Heme Complexes Research Articles

ChemInform Abstract: Redox Cycling in the Activation of Peroxides by Iron Porphyrin and Manganese Complexes. ′Catching′ Catalytic Active Intermediates

AbstractReview: 261 refs.

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations.

In vertebrates, most iron is present as heme or is chelated by proteins. Thus, Gram-positive pathogens such as Staphylococcus aureus have evolved an iron-regulated surface determinant (Isd) system that transports heme across thick cell walls into the cytoplasm. Recent studies have demonstrated that heme is rapidly transferred between the NEAr Transporter (NEAT) domains of the Isd system, despite its high affinity toward each domain, suggesting the presence of an intermediate NEAT•heme•NEAT complex. In the present study, we performed short restrained molecular dynamics (MD) simulations to dock the acceptor NEAT domain to the donor NEAT•heme complex and obtained models where the two NEAT domains were arranged with two-fold pseudo symmetry around the heme molecule. After turning off the restraints, complex structures were stably maintained during subsequent unrestrained MD simulations, except for the hydrogen bond between the propionate group of the heme molecule and the donor NEAT domain, potentially facilitating the transition of heme from the donor to the acceptor. Subsequent structural optimization using the quantum mechanics/molecular mechanics (QM/MM) method showed that two tyrosine residues, one from each NEAT domain, were simultaneously coordinated to the ferric heme iron in the intermediate complex only if they were deprotonated. Based on these results, we propose a reaction scheme for heme transfer between NEAT domains.

Monitoring Changes in the Redox State of Myoglobin in Cardiomyocytes by Raman Spectroscopy Enables the Protective Effect of NO Donors to Be Evaluated.

Raman microspectroscopy has been used to monitor changes in the redox and ligand-coordination states of the heme complex in myoglobin during the preconditioning of ex vivo cardiomyocytes with pharmacological drugs that release nitric oxide (NO). These chemical agents are known to confer protection on heart tissue against ischemia-reperfusion injury. Subsequent changes in the redox and ligand-coordination states during experimental simulations of ischemia and reperfusion have also been monitored. We found that these measurements, in real time, could be used to evaluate the preconditioning treatment of cardiomyocytes and to predict the likelihood of cell survival following a potentially lethal period of ischemia. Evaluation of the preconditioning treatment was done at the single-cell level. The binding of NO to myoglobin, giving a 6-coordinate ferrous-heme complex, was inferred from the measured Raman bands of a cardiomyocyte by comparison to pure solution of the protein in the presence of NO. A key change in the Raman spectrum was observed after perfusion of the NO-donor was completed, where, if the preconditioning treatment was successful, the bands corresponding to the nitrosyl complex were replaced by bands corresponding to metmyoglobin, Mb(III). An observation of Mb(III) bands in the Raman spectrum was made for all of the cardiomyocytes that recovered contractile function, whereas the absence of Mb(III) bands always indicated that the cardiomyocyte would be unable to recover contractile function following the simulated conditions of ischemia and reperfusion in these experiments.

Design and engineering of a man-made diffusive electron-transport protein

Maquettes are man-made cofactor-binding oxidoreductases designed from first principles with minimal reference to natural protein sequences. Here we focus on water-soluble maquettes designed and engineered to perform diffusive electron transport of the kind typically carried out by cytochromes, ferredoxins and flavodoxins and other small proteins in photosynthetic and respiratory energy conversion and oxido-reductive metabolism. Our designs were tested by analysis of electron transfer between heme maquettes and the well-known natural electron transporter, cytochrome c. Electron-transfer kinetics were measured from seconds to milliseconds by stopped-flow, while sub-millisecond resolution was achieved through laser photolysis of the carbon monoxide maquette heme complex. These measurements demonstrate electron transfer from the maquette to cytochrome c, reproducing the timescales and charge complementarity modulation observed in natural systems. The ionic strength dependence of inter-protein electron transfer from 9.7×106M−1s−1 to 1.2×109M−1s−1 follows a simple Debye–Hückel model for attraction between +8 net charged oxidized cytochrome c and −19 net charged heme maquette, with no indication of significant protein dipole moment steering. Successfully recreating essential components of energy conversion and downstream metabolism in man-made proteins holds promise for in vivo clinical intervention and for the production of fuel or other industrial products. This article is part of a Special Issue entitled Biodesign for Bioenergetics — the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Alzheimer's Disease: A Heme-Aβ Perspective.

