncated hemoglobin vibrational dynamics

We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides Calphas for all residues but glycines in the coarse-graining procedure, without leading to an increase in the degrees of freedom (beta Gaussian Model). Normalized covariance matrix and deformation along slowest modes with collective character are analyzed, pointing out anticorrelations between functionally relevant sites for the proteins under study. In particular, we underline the functional motions of an extended tunnel-cavity system running inside the protein matrix, which provide a pathway for small ligands binding with the iron in the heme group. We give a rough estimate of the order of magnitude of the relaxation times of the slowest two overdamped modes and compare results with previous studies on globins.     

Evolutionary conservation of protein vibrational dynamics

The aim of the present work is to study the evolutionary divergence of vibrational protein dynamics. To this end, we used the Gaussian Network Model to perform a systematic analysis of normal mode conservation on a large dataset of proteins classified into homologous sets of family pairs and superfamily pairs. We found that the lowest most collective normal modes are the most conserved ones. More precisely, there is, on average, a linear correlation between normal mode conservation and mode collectivity. These results imply that the previously observed conservation of backbone flexibility (B-factor) profiles is due to the conservation of the most collective modes, which contribute the most to such profiles. We discuss the possible roles of normal mode robustness and natural selection in the determination of the observed behavior. Finally, we draw some practical implications for dynamics-based protein alignment and classification and discuss possible caveats of the present approach.     

Carbohydrate functionalization using cationic iron carbonyl complexes

Cationic iron carbonyl cyclohexadiene complexes were employed in the derivatization of the 3-OH position of unprotected and protected methyl beta-D-galactopyranosides using two different approaches, giving access to galactopyranosides with an aromatic or cyclohexadienoic functionality in this position.     

Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations

A linear correlation between harmonic and anharmonic frequencies of water calculated at B3LYP level of theory was observed with a number of basis sets. Similar relationships were found in both the gas phase and solution for several small molecules. The best correlation was found for C = O stretch mode in formaldehyde, formamide and N-methylacetamide. The average difference between B3LYP harmonic and anharmonic ν(C = O) frequencies calculated with several basis sets in these molecules was 30 cm(-1). The ad hoc correction of -30 cm(-1), added to harmonic frequencies of two different carbonyl groups present in a structure of a larger molecule was tested as a fast way of predicting anharmonic frequencies without elaborated calculations. The proposed approach was tested successfully on a larger molecule of E and Z isomers of N-acetyl-α,β-dehydrophenylalanine N',N'-dimethylamide [Ac-(E/Z)-ΔPhe-NMe(2)] and the estimated anharmonic ν(C = O) frequencies were close to directly calculated results.     

Electrochemistry and spectroscopy of sulfate and thiosulfate complexes of iron porphyrins

The electrochemical and spectroscopic properties of the complex formed by the addition of thiosulfate to ferric porphyrins were examined. The NMR spectrum of the thiosulfate-ferric porphyrin complex was consistent with a high-spin ferric complex, while the EPR spectrum at liquid nitrogen temperatures indicated that the complex under these conditions was low-spin. Such behavior has been previously observed for other ferric porphyrin complexes. The visible spectra were characterized by a shift in the Soret band to higher energies, with smaller changes in the longer wavelength region. The complex was reasonably stable in DMF, but slowly reduced over several hours to Fe^II(TPP) and S₄O₆ ²⁻. The voltammetric behavior of the thiosulfate complex in DMF consists of two waves, the first of which was irreversible. The ferric/ferrous reduction in the presence of thiosulfate was shifted negatively about 400 mV, compared to the Fe(TPP)(Cl) reduction. The visible, NMR and EPR spectra were most consistent with a Fe-S bonded ferric porphyrin-thiosulfate complex, Fe(P)(SSO₃)⁻. The kinetics of the reduction of ferric porphyrin by thiosulfate in DMSO indicated an autocatalytic mechanism, where the first step is the formation of the catalyst. The identity of the catalyst could not be determined because it must be present at low concentrations, but it is formed from the reaction of the ferric complex with thiosulfate. Coordination of thiosulfate to the porphyrin was not necessary for the reduction to occur, and the reduction of Fe(TPP)(Cl) by thiosulfate was accelerated by the addition of sulfate. Under these conditions, sulfate had replaced thiosulfate as the axial ligand for the ferric porphyrin. In the presence of sulfate, the reduction occurred in a single kinetic pseudo-first order step.     

