Evaluation of electron-withdrawing group effects on heme binding in designed proteins: implications for heme a in cytochrome c oxidase

Heme a, the metalloporphyrin cofactor unique to cytochrome c oxidases, differs from the more common heme b by two chemical modifications, a C-2 hydroxyethylfarnesyl group and a C-8 formyl group. To elucidate a role of the C-8 formyl group, we compare the heme affinity, spectroscopy, and electrochemistry of a heme a mimic, Fe(diacetyldeuterioporphyrin IX) or Fe(DADPIX), with heme b, Fe(protoporphryrin IX) or Fe(PPIX), incorporated into a designed heme protein. The [Delta7-H3m]2 protein ligand, or maquette, selected for this study contains two equivalent bis-(3-methyl-L-histidine) heme binding sites within a four-alpha-helix bundle scaffold. The spectroscopic data on Fe(PPIX) and Fe(DADPIX) bound to [Delta7-H3m]2 demonstrate that these complexes are excellent synthetic analogues for natural cytochromes b and a, respectively. Comparison of the spectroscopic, electrochemical, and equilibrium thermodynamic data measured for the Fe(PPIX)-[Delta7-H3m]2 maquette with the previously reported Fe(PPIX)-[Delta7-His]2 complex demonstrates that changing the heme axial ligands to 3-methyl-L-histidine from L-histidine does not alter the resulting heme protein properties significantly in either oxidation state. Heme binding studies demonstrate that [Delta7-H3m]2 binds two ferrous Fe(DADPIX) or Fe(PPIX) moieties with similar dissociation constant values. However, in the ferric state, the data show that [Delta7-H3m]2 only binds a single Fe(DADPIX) and that one 2500-fold weaker than oxidized Fe(PPIX). The data demonstrate that the 4.6 kcal mol(-1) weakened affinity of [Delta7-H3m]2 for oxidized Fe(DADPIX) results in the majority of the 160 mV, 3.7 kcal mol(-1), positive shift in the heme reduction potential relative to Fe(PPIX). These data indicate that a role of the formyl group on heme a is to raise the iron reduction potential, thus making it a better electron acceptor, but that it does so by destabilizing the affinity of bis-imidazole sites for the ferric state.     

阿霉素的光谱电化学研究

利用循环伏安、紫外可见光谱电化学、荧光光谱电化学、圆二色光谱电化学等方法研究了阿霉素(ADM)在石墨电极上的电化学行为.结果发现,阿霉素在+0.2～+0.7V和-0.2～-0.7V范围内分别出现一对氧化还原峰.正电位下,蒽环上的酚羟基发生单电子氧化,并伴随后续化学反应.负电位范围内,阿霉素经历ECE电极反应过程,即蒽醌经单电子还原生成半醌自由基,半醌可发生不可逆的化学反应,脱去配氧糖基,转变为7-去氧柔毛霉醌(7-deoxyadriamycinone),后者在更负的电位下形成一对可逆的新的氧化还原峰.     

Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.     

Cryoradiolytic reduction of heme proteins: Maximizing dose-dependent yield

Radiolytic reduction in frozen solutions and crystals is a useful method for generation of trapped intermediates in protein-based radical reactions. In this communication we define the conditions which provide the maximum yield of one electron-reduced myoglobin at 77 K using ⁶⁰Co γ-irradiation in aqueous glycerol glass. The yield reached 50% after 20 kGy, was almost complete at ∼160 kGy total dose, and does not depend on the protein concentration in the range 0.01–5 mM.     

Photon echo spectroscopy of porphyrins and heme proteins: effects of quasidegenerate electronic structure on the peak shift decay

Three pulse photon echo peak shift spectroscopy and transient grating measurements on Zn-substituted cytochrome c, Zn-tetraphenylporphyrin, and Zn-protoporphyrin IX are reported. The effects of protein conformation, axial ligation, and solvent are investigated. Numerical simulations of the peak shift and transient grating experiments are presented. The simulations employed recently derived optical response functions for square-symmetric molecules with doubly degenerate excited states. Simulations exploring the effects of excited-state energy splitting, symmetric and asymmetric fluctuations, and excited-state lifetime show that the time scales of the peak shift decay in the three-level system largely reflect the same dynamics as in the two-level system. However, the asymptotic peak shift, which is a clear indicator of inhomogeneous broadening in a two-level system, must be interpreted more carefully for three-level systems, as it is also influenced by the magnitude of the excited-state splitting. The calculated signals qualitatively reproduce the data.     