Redox active iron is utilized in biology for various electron transfer and catalytic reactions essential for life, yet this same chemistry mediates the formation of partially reduced oxygen species (PROS). Oxidative stress derived from the iron accumulated in the amyloid plaques originating from amyloid β (Aβ) peptides and neurofibrillary tangles derived from hyperphosphorylated tau proteins has been implicated in the pathogenesis of Alzheimer's disease (AD). Altered heme homeostasis leading to dysregulation of expression of heme proteins and heme deposits in the amyloid plaques are characteristic of the AD brain. However, the pathogenic significance of heme in neurodegeneration in AD has been unappreciated due to the lack of detailed understanding of the chemistry of the interaction of heme and Aβ peptides. As a result, the biochemistry and biophysics of heme complexes of Aβ peptides (heme-Aβ) remained largely unexplored. In this Account, we discuss the active site environment of heme bound Aβ complexes, which involves three amino acid residues unique in mammalian Aβ (Arg5, Tyr10, and His13) and missing in Aβ from rodents, which do not get affected by AD. The histidine residue binds heme, while the arginine and the tyrosine act as key second sphere residues of the heme-Aβ active site that play a crucial role in its reactivity. Generation of PROS, enhanced peroxidase activity, and oxidation of neurotransmitters such as serotonin (5-HT) are all found to be catalyzed by heme-Aβ in in vitro assays, and these reactivities can potentially be linked to the observed neuropathologies in AD brain. Association of Cu with heme-Aβ leads to the formation of heme-Cu-Aβ. The heme-Cu-Aβ complex produces a greater amount of PROS than reduced heme-Aβ or Cu-Aβ alone. Nitric oxide (NO), a signaling molecule, is found to ameliorate the detrimental effects of heme-Aβ and Cu bound heme-Aβ complexes by detaching heme from the heme-Aβ complex and releasing it into the environment solution. Heme-Aβ complexes show fast electron transfer with oxidized cytochrome c and rapid heme transfer with apomyoglobin and aponeuroglobin. NO, cytochrome c, and apoglobins can all lead to reduction in PROS generated by reduced heme-Aβ. Synthetic analogues of heme, offering a hydrophobic distal environment, have been used to trap oxygen bound intermediates, which provides insight into the mechanism of PROS generation by reduced heme-Aβ. Artificial constructs of Aβ on nonbiological platforms are used not only to stabilize metastable and physiologically relevant large and small amyloid aggregates but also to monitor the interaction of various drug candidates with heme and Cu bound Aβ aggregates, representing a tractable avenue for testing therapeutic agents targeting metals and cofactors in AD.

A Ferric-Peroxo Intermediate in the Oxidation of Heme by IsdI.

The canonical heme oxygenases (HOs) catalyze heme oxidation via a heme-bound hydroperoxo intermediate that is stabilized by a water cluster at the active site of the enzyme. In contrast, the hydrophobic active site of IsdI, a heme-degrading enzyme from Staphylococcus aureus, lacks a water cluster and is expected to oxidize heme by an alternative mechanism. Reaction of the IsdI-heme complex with either H2O2 or m-chloroperoxybenzoic acid fails to produce a specific oxidized heme iron intermediate, suggesting that ferric-hydroperoxo or ferryl derivatives of IsdI are not involved in the catalytic mechanism of this enzyme. IsdI lacks a proton-donating group in the distal heme pocket, so the possible involvement of a ferric-peroxo intermediate has been evaluated. Density functional theory (DFT) calculations indicate that heme oxidation involving a ferric-peroxo intermediate is energetically accessible, whereas the energy barrier for a reaction involving a ferric-hydroperoxo intermediate is too great in the absence of a proton donor. We propose that IsdI catalyzes heme oxidation through nucleophilic attack by the heme-bound peroxo species. This proposal is consistent with our previous demonstration by nuclear magnetic resonance spectroscopy that heme ruffling increases the susceptibility of the meso-carbon of heme to nucleophilic attack.

