Binding mechanism of disulfide species to ferric hemeproteins: The case of metmyoglobin

The interactions of the heme iron of hemeproteins with sulfide and disulfide compounds are of potential interest as physiological signaling processes. While the interaction with hydrogen sulfide has been described computationally and experimentally, the reaction with disulfide, and specifically the molecular mechanism for ligand binding has not been studied in detail. In this work, we study the association process for disulfane and its conjugate base disulfanide at different pH conditions. Additionally, by means of advanced sampling techniques based on multiple steered molecular dynamics, we provide free energy profiles for ligand migration for both acid/base species, showing a similar behavior to the previously reported for the related H2S/HS¯ pair. Finally, we studied the ligand interchange reaction (H2O/H2S, HS¯ and H2O/HSSH, HSS¯) by means of hybrid quantum mechanics-molecular mechanics calculations. We show that the anionic species are able to displace more efficiently the H2O bound to the iron, and that the H-bond network in the distal cavity can help the neutral species to perform the reaction. Altogether, we provide a molecular explanation for the experimental information and show that the global association process depends on a fine balance between the migration towards the active site and the ligand interchange reaction.

Reduction of metmyoglobin by inorganic disulfide species

The mechanism of the metal centered reduction of metmyoglobin (MbFeIII) by inorganic disulfide species has been studied by combined spectroscopic and kinetic analyses, under argon atmosphere. The process is kinetically characterized by biexponential time traces, for variable ratios of excess disulfide to protein, in the pH interval 6.6-8.0. Using UV-vis and resonance Raman spectroscopies, we observed that MbFeIII is converted into a low spin hexacoordinated ferric complex, tentatively assigned as MbFeIII(HSS-)/MbFeIII(SS2-), in an initial fast step. The complex is slowly converted into a pentacoordinated ferrous form, assigned as MbFeII according to the resonance Raman records. The reduction is a pH-dependent process, but independent of the initial disulfide concentration, suggesting the unimolecular decomposition of the intermediate complex following a reductive homolysis. We estimated the rate of the fast formation of the complex at pH 7.4 (kon = 3.7 × 103 M-1 s-1), and a pKa2 = 7.5 for the equilibrium MbFeIII(HSS-)/MbFeIII(SS2-). Also, we estimated the rate for the slow reduction at the same pH (kred = 10-2 s-1). A reaction mechanism compliant with the experimental results is proposed. This mechanistic study provides a differential kinetic signature for the reactions of disulfide compared to sulfide species on metmyoglobin, which may be considered in other hemeprotein systems.

Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species

The mechanism of the metal centered reduction of metmyoglobin (MbFeIII) by sulfide species (H2S/HS-) under an argon atmosphere has been studied by a combination of spectroscopic, kinetic, and computational methods. Asymmetric S-shaped time-traces for the formation of MbFeII at varying ratios of excess sulfide were observed at pH 5.3 < pH < 8.0 and 25 °C, suggesting an autocatalytic reaction mechanism. An increased rate at more alkaline pHs points to HS- as relevant reactive species for the reduction. The formation of the sulfanyl radical (HS•) in the slow initial phase was assessed using the spin-trap phenyl N-tert-butyl nitrone. This radical initiates the formation of S-S reactive species as disulfanuidyl/ disulfanudi-idyl radical anions and disulfide (HSSH•-/HSS•2- and HSS-, respectively). The autocatalysis has been ascribed to HSS-, formed after HSSH•-/HSS•2- disproportionation, which behaves as a fast reductant toward the intermediate complex MbFeIII(HS-). We propose a reaction mechanism for the sulfide-mediated reduction of metmyoglobin where only ferric heme iron initiates the oxidation of sulfide species. Beside the chemical interest, this insight into the MbFeIII/sulfide reaction under an argon atmosphere is relevant for the interpretation of biochemical aspects of ectopic myoglobins found on hypoxic tissues toward reactive sulfur species.