Syntheses of di-hydrocarbyl derivatives of carbonyl phosphine complexes of iron

Complexes cis,trans-Fe(CO)₂(PMe₃)₂RR′ (R = CH₃, R′ = Ph (2); R = CH₃, R′ = CHCH₂ (3); R = CHCH₂, R′ = Ph (4); R = R′ = CHCH₂ (5); R = R′ = CH₃ (6)) were prepared by reaction of cis,trans-Fe(CO)₂(PMe₃)₂RCl (1) with organolithium reagents LiR′. All complexes were characterized in solution by IR and ¹H, ³¹P and, in a few cases, ¹³C NMR mono- and bi-dimensional spectroscopies. Complexes 5 and 6 were structurally characterized by X-ray diffractometric methods. In solution complexes 2, 3 and 4 undergo slowly coupling of the σ-hydrocarbyl substituents leading to Fe(CO)₃(PMe₃)₂ and other decomposition products. Complex 6 was very stable in solution in the absence of nucleophiles and in the solid state. Complex 5 transformed through intramolecular coupling of the vinyl groups into Fe(CO)(PMe₃)₂(η⁴-butadiene) (7), which was characterized in solution by IR and NMR spectroscopies.     

Noncovalent interactions of peptides with porphyrins in aqueous solution: conformational study using vibrational CD spectroscopy.

Noncovalent interactions of poly(L-lysine) (PL), oligopeptides L-lysyl-L-alanyl-L-alanine and (L-lysyl-L-alanyl-L-alanine)(2) with meso-tetrakis(4-sulfonatophenyl)porphine (TPPS), and poly(L-glutamic acid) (PLGA) with meso-tetrakis(1-methyl-4-pyridyl)porphine tetra-p-tosylate (TMPyP) in aqueous solutions have been studied using combination of spectroscopic methods: Vibrational circular dichroism (VCD) spectroscopy in the mid-infrared region provides a direct information on conformational changes of the polypeptides and oligopeptides caused by interactions with porphyrins; ultraviolet-visible absorption, fluorescence, and electronic circular dichroism (ECD) reveal the aggregation characterization of the porphyrin part of the complexes. Interactions of TPPS with tripeptide, hexapeptide, and PL containing about ten amino acid residues in the molecular chain are accompanied with the changes of VCD patterns in the amide I' region. In these cases, the conformation of the oligopeptide part of complexes is obviously influenced by interactions with TPPS and partial changes of random coil structure are observed in VCD. When PL was composed of the hundreds of lysine residues, just a weak intensity decrease was detected and the shape of VCD spectrum typical for the random coil structure was preserved. As follows from the uv-vis absorption and fluorescence spectra, porphyrin molecules are attached to peptides by electrostatic interaction as a monomer or dimer and interaction between porphyrin and peptide depends on the polypeptide chain length. For the PLGA-TMPyP system with PLGA containing from tens to hundreds of glutamic acid residues in the chain, the VCD spectra were unchanged when TMPyP was presented in the aqueous solution of PLGA and random coil conformation of PLGA-TMPyP aggregates was preserved.     

Synthesis and reactivity of iron carbonyl clusters containing alkynethiolate ligands

The new cluster Li[Fe₃(μ₃,η¹-SCCFc)(CO)₉] reacts with ClAuPPh₃ to afford compound [Fe₃Au(μ₄,η²-CCFc)(CO)₉(PPh₃)], which exhibits an isomeric equilibrium in solution with the cluster [Fe₃Au(μ₃,η²-CCFc)(CO)₉(PPh₃)].The rupture of C-S bonds in the thioethers Me₃SiCCSCCR (R = Fc, SiⁱPr₃) in the presence of Fe₃(CO)₁₂, yields to the clusters [Fe₃(μ-SCCSiⁱPr₃)(μ-CCSiMe₃)(CO)₉] and [Fe₃(μ,η²-(SiⁱPr₃)CCCCSiMe₃)(μ₃-S)(CO)₉] together with the unexpected compounds [Fe₂(μ-SCC(H)R)(CO)₆] (R = SiMe₃, SiⁱPr₃).Additionally, the dinuclear derivatives [Fe₂(μ-SCCR)(μ-CCR′)(CO)₆] (R = Fc, R′ = SiMe₃; R = SiMe₃, R′ = Fc; R = SiMe₃; R′ = SiⁱPr₃) have also been obtained. These compounds have been spectroscopically characterized and the crystal structure of some of them has been solved.     