Effects Of Polyphenols On The Endogenous Formation Of Nitroso Compounds In Simulated Gastric Conditions

There is considerable epidemiological evidence supporting a positive association between red and processed meat intake and risk of colorectal cancer. There are several potential mechanism for this positive association, in particular the formation of carcinogenic N-nitroso compounds. Previously, we could show a close relationship between red meat and ATNC (apparent total nitroso compounds) formation. Polyphenols can reduce the formation of N-nitroso compounds in vitro. In this study, we have investigated the protective effect of different polyphenols in a simulated gastric system. The in vitro effect of quercetin, rutin, (-)-epicatechin, rosmarinic acid, ascorbic acid and several plant extracts containing these compounds were tested in an acidic gastric juice environment (bovine serum albumin, haemin and haemoglobin were dissolved in 7mM HCl, pH2.2, 1 mM NaNO2 were added to start the reaction). Different classes nitroso compounds were determined using chemical denitrosation with chemiluminescence detection. This enabled us not only to measure ATNC but also nitrosothiols and iron-nitrosyl (nitrosyl haem) complexes separately to have more information of the mechanism. The highest concentration of ATNC were observed after 20 mins of reaction time, while nitrite concentrations gradually decreased to almost 0 µmol/L. The formation of nitroso compounds were investigated in a simplified stomach environment to simulate high nitrate and high red meat intake with and without the addition of polyphenols. Our results did not show a consistent effect of phenolic compounds on the formation of total nitroso compounds, nitrosothiols or iron-nitrosyl complexes.

Direct analysis of intact biological macromolecules by low-energy, fiber-based femtosecond laser vaporization at 1042 nm wavelength with nanospray postionization mass spectrometry.

A fiber-based laser with a pulse duration of 435 fs and a wavelength of 1042 nm was used to vaporize biological macromolecules intact from the condensed phase into the gas phase for nanospray postionization and mass analysis. Laser vaporization of dried standard protein samples from a glass substrate by 10 Hz bursts of 20 pulses having 10 μs pulse separation and <50 μJ pulse energy resulted in signal comparable to a metal substrate. The protein signal observed from an aqueous droplet on a glass substrate was negligible compared to either a droplet on metal or a thin film on glass. The mass spectra generated from dried and aqueous protein samples by the low-energy, fiber laser were similar to the results from high-energy (500 μJ), 45-fs, 800-nm Ti:sapphire-based femtosecond laser electrospray mass spectrometry (LEMS) experiments, suggesting that the fiber-based femtosecond laser desorption mechanism involves a nonresonant, multiphoton process, rather than thermal- or photoacoustic-induced desorption. Direct analysis of whole blood performed without any pretreatment resulted in features corresponding to hemoglobin subunit-heme complex ions. The observation of intact molecular ions with low charge states from protein, and the tentatively assigned hemoglobin α subunit-heme complex from blood suggests that fiber-based femtosecond laser vaporization is a "soft" desorption source at a laser intensity of 2.39 × 10(12) W/cm(2). The low-energy, turnkey fiber laser demonstrates the potential of a more robust and affordable laser for femtosecond laser vaporization to deliver biological macromolecules into the gas phase for mass analysis.

A simple and label-free electrochemical method for detection of beta-site amyloid precursor protein cleaving enzyme and screening of its inhibitor

Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) is an aspartic protease that promotes the production of beta-amyloid (Aβ) peptides from beta-site amyloid precursor protein. Pharmacological reduction of Aβ production by inhibiting BACE1 has emerged as a promising target for the treatment of Alzheimer's disease (AD). In this work, we reported a simple electrochemical method for detection of BACE1 and screening of its inhibitor. This method made use of an unlabeled peptide that comprises a segment of beta-site amyloid precursor protein with the Swiss mutation. The peptide–heme complex formed on the electrode surface showed strong electrocatalytic O2 reduction. Cleavage of the peptide by BACE1 detached the heme-binding fragment from the electrode surface, leading to a remarkable decrease in the electrochemical signal. Suppression of BACE1 by the inhibitor yielded a larger voltammetric signal. The IC50 of the inhibitor tested by this method (15.7nM) was in agreement with that reported. The proposed method could serve as a promising alternative to the traditional methods for probing of BACE1 activity and screening of BACE1 inhibitor owing to its simplicity, high sensitivity and low assay cost.