Reactivity of inorganic sulfide species towards a pentacoordinated heme model system

The reactivity of inorganic sulfide towards ferric bis(N-acetyl)- microperoxidase 11 in sodium dodecyl sulfate has been explored by means of visible absorption and resonance Raman spectroscopies. The reaction has been previously studied in buffered solutions at neutral pH and in the presence of excess sulfide, revealing the formation of a moderately stable hexacoordinated low spin ferric sulfide complex that yields the ferrous form in the hour's timescale. In the surfactant solution, instead, the ferrous form is rapidly formed. The spectroscopic characterization of the heme structure in the surfactant milieu revealed the stabilization of a major ferric mono-histidyl high spin heme, which may be ascribed to out of plane distortions prompting the detachment of the axially ligated water molecule, thus leading to a differential reactivity. The ferric bis(N-acetyl)- microperoxidase 11 in sodium dodecyl sulfate provides a model for pentacoordinated heme platforms with an imidazole-based ligand.

Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin

Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations-a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism-the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.

A fluorescence nanoscopy marker for corticotropin-releasing hormone type 1 receptor: computer design, synthesis, signaling effects, super-resolved fluorescence imaging, and in situ affinity constant in cells

A new fluorescent marker for CRHR1 shows an antagonist effect and suitability for super resolution fluorescence microscopy.

Reactivity of inorganic sulfide species toward a heme protein model

The reactivity of inorganic sulfide species toward heme peptides was explored under biorelevant conditions in order to unravel the molecular details of the reactivity of the endogenous hydrogen sulfide toward heme proteins. Unlike ferric porphyrinates, which are reduced by inorganic sulfide, some heme proteins can form stable Fe(III)-sulfide adducts. To isolate the protein factors ruling the redox chemistry, we used as a system model, the undecapeptide microperoxidase (MP11), a heme peptide derived from cytochrome c proteolysis that retains the proximal histidine bound to the Fe(III) atom. Upon addition of gaseous hydrogen sulfide (H2S) at pH 6.8, the UV-vis spectra of MP11 closely resembled those of the low-spin ferric hydroxo complex (only attained at an alkaline pH) and cysteine or alkylthiol derivatives, suggesting that the Fe(III) reduction was prevented. The low-frequency region of the resonance Raman spectrum revealed the presence of an Fe(III)-S band at 366 cm(-1) and the general features of a low-spin hexacoordinated heme. Anhydrous sodium sulfide (Na2S) was the source of sulfide of choice for the kinetic evaluation of the process. Theoretical calculations showed no distal stabilization mechanisms for bound sulfide species in MP11, highlighting a key role of the proximal histidine for the stabilization of the Fe(III)-S adducts of heme compounds devoid of distal counterparts, which is significant with regard to the biochemical reactivity of endogenous hydrogen sulfide.

Reactivity of iron(II)-bound nitrosyl hydride (HNO, nitroxyl) in aqueous solution

The reactivity of coordinated nitroxyl (HNO) has been explored with the [Fe(II)(CN)(5)HNO](3-) complex in aqueous medium, pH 6. We discuss essential biorelevant issues as the thermal and photochemical decompositions, the reactivity toward HNO dissociation, the electrochemical behavior, and the reactions with oxidizing and reducing agents. The spontaneous decomposition in the absence of light yielded a two-electron oxidized species, the nitroprusside anion, [Fe(II)(CN)(5)NO](2-), and a negligible quantity of N(2)O, with k(obs)≈5×10(-7)s(-1), at 25.0°C. The value of k(obs) represents an upper limit for HNO release, comparable to values reported for other structurally related L ligands in the [Fe(II)(CN)(5)L](n-) series. These results reveal that the FeN bond is strong, suggesting a significant σ-π interaction, as already postulated for other HNO-complexes. The [Fe(II)(CN)(5)HNO](3-) ion showed a quasi-reversible oxidation wave at 0.32 V (vs normal hydrogen electrode), corresponding to the [Fe(II)(CN)(5)HNO](3-)/[Fe(II)(CN)(5)NO](3-),H(+) redox couple. Hexacyanoferrate(III), methylviologen and the nitroprusside ion have been selected as potential oxidants. Only the first reactant achieved a complete oxidation process, initiated by a proton-coupled electron transfer reaction at the HNO ligand, with nitroprusside as a final oxidation product. Dithionite acted as a reductant of [Fe(II)(CN)(5)HNO](3-), in a 4-electron process, giving NH(3). The high stability of bound HNO may resemble the properties in related Fe(II) centers of redox active enzymes. The very minor release of N(2)O shows that the redox conversions may evolve without disruption of the FeN bonds, under competitive conditions with the dissociation of HNO.