Inclusion chemistry for the modeling of heme proteins

Early attention to the modeling of heme proteins is enhancing the understanding of biochemistry. Those studies are also contributing to the development of techniques for the modeling of still more intricate, multifunctional, variously selective natural systems. Selectivity in simple systems may involve the molecular capability to bind only one of a family of related species or it may mean the ability to select and control one of a number of possible functions of a given bound species. Complicated systems simultaneously combine the two kinds of simple selectivities for two or more different classes of guest, often with synergistic interrelationships. The subject is developed around examples of binary, tertiary, and quarternary complexes designed to model the behavior of monooxygenases.     

Reactions of heme proteins with carbonate radical anion

Reactions of radiolytically generated CO₃ ^•− with some ferric heme proteins, catalase, cytochrome c, and horseradish peroxidase (HRP), were studied. Carbonate radical anion oxidized amino acid residues of these proteins, but did not react directly with heme iron. HRP and catalase lost about 30% and 20% of their activity, respectively, after the reaction with 100 μM of CO₃ ^•−. The rate constants of the reactions of CO₃ ^•− with the investigated proteins measured by the pulse radiolysis method at pH 8–8.4 and 10 varied from 1.0 × 10⁸ M⁻¹ s⁻¹ (for cytochrome c) to 3.7 × 10⁹ M⁻¹ s⁻¹ (for catalase).     

On-line chemiluminescence detection for isoelectric focusing of heme proteins on microchips

In this paper we present a sensitive chemiluminescence (CL) detection of heme proteins coupled with microchip IEF. The detection principle was based on the catalytic effects of the heme proteins on the CL reaction of luminol-H2O2 enhanced by para-iodophenol. The glass microchip and poly(dimethylsiloxane) (PDMS)/glass microchip for IEF were fabricated using micromachining technology in the laboratory. The modes of CL detection were investigated and two microchips (glass, PDMS/glass) were compared. Certain proteins, such as cytochrome c, myoglobin, and horseradish peroxidase, were focused by use of Pharmalyte pH 3-10 as ampholytes. Hydroxypropylmethylcellulose was added to the sample solution in order to easily reduce protein interactions with the channel wall as well as the EOF. The focused proteins were transported by salt mobilization to the CL detection window. Cytochrome c, myoglobin, and horseradish peroxidase were well separated within 10 min on a glass chip and the detection limits (S/N=3) were 1.2x10(-7), 1.6x10(-7), and 1.0x10(-10) M, respectively.     

Direct electrochemistry and electrocatalysis of heme proteins on SWCNTs-CTAB modified electrodes

Direct electrochemistry and electrocatalysis of heme proteins including hemoglobin (Hb), myoglobin (Mb) and horseradish peroxidase (HRP) were studied with the protein incorporated single walled carbon nanotubes (SWCNTs)-cetylramethylammonium bromide (CTAB) nanocomposite film modified glassy carbon electrodes (GCEs). The incorporated heme proteins were characterized with Fourier transform infrared spectroscopy (FTIR), ultraviolet visible (UV) spectroscopy, atomic force microscopy (AFM) and electrochemistry, indicating the heme proteins in SWCNTs-CTAB nanocomposite films keep their secondary structure similar to their native states. The direct electron transfer between the heme proteins in SWCNTs-CTAB films and GCE was investigated. The electrochemical parameters such as formal potentials and apparent heterogeneous electrontransfer rate constants (k_s) were estimated by square wave voltammetry with nonlinear regression analysis. The heme protein-SWCNT-CTAB electrodes show excellent electrocatalytic activities for the reduction of H₂O₂ and NO₂⁻, which have been utilized to determine the concentrations of H₂O₂ and NO₂⁻.     