Photoexcitation Dynamics of Cyanate‐ligated Ferric Heme Proteins Probed by Femtosecond Vibrational Spectroscopy#

The photoexcitation dynamics of cyanate‐ligated ferric myoglobin (MbNCO) and hemoglobin (HbNCO) in D2O at 293 K after excitation with a visible pulse was investigated by probing the anti‐symmetric stretching (ν1) mode of the NCO − ion bound to Mb or Hb using femtosecond vibrational spectroscopy. The ν1 mode of NCO in MbNCO or HbNCO in D2O shows one absorption feature near 2158 cm−1, which is similar to that of the free anion in D2O (2160 cm−1). The absorption feature of MbNCO was described by two absorption bands, i.e., one major band (90%) peaked at 2157 cm−1 with a full width at half maximum (FWHM) of 11 cm−1 and a minor band (10%) at 2143 cm−1 with an FWHM of 12 cm−1. In HbNCO, the major (82%) and minor (18%) bands are at 2159 (FWHM of 14 cm−1) and 2145 cm−1 (FWHM of 14 cm−1), respectively. The major and minor bands were attributed to the high‐ and low‐spin heme complexes, respectively. The photoexcited MbNCO and HbNCO undergo a rapid electronic relaxation with a time constant smaller than 0.4 ps, followed by thermal relaxation with a time constant of 8 ± 1 ps. No measurable absorption band for the photodeligated NCO − was detected, indicating that the photodeligation quantum yield of NCO −‐bound ferric heme proteins is negligible. The characteristics of the thermal and electronic relaxations are independent of both the excitation wavelengths used (575 and 400 nm) and heme proteins probed (Mb and Hb). Although the interaction between the cyanate and Fe3+ of the heme in Mb and Hb may be weak as suggested by the negligible shift in the band position of the cyanate upon ligand binding, the photodissociation of NCO − by a visible pulse is not significant. This finding is consistent with the negligible photodeligation observed for most of the other anion‐ligated ferric heme proteins.

Binding of azole drugs to heme: A combined MS/MS and computational approach

The binding properties of azole drugs toward ferric heme have been examined, focusing on well known antifungal drugs bearing imidazole and triazole heteroaromatic rings. These drugs are known to act as inhibitors of the Candidaalbicans P450 sterol 14α-demethylase enzyme, through binding to the heme prosthetic group. Absolute binding energies have been determined experimentally by energy variable collision induced dissociation experiments performed on the selected ionic complexes and evaluated theoretically using density functional theory, within the Car–Parrinello Molecular Dynamics method. The two series display some agreement in the relative binding energies data. These findings suggest that the combined ab initio and mass spectrometric approach may prove fruitful in assaying complexes between a prosthetic group and an array of ligands of potential pharmacological activity. It is shown that the axial interaction of the imidazole-based drugs with iron(III) is somewhat stronger than that of the triazole-based drugs. This general observation fails if specific interactions remote from the metal center come into play. For example, a hydrogen bond interaction is established in the ferric heme complex with fluconazole, a drug of the triazole family owning a hydroxyl group prone to interact with the carbonyl oxygen of a propionyl group on the periphery of protoporphyrin IX. However, the relatively uniform values for both the experimental and theoretically calculated binding energies underline the important role played by the prosthetic group environment in tuning the heme interaction with biological and xenobiotic molecules and ultimately in modulating enzyme activity.

EPR Analysis of Imidazole Binding to Methanosarcina acetivorans Protoglobin

Protoglobins form an unusual class of globin proteins with surprising structural features, such as a highly ruffled heme. Electron paramagnetic resonance spectra of the frozen solution of the ferric imidazole complex of Methanosarcina acetivorans protoglobin reveal the existence of two low-spin ferric heme complexes. Hyperfine sublevel correlation spectroscopy was used to study the imidazole complex of this protoglobin as well as the imidazole complex of horse heart myoglobin for comparison. The spin Hamiltonian values obtained for the dominant contribution of the imidazole-ligated protoglobin agree with a heme conformation in which the plane of the exogenous imidazole is turned more than 30° versus the imidazole plane of the proximal histidine ligand. In turn, the electron paramagnetic resonance data of the minority complex indicate a second conformer, in which the two ligand planes are aligned almost parallel to each other with a lengthened iron–nitrogen bond for the exogenous imidazole ligand.