Disproportionation of hydroxylamine by water-soluble iron(III) porphyrinate compounds

The reactions of hydroxylamine (HA) with several water-soluble iron(III) porphyrinate compounds, namely iron(III) meso-tetrakis-(N-ethylpyridinium-2yl)-porphyrinate ([Fe(III)(TEPyP)](5+)), iron(III) meso-tetrakis-(4-sulphonatophenyl)-porphyrinate ([Fe(III)(TPPS)](3-)), and microperoxidase 11 ([Fe(III)(MP11)]) were studied for different [Fe(III)(Porph)]/[HA] ratios, under anaerobic conditions at neutral pH. Efficient catalytic processes leading to the disproportionation of HA by these iron(III) porphyrinates were evidenced for the first time. As a common feature, only N(2) and N(2)O were found as gaseous, nitrogen-containing oxidation products, while NH(3) was the unique reduced species detected. Different N(2)/N(2)O ratios obtained with these three porphyrinates strongly suggest distinctive mechanistic scenarios: while [Fe(III)(TEPyP)](5+) and [Fe(III)(MP11)] formed unknown steady-state porphyrinic intermediates in the presence of HA, [Fe(III)(TPPS)](3-) led to the well characterized soluble intermediate, [Fe(II)(TPPS)NO](4-). Free-radical formation was only evidenced for [Fe(III)(TEPyP)](5+), as a consequence of a metal centered reduction. We discuss the catalytic pathways of HA disproportionation on the basis of the distribution of gaseous products, free radicals formation, the nature of porphyrinic intermediates, the Fe(II)/Fe(III) redox potential, the coordinating capabilities of each complex, and the kinetic analysis. The absence of NO(2)(-) revealed either that no HAO-like activity was operative under our reaction conditions, or that NO(2)(-), if formed, was consumed in the reaction milieu.

Theoretical insight into the hydroxylamine oxidoreductase mechanism

The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe(III)NO intermediate, while behaving indifferently in the Fe(II)NO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe(III)H(2)O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates.

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.

Effect of nitroxyl on the hamster retinal nitridergic pathway

There is a growing body of evidence on the role of nitric oxide (NO) in retinal physiology. Recently, interest has developed in the functional role of an alternative redox form of NO, namely nitroxyl (HNO/NO(-)), because it is formed by a number of diverse biochemical reactions. The aim of the present report was to comparatively analyze the effect of HNO and NO on the retinal nitridergic pathway in the golden hamster. For this purpose, sodium trioxodinitrate (Angeli's salt) and diethylammonium (Z)-1-(N,N-diethylamino)diazen-1-ium-1,2-diolate (DEA/NO) were used as HNO and NO releasers, respectively. Angeli's salt and DEA/NO significantly decreased nitric oxide synthase activity. In addition, Angeli's salt (but not DEA/NO) significantly decreased l-arginine uptake. DEA/NO significantly increased cGMP accumulation at low micromolar concentrations, while Angeli's salt affected this parameter with a threshold concentration of 200muM. Although Angeli's salt and DEA/NO significantly diminished reduced glutathione and protein thiol levels in a similar way, DEA/NO was significantly more effective than AS in increasing S-nitrosothiol levels. None of these compounds increased retinal lipid peroxidation. These results suggest that HNO could regulate the hamster retinal nitridergic pathway by acting through a mechanism that only partly overlaps with that involved in NO response.

Effect of nitroxyl on human platelets function

There is a growing body of evidence on the role of nitric oxide (NO) in human platelet physiology regulation. Recently, interest has developed in the functional role of an alternative redox form of NO, namely nitroxyl (HNO/NO-), because it is formed by a number of diverse biochemical reactions. The aim of the present study was to comparatively analyze the effect of HNO and NO on several functional parameters of human platelets. For this purpose, sodium trioxodinitrate (Angeli's salt,AS) and sodium nitroprusside (SNP) were used as HNO and NO releasers, respectively. BothAS and SNP significantly inhibited platelet aggregation and ATP release induced by different agonists and adrenaline. AS or SNP did not modify the expression of platelet glycoproteins (Ib, IIb-IIIa, la-IIa, IV), whereas they substantially decreased the levels of CD62P, CD63 and of PAC-1 (a platelet activated glycoprotein IIb/IIIa epitope) after the stimulation with ADP. AS and SNP significantly increased cGMP accumulation in a 1H-[1,2,4]oxadiazolo [4,3-a] quinoxalin-1-one (ODQ)-sensitive manner. However, while L-cysteine reduced the effect of AS, it increased the effect of SNP on this parameter. Accordingly, a differential effect of L-cysteine was observed on the antiaggregatory effect of both compounds. In summary, these results indicate that HNO is an effective inhibitor of human platelet aggregation.