Photochemically driven models of oxygenases based on the use of iron porphyrins

Photoexcited iron porphyrins can be used to mimic the catalytic activity of cytochrome P-450 oxygenases both in the reduction of halogenated alkanes and in the oxidation of hydrocarbons by O₂ itself at room temperature and atmospheric pressure. The results reported indicate that there is a similarity and a complementarity of photonic activation with other more conventional methods of activation of model systems of oxygenases. In fact, by irradiating at suitable wavelengths, it is possible to induce redox reactions which mimic those of natural oxygenases, avoiding the difficulties caused by parallel processes which could be expected when chemical reagents are used. These processes occur with good turnover values of the photocatalyst and in mild temperature and pressure conditions. By controlling the reaction environment, it is possible to address the selectivity of the process. In this regard, the very recent results obtained after heterogenization of the photocatalysts inside membranes of Nafion® are particularly promising for the development of new biomimetic photocatalysts in heterogeneous or organized systems.     

Effects of porphyrins and inorganic iron on the growth of Prevotella intermedia

We demonstrated earlier that hemin-iron-containing compounds which include hemin, human hemoglobin, bovine hemoglobin, and bovine catalase stimulate the growth of Prevotella intermedia [Leung, Subramaniam, Okamoto, Fukushima, Lai, FEMS Microbiol. Lett. 162 (1998) 227-233]. However, the contributions of tetrapyrrole porphyrin ring in these hemin-iron sources as well as inorganic iron for the growth of this organism have not been determined. The purpose of this study was to examine the effects of porphyrins, host iron-binding proteins, and various inorganic iron sources on the growth of hemin-iron depleted P. intermedia. Protoporphyrin IX and protoporphyrin IX-zinc, either in the presence or absence of supplemented ferrous or ferric iron, promoted the growth of P. intermedia at a rate that was comparable to that of the hemin control. On the other hand, neither the host iron proteins, transferrin and lactoferrin, nor the inorganic iron sources which included ferrous chloride, ferric chloride, ferric citrate, ferric nitrate, and ferric ammonium citrate at concentrations up to 200 microM stimulated the growth of hemin-iron-restricted P. intermedia. The results suggest that P. intermedia only use iron in a specific form and that the porphyrin-ring structure is essential for the growth of P. intermedia as in the case of other related organisms.     

DFT study on the reactivity of iron porphyrins tuned by ring substitution

The effect of beta-substituents (-NO2, -Br, -OCH3) in the reactivity of Fe(II) and Fe(III) porphyrins is studied by means of density functional theory (DFT) calculations. The binding of nitric oxide, carbon monoxide and dioxygen (NO, CO, O2) was explored due to the relevance of their interactions in the chemistry of heme proteins and in biomimetic catalysis. The binding capability (BC) of the porphyrins was found to be strongly modulated both by the donor and attractor substituents used in the work. Unexpectedly, we found that the BC of Fe(II) porphyrins is mainly decreased for the diatomic ligands, when both donor or withdrawing substituents were considered. This effect was particularly significant when the ligand was oxygen. The correlation of Fe-X and X-O (X=N, C, O) bond distances is explained in terms of backdonation effects.     

Reaction of chlorocruorin with heme iron ligands and carbonyl reagents.

Chlorocruorin was purified from Potamilla leptochaeta and the spectral properties of its derivatives wwere investigated. Ferri- or ferrochlorocruorin did not exhibits a ferrihemochrome or ferrohemochrome spectrum, respectively. Oxy- and carbonmonoxy-ferrochlorocruorin did show ferrohemochrome-type spectra. Ferrihemochromes were formed, however, when oxy-or ferrichlorocruorin was treated with 0.02-0.05% SDS, and they were transformed to ferrohemochromes by reduction with sodium dithionite. Ferrihemochrome formation was also brought about by increasing the pH of a ferrichlorocruorin solution to 9, or by liganding of extrinsic imidazole or cyanide to the ferric pigment. Therefore, it is apparent that at least one of the coordination positions on the heme iron in ferri-and ferrochlorocruorin is vacant or occupied by a weak-field ligand. Titration studies of ferrichlorocruorin with imidazole indicated that this supposedly vacant coordination position was occupied first by the imidazole, and that the intrinsic ligand of protein orgin was replaced finally at higher concentrations. The extrinsic ligands in the cyanide and imidazole complexes of ferrichlorocruorin were excluded from their coordination positions as the protein moiety assumed conformations inherent to the reduced pigment. Spectral analyses indicated that the intrinsic ligand is an imidazole moiety of a histidyl residue. When chlorocruorin was intact, carbonyl reagents such as cyanide and sodium bisulfite did not add to the formyl group of chlorocruoreheme. When the protein conformation was perturbed by SDS, addition to ferrichlorocruorin occurred appreciably. This addition was accelerated if the heme iron coordination position had been occupied by strong field ligands,and was reversed to some extent as the chlorocruorin complexes were reduced.     