The Heme-Bound Human BK Channel Gating Ring is a Co Sensor

Carbon monoxide (CO) is a recognized gasotransmitter that regulates BK channel activity, causing vasodilatory effects. It is thought that CO interacts with the intracellular portion of BK channels, which consists of the assembly of structural domains RCK1 and RCK2 into the ligand-sensing Gating Ring superstructure. Several mechanisms have been proposed to account for the BK/CO interaction (Heinemann et al., Chem Commun 2014). We have tested the hypothesis that CO interacts with BK channels via heme, which associates with the RCK1-RCK2 linker region, previously described as the BK Cytochrome-c-like domain (Yusifov et al., Biophysical J, 2709-Pos 2014). We investigated the molecular interaction of CO with the purified human BK channel Gating Ring using absorption spectroscopy: we found that the spectrum of the Gating Ring complexed with the reduced form of heme [Fe(II) protoporphyrin-IX] was significantly altered in the presence of CO and produced a Soret peak at 422 nm and β/α bands at 538 and 574 nm, typical spectral characteristic of hemoproteins complexed with CO. Furthermore, CO-dependent conformational changes were assessed using ANS (8-Anilino-1-naphthalenesulfonic acid) fluorescence spectra of the Gating Ring/reduced heme complex in the presence of increasing [CO]. The intensity of GR/ANS emission diminished in a [CO]-dependent manner (K0.5=54±3.8nM), indicating less ANS association, and therefore the occurrence of CO-dependent GR structural rearrangements. On the contrary, when heme was substituted by protoporphyrin-IX, a heme analog that lacks iron, CO addition did not alter ANS fluorescence. These results suggest that, in BK channels, the Heme/Cytochrome-c-like domain complex acts as a CO sensor, binding CO via heme and inducing a conformational change to the BK channel Gating Ring at submicromolar [CO]. This structural transition likely represents one of the mechanisms underlying the CO-dependent regulation of the human BK channel.

Probe the Heme Iron Ligand and Conformational Change of Misfolded States of Cytochrome C through EPR Spectroscopy

Cytochrome c is a heme-protein existing in the membrane of mitochrondria which plays a pivotal role in apoptosis. Besides its important biological functions, it is a model system for protein folding and unfolding studies. Recently, Soffer et al. [Soffer et al. Biochemistry 2013, 52, 1397−1408] claimed that a meta-stable misfolded state of horse heart ferricytochreome c could be obtained after exposing the protein to the ferricyanide solution at very alkaline pH for an extended period of time, and it did not undergo any remarkable change in its secondary and tertiary structures upon adjusting the solution to folding promoting conditions at neutral pH. Yet the axial coordination of the heme iron as well as the electronic structures for the misfolded protein remained undetermined. For this purpose, in this work, electron paramagnetic resonance (EPR) spectra of the misfolded protein in the solution at different pH values were recorded, and DFT calculation was conducted to predict the EPR g-tensor at different axial ligand configurations. Our EPR data indicate that the misfolded protein at very alkaline condition exhibits a hexacoordinated low spin state, while at pH 5 the protein adapt the configuration similar to the native-like low-spin ferric heme complex which possesses a histidine/methionine coordination environment. For pH value between 6 and 7, the EPR spectra appear to be the superposition of the two species. With the aid of DFT calculation, also checked by the EPR and other spectroscopic data, the possible hexacoordinated low spin state with a hydroxyl ion as the proximal ligand and the pentacoordinated quantum mixed state of the heme iron for misfolded protein at different folding conditions were discussed. This work was partially supported by Hundred Talents Program of Chinese Academy of Sciences.

Probing the ligand recognition and discrimination environment of the globin-coupled oxygen sensor protein YddV by FTIR and time-resolved step-scan FTIR spectroscopy.

YddV is a newly discovered signal transducer heme protein that recognizes O2 and CO. Structural differences in the ligand-bound heme complex in YddV reflect variations in catalytic regulation by O2 and CO. Time-resolved step-scan (TRS(2)) FTIR studies of the wild type and of the important in oxygen recognition and stability of the heme Fe(II)-O2 complex L65M, L65T, Y43A, Y43F and Y43W mutants were performed to determine the site-specific protein dynamics following carbon monoxide (CO) photodissociation. These mutations were designed to perturb the electrostatic field near the iron-bound gaseous ligand (CO) and also to allow us to investigate the communication pathway between the distal residues of the protein and heme. TRS(2)-FTIR spectra of YddV-heme-CO show that the heme propionates are in protonated and deprotonated states. Moreover, the rate of decay of the vibrations of amide I is on a time scale that coincides with the rate of rebinding of CO, which suggests that there is coupling between ligation dynamics in the distal heme environment and (i) relaxation of the protein backbone and (ii) the environment sensed by the heme propionates. The fast recombination rates in L65M, L65T and Y43W imply a significant role of L65 and Y43 in controlling the ligand dynamics. The implications of these results with respect to the role of the heme propionates and the charged or proton-donating residues in the distal pocket, which are crucial for stabilizing bound gaseous ligands, are discussed.