Discrimination of nitroxyl and nitric oxide by water-soluble Mn(III) porphyrins

The water-soluble manganese(III) meso-tetrakis (N-ethylpyridinium-2-yl) porphyrin (Mn(III)TEPyP) and manganese(III) meso-(tetrakis(4-sulfonato-phenyl)) porphyrinate (Mn(III)TPPS) are able to chemically distinguish between HNO and NO donors, reacting with the former in a fast, efficient, and selective manner with concomitant formation of the {MnNO}(7) complex (k(on(HNO)) approximately equal to 10(5) M(-1) s(-1)), while they are inert or react very slowly with NO donors. DFT calculations and kinetic data suggest that HNO trapping is operative at least in the case of Mn(III)TPPS, while catalytic decomposition of the HNO donors (sodium trioxodinitrate and toluene sulfohydroxamic acid) seems to be the main pathway for Mn(III)TEPyP. In the presence of oxygen, the product Mn(II)TEPyP(NO) oxidizes back to Mn(III)TEPyP, making it possible to process large ratios of nitroxyl donor with small amounts of porphyrin.

On how the conformation of biliverdins influences their reduction to bilirubins: a biological and molecular modeling study

The cyclic 2,18-bridged biliverdin (2) is excreted in rat bile without reduction to the corresponding bilirubin. Conformational analysis, employing an optimized Monte Carlo method and a mixed Monte Carlo/stochastic dynamics, reveals that biliverdin IXalpha (1) and the cyclic analogue 2 adopt 'lock washer' conformations, stabilized by the presence of intramolecular hydrogen bonds between N23...H22N and, to a lesser extent, between N23...H24N. Although 2 is very similar in overall shape to 1, the former adopts a 'locked lock washer' conformation unable to undergo fluctuations, thus possibly hampering a proper recognition by biliverdin reductase.

Fast nitroxyl trapping by ferric porphyrins

Iron(II) porphyrin nitrosyl complexes are obtained in high yields from the reaction of iron(III) porphyrins with the nitroxyl donors sodium trioxodinitrate and toluensulfohydroxamic acid. The reaction was found to proceed both in organic solvents and in aqueous media from iron(III) (meso-tetraphenyl) porphyrinate ([FeIII(TPP)]+) and iron(III) meso-tetrakis (4-sulfonatophenyl) porphyrinate ([FeIII(TPPS)]3-) or iron(III) protoporphyrin IX, respectively. The kinetic rate constant for the reaction of ([FeIII(TPPS)]3-) with sodium trioxodinitrate (kon) was estimated to be 1.00 +/- 0.04 x 107 M-1 s-1. As well as resulting in a versatile method for obtaining ferrous nitrosyl porphyrins, the reaction points at ferric porphyrins as efficient nitroxyl traps and provides a tool to model nitroxyl reactivity toward hemeproteins.

Exploring the conformation of bilirubins with natural and unnatural analogues: use of positional and bridged isomers of bilirubin IXalpha

Unlike bilirubin IXalpha (1), the isomers bilirubin IXdelta (2) and neobilirubin IXbeta (3) do not require conjugation with glucuronic acid in order to be excreted. A conformational analysis employing an optimized Monte Carlo method and a mixed Monte Carlo stochastic dynamics reveals that isomer 2 exhibits a structure more closed than the well known 'ridge-tile' conformation of 1. The change in the position of both propionic acid chains causes the loss of at least four hydrogen bonds. On the other hand, the change in the configuration of the distal dipyrrinone and the blockage of the lactamic nitrogen by the presence of a bridge in isomer 3 results in an open and more elongated structure, where the chance of hydrogen bond formation in this region is obliterated. The resulting molecular models for these compounds are consistent with 1H NM R, UV-vis, and TLC data.