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: ¹³C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, ¹³C′/¹³C′-¹³C^α CSA/dipolar and ¹³C′/¹³C′–¹⁵N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.     

Long-range charge transport through double-stranded DNA mediated by manganese or iron porphyrins

Guanine oxidation by electron transfer results in the formation of a guanine radical cation, which is at the origin of long-range charge transport through double-stranded DNA. It is possible to observe guanine lesions at a long distance from the oxidative reagent covalently bound to DNA owing to the migration of the positive hole in the DNA pi-stacks. This phenomenon of long-range hole transport is classically studied in the literature with photosensitizers used as one-electron oxidants. It is shown in the present work that the process of long-range charge transport and the concomitant formation of guanine lesions at a long distance can be observed also in the case of two-electron oxidants. This is the signature of the formation of a transient guanine radical cation in the course of the two-electron abstraction process and consequently evidence of the separated one plus one electron abstraction steps. Long-range charge transport is likely to be a universal mechanism for any two-electron oxidant acting by electron abstraction provided that the second electron abstraction is slower than hole transfer.     

It is still not for the old iron: adjuvant effects of carbonyl iron in experimental autoimmune encephalomyelitis induction

Experimental autoimmune encephalomyelitis (EAE) is a model of multiple sclerosis. Dark Agouti rats immunized with spinal cord homogenate (SCH) and carbonyl iron (CI), as an adjuvant, develop severe hyperacute form of EAE. They succumb to EAE earlier and have higher clinical scores and lethality rate in comparison to counterparts immunized with SCH + complete Freund's adjuvant. There is no difference in the number of cells or in histological presentation of the CNS infiltrates of rats immunized with the two adjuvants. However, there are more granulocytes, NK and NKT cells, and less CD4(+) T cells in the spinal cord infiltrates of SCH + CI-immunized animals. Nitric oxide (NO)-generating enzyme inducible NO synthase have higher expression in spinal cord of SCH + CI-immunized rats, and this corresponds to more intensive nitrotyrosine formation in the CNS tissue of these rats. Abundant infiltration of granulocytes and NK cells into the CNS and excessive generation of peroxynitrite within the CNS of SCH + CI-immunized rats might account for the severe neurological deficits induced by immunization with CI. These factors should be closely examined in the fulminant forms of multiple sclerosis and acute disseminated encephalomyelitis, as they could represent a promising targets for therapy.     

Quantitative studies of ribosome conformational dynamics

The ribosome is a dynamic machine that undergoes many conformational rearrangements during the initiation of protein synthesis. Significant differences exist between the process of protein synthesis initiation in eubacteria and eukaryotes. In particular, the initiation of eukaryotic protein synthesis requires roughly an order of magnitude more initiation factors to promote efficient mRNA recruitment and ribosomal recognition of the start codon than are needed for eubacterial initiation. The mechanisms by which these initiation factors promote ribosome conformational changes during stages of initiation have been studied using cross-linking, footprinting, site-directed probing, cryo-electron microscopy, X-ray crystallography, fluorescence spectroscopy and single-molecule techniques. Here, we review how the results of these different approaches have begun to converge to yield a detailed molecular understanding of the dynamic motions that the eukaryotic ribosome cycles through during the initiation of protein synthesis.     

Picosecond dynamics of the glutamate receptor in response to agonist-induced vibrational excitation

Conformational changes of proteins are dominated by the excitation and relaxation processes of their vibrational states. To elucidate the mechanism of receptor activation, the conformation dynamics of receptors must be analyzed in response to agonist-induced vibrational excitation. In this study, we chose the bending vibrational mode of the guanidinium group of Arg485 of the glutamate receptor subunit GluR2 based on our previous studies, and we investigated picosecond dynamics of the glutamate receptor caused by the vibrational excitation of Arg485 via molecular dynamics simulations. The vibrational excitation energy in Arg485 in the ligand-binding site initially flowed into Lys730, and then into the J-helix at the subunit interface of the ligand-binding domain. Consequently, the atomic displacement in the subunit interface around an intersubunit hydrogen bond was evoked in about 3 ps. This atomic displacement may perturb the subunit packing of the receptor, triggering receptor activation.