Dendrimers with Porphyrin Cores: Synthetic models for globular heme proteins

Dendritic iron porphyrins were synthesized as functional mimics of globular electron-transfer heme proteins. The cascade molecules 1 · Zn ? 3 Zn of first to third generation were obtained starting from the (meso-diarylporphyrin) zinc 6 · Zn which contains four carboxylate arms for attachment of the poly(ether-amide) dendritic branches by peptide-coupling methodology (Scheme 1). Generation 3 compound 3 · Zn with 108 methyl-carboxylate end groups has a molecular weight of 19054. D, and computer modeling suggests that its structure is globular and densely-packed, measuring ca. 4 nm in diameter and, therefore, similar in dimensions to the electron-transfer protein cytochrome-c. Starting from the generation 1 poly(carboxylic acid) 11 · Zn and the generation 2 analog 12 · Zn the dendritic Zn^II porphyrins 4 · Zn and 5 · Zn , respectively, were obtained by esterification with triethyleneglycol monomethyl ether (Schemes 3 and 4). Demetallation followed by insertion of Fe^II and in situ oxidation afforded the water-soluble dendritic iron porphyrins 4 FeCl and 5 FeCl . The electrochemical behavior of esters 1 · Zn ? 3 · Zn in organic solvents changed smoothly with increasing dendritic generation (Table 1). Progressing from 1 · Zn to 3 · Zn in THF, the first porphyrin-centered oxidation and reduction potentials become more negative by 320 and 210mV, respectively. These changes were attributed to strong microenvironmental effects imposed on the electroactive core by the densely packed dendritic surroundings. The electrochemical properties of 4 · FeCl and 5 · FeCl were investigated by cyclic voltammetry in both CH₂Cl₂ and H₂O (Tables 2 and 3). Progressing from 4 · FeCl to 5 · FeCl in CH₂Cl₂, the redox potential of the biologically relevant Fe^III/Fe^II couple remained virtually unchanged, whereas in aqueous solution, 5 FeCl exhibited a potential 420 mV more positive than did 4 FeCl. The large difference between these potentials in H₂O was attributed to differences in solvation of the core electrophore. Whereas the relatively open dendritic branches in 4 · Fecl do not impede access of bulk solvent to the central core, the densely packed dendritic superstructure of 5 · FeCl significantly reduces contact between the heme and external solvent. As a result, the more charged Fe^III state is destabilized relative to Fe^II, and the redox potential is strongly shifted to a more positive value.     

Spectroelectrochemistry on electroactive self-assembled monolayers: Cyclic voltammetry coupled to spectrophotometry

We present a spectroelectrochemical bench involving an electrochemical/spectrophotometric coupling dedicated to probe electroactive self-assembled monolayers (SAMs). This bench is validated by the study of the oxidation of a 5,5′-disubstituted-2,2′-bithiophene immobilized on Au substrate, producing a reversible dimerization of the radical cation (i.e. EC_Dim process) leading to a dimer. A direct comparison between thin layer spectroelectrochemistry in solution and spectroelectrochemistry on SAMs shows that a SAM could be viewed as a highly concentrated solution.     

Charge heterogeneity of surfaces: mapping and effects on surface forces

The DLVO theory treats the total interaction force between two surfaces in a liquid medium as an arithmetic sum of two components: Lifshitz–van der Waals and electric double layer forces. Despite the success of the DLVO model developed for homogeneous surfaces, a vast majority of surfaces of particles and materials in technological systems are of a heterogeneous nature with a mosaic structure composed of microscopic and sub-microscopic domains of different surface characteristics. In such systems, the heterogeneity of the surface can be more important than the average surface character. Attractions can be stronger, by orders of magnitude, than would be expected from the classical mean-field DLVO model when area-averaged surface charge or potential is employed. Heterogeneity also introduces anisotropy of interactions into colloidal systems, vastly ignored in the past. To detect surface heterogeneities, analytical tools which provide accurate and spatially resolved information about material surface chemistry and potential — particularly at microscopic and sub-microscopic resolutions — are needed.Atomic force microscopy (AFM) offers the opportunity to locally probe not only changes in material surface characteristic but also charges of heterogeneous surfaces through measurements of force–distance curves in electrolyte solutions. Both diffuse-layer charge densities and potentials can be calculated by fitting the experimental data with a DLVO theoretical model. The surface charge characteristics of the heterogeneous substrate as recorded by AFM allow the charge variation to be mapped. Based on the obtained information, computer modeling and simulation can be performed to study the interactions among an ensemble of heterogeneous particles and their collective motions. In this paper, the diffuse-layer charge mapping by the AFM technique is briefly reviewed, and a new Diffuse Interface Field Approach to colloid modeling and simulation is briefly discussed.     