Nitration of Y10 in Aβ1-40: is it a compensatory reaction against oxidative/nitrative stress and Aβ aggregation?

Amyloid β peptide (Aβ) aggregation is considered to be a crucial pathological biomarker of Alzheimer's disease (AD). It was found that Aβ and heme can form an Aβ-heme complex, which results in increased heme pseudoperoxidase activity. Recently, we found that increasing pseudoperoxidase activity induces elevated tyrosine nitration on Aβ in the presence of nitrite and hydrogen peroxide. However, the nature of tyrosine nitration of Aβ and its physiologic significance are still unknown. In this study, we revealed that Aβ1-40 can be nitrated in vitro by binding to heme in the presence of nitrite and hydrogen peroxide. Moreover, we found that tyrosine nitration had little effect on Aβ1-40's binding activity with heme. A TMB assay also revealed that the peroxidase activity of the heme-Aβ1-40Y10(3N)T (tyrosine 10 was replaced with 3-nitrtotyrosine in Aβ1-40) complex was moderately increased compared with that of the heme-Aβ1-40 complex. Furthermore, Thioflavin T fluorescence and transmission electron microscopic characterization indicated that tyrosine nitration significantly decreased the aggregation of Aβ1-40. In addition, a cytotoxicity test verified that wild-type Aβ1-40 was more cytotoxic than that of Aβ1-40Y10(3N)T. These results suggest that nitration of Aβ1-40 might be an Aβ detoxicant process and a compensatory reaction to nitrative stress. Our findings may lead to a detailed understanding of the function of Aβ1-40 and may be helpful in preventing and curing AD.

A ripening associated peroxidase from papaya having a role in defense and lignification: Heterologous expression and in-silico and in-vitro experimental validation

Fruit ripening associated full length cDNA of a peroxidase from papaya was cloned and heterologously expressed. The expressed peroxidase was activated by in-vitro re-folding in the presence of hemin and calcium. The purified recombinant peroxidase exhibited broad substrate affinity in the order of o-dianisidine>pyrogallol>guaiacol and was found to be a homotetramer of 155kDa with each subunit having a size of 38kDa. The basis of the distinctive preferences for various substrates was investigated through in-silico molecular modeling approaches. Thus, when the modeled papaya peroxidase–heme complex was docked with these substrates, the in-silico binding efficiency was found to be in agreement with those of wet lab results with the involvement of Arg37, Phe40, His41, Pro137, Asn138, His139, His167, and Phe239 as the common interacting residues in all the cases. However, the binding of the different substrates were found to be associated with conformational changes in the peroxidase. Thus, in the case of o-dianisidine (the most efficient substrate), the protein was folded in the most compact fashion when compared to guaiacol (the least efficient substrate). Protein function annotation analyses revealed that the papaya peroxidase may have biological roles in oxidation-reduction processes, stresses, defense responses etc. In order to further validate its role in lignifications, the papaya peroxidase was compared with a lignin biosynthetic peroxidase from Leucaena leucocephala, a tree legume. Thus, based on 3D structure superimposition and docking, both peroxidases exhibited a great extent of similarity suggesting the papaya peroxidase having a role in lignification (defense response) too. The predicted functions of papaya peroxidase in defense response and lignification were further validated experimentally using qRT-PCR analyses and measurement of oxidation of coniferyl alcohol.

Pressure effects reveal that changes in the redox states of the heme iron complexes in the sensor domains of two heme-based oxygen sensor proteins, EcDOS and YddV, have profound effects on their flexibility.

The catalytic activity of a heme-based oxygen sensor phosphodiesterase from Escherichiacoli (EcDOS) towards cyclic diGMP is regulated by the redox state of the heme iron complex in the enzyme's sensing domain and the association of external ligands with the iron center. Specifically, the Fe(II) complex is more active towards cyclic diGMP than the Fe(III) complex, and its activity is further enhanced by O2 or CO binding. In order to determine how the redox state and coordination of the heme iron atom regulate the catalytic activity of EcDOS, we investigated the flexibility of its isolated N-terminal heme-binding domain (EcDOS-heme) by monitoring its spectral properties at various hydrostatic pressures. The most active form of the heme-containing domain, i.e. the Fe(II)-CO complex, was found to be the least flexible. Conversely, the oxidized Fe(III) forms of EcDOS-heme and its mutants had relatively high flexibilities, which appeared to be linked to the low catalytic activity of the corresponding intact enzymes. These findings corroborate the suggestion, made on the basis of crystallographic data, that there is an inverse relationship between the flexibility of the heme-containing domain of EcDOS and its catalytic activity. The Fe(II)-CO form of the heme domain of a second heme-based oxygen sensor, diguanylate cyclase (YddV), was also found to be quite rigid. Interestingly, the incorporation of a water molecule into the heme complex of YddV caused by mutation of the Leu65 residue reduced the flexibility of this heme domain. Conversely, mutation of the Tyr43 residue increased its flexibility.

Electrochemistry and molecular modeling of the hemoglobin–benzene interaction with a nanocrystalline mixed metal oxide

Nanocrystalline mixed metal oxides of various metal cations were synthesized and were then used for the construction of a new modified carbon paste electrode. Hemoglobin (Hb) was entrapped on the surface of this electrode using an alginate biocompatible biopolymer that crosslinked with the calcium ions. Spectroscopic studies were done to determine the characteristics of the biopolymer matrix and the effects of benzene on Hb. The direct electrochemistry of Hb using the proposed method and its application in Hb interaction with benzene were investigated using an electrochemical method. The heme complexes with imidazole and histidine were also entrapped on the surface of the electrode and the effect of benzene on these complexes was also studied. The Hill binding parameters were obtained for the Hb–benzene, imidazole-heme–benzene and histidine-heme–benzene interactions. A molecular docking simulation was used for theoretical studies and the data obtained were compared with experimental results. A good agreement was observed between the theoretical and experimental results. The Hb electrode can be used for benzene determination in water and aqueous solutions because of the linear relationship between benzene concentration and the peak current decreases with good linearity. The proposed sensor has advantages such as it has an easy, simple and inexpensive preparation method, shows good linearity and low detection and good quantification limits, good reproducibility and sensitivity, and has a relatively long life time (about 15 days) that is because of the alginate biopolymer biocompatible matrix.

Factors affecting hydrogen-tunneling contribution in hydroxylation reactions promoted by oxoiron(IV) porphyrin π-cation radical complexes.

Hydrogen atom transfer with a tunneling effect (H-tunneling) has been proposed to be involved in aliphatic hydroxylation reactions catalyzed by cytochrome P450 and synthetic heme complexes as a result of the observation of large hydrogen/deuterium kinetic isotope effects (KIEs). In the present work, we investigate the factors controlling the H-tunneling contribution to the H-transfer process in hydroxylation reaction by examining the kinetics of hydroxylation reactions at the benzylic positions of xanthene and 1,2,3,4-tetrahydronaphthalene by oxoiron(IV) 5,10,15,20-tetramesitylporphyrin π-cation radical complexes ((TMP(+•))Fe(IV)O(L)) under single-turnover conditions. The Arrhenius plots for these hydroxylation reactions of H-isotopomers have upwardly concave profiles. The Arrhenius plots of D-isotopomers, clear isosbestic points, and product analysis rule out the participation of thermally dependent other reaction processes in the concave profiles. These results provide evidence for the involvement of H-tunneling in the rate-limiting H-transfer process. These profiles are simulated using an equation derived from Bell's tunneling model. The temperature dependence of the KIE values (k(H)/k(D)) determined for these reactions indicates that the KIE value increases as the reaction temperature becomes lower, the bond dissociation energy (BDE) of the C-H bond of a substrate becomes higher, and the reactivity of (TMP(+•))Fe(IV)O(L) decreases. In addition, we found correlation of the slope of the ln(k(H)/k(D)) - 1/T plot and the bond strengths of the Fe═O bond of (TMP(+•))Fe(IV)O(L) estimated from resonance Raman spectroscopy. These observations indicate that these factors modulate the extent of the H-tunneling contribution by modulating the ratio of the height and thickness of the reaction barrier.