Insight into heme protein redox potential control and functional aspects of six-coordinate ligand-sensing heme proteins from studies of synthetic heme peptides

We describe detailed studies of peptide-sandwiched mesohemes PSMA and PSMW, which comprise two histidine (His)-containing peptides covalently attached to the propionate groups of iron mesoporphyrin II. Some of the energy produced by ligation of the His side chains to Fe in the PSMs is invested in inducing helical conformations in the peptides. Replacing an alanine residue in each peptide of PSMA with tryptophan (Trp) to give PSMW generates additional energy via Trp side chain-porphyrin interactions, which enhances the peptide helicity and stability of the His-ligated state. The structural change strengthened His-FeIII ligation to a greater extent than His-FeII ligation, leading to a 56-mV negative shift in the midpoint reduction potential at pH 8 (Em,8 value). This is intriguing because converting PSMA to PSMW decreased heme solvent exposure, which would normally be expected to stabilize FeII relative to FeIII. This and other results presented herein suggest that differences in stability may be at least as important as differences in porphyrin solvent exposure in governing redox potentials of heme protein variants having identical heme ligation motifs. Support for this possibility is provided by the results of studies from our laboratories comparing the microsomal and mitochondrial isoforms of mammalian cytochrome b5. Our studies of the PSMs also revealed that reduction of FeIII to FeII reversed the relative affinities of the first and second His ligands for Fe (K2III > K1III; K2II < K1II). We propose that this is a consequence of conformational mobility of the peptide components, coupled with the much greater ease with which FeII can be pulled from the mean plane of a porphyrin. An interesting consequence of this phenomenon, which we refer to as "dynamic strain", is that an exogenous ligand can compete with one of the His ligands in an FeII-PSM, a reaction accompanied by peptide helix unwinding. In this regard, the PSMs are better models of neuroglobin, CooA, and other six-coordinate ligand-sensing heme proteins than of stably bis(His)-ligated electron-transfer heme proteins such as cytochrome b5. Exclusive binding of exogenous ligands by the FeII form of PSMA led to positive shifts in its Em,8 value, which increases with increasing ligand strength. The possible relevance of this observation to the function of six-coordinate ligand-sensing heme proteins is discussed.     

Electron transfer of heme proteins on the ITO electrode in polymer solvents

The redox reaction of poly(ethylene oxide) (PEO)-modified hemoglobin (PEO–Hb) was analyzed in PEO oligomers with cyclic voltammetry. The PEO–Hb was made soluble in PEO with molecular weight of 200 (PEO₂₀₀) containing 0.5 M KCI. Quasi-reversible redox signals of PEO–Hb were obtained by using an indium tin oxide (ITO) glass working electrode. PEO–Hb, cast on the ITO electrode, also showed the redox response in PEO with molecular weight of 400 (PEO₄₀₀). The peak current of PEO–Hb on the ITO electrode gradually increased during potential cycling. The effect of the scan rate on the quantity of electricity (Q) was analyzed after the peak current reached a constant value. The constant Q value was observed at the scan rate ranging from 30 to 500 mV/sec. The number of reactive PEO–Hb molecules was estimated from this constant Q-value. It was suggested that the electron transfer was carried out at the first layer of the PEO–Hb which was in direct contact with the ITO electrode. The quantity of electricity of PEO–Hb increased when the ITO electrode was first washed in an aqueous medium with ultrasonicator. This strongly suggested that the more effective surface area of the ITO electrode turned to be covered with PEO–Hb when the microporous region of the ITO particles was more hydrated.     

Modelling of solid-liquid adsorption: effects of adsorbent heterogeneity

Effects of adsorbent heterogeneity on the adsorption of cobalt phthalocyanine dye on activated carbon have been studied. Adsorption experiments were carried out by varying the temperature and adsorbent mass in batch adsorbers and, in addition, the adsorbent particle size and fluid flow rate in a continuous stirred tank reactor (CSTR)-type adsorber in order to investigate the equilibrium and the kinetics of adsorption.The Brunauer-Emmett-Teller (BET), Langmuir with uniform distribution (LUD) and Langmuir-Freundlich equations are able to represent the equilibrium data with similar accuracy within the range of measurements. Reasonably large values of the heterogeneity parameter (2.69–2.86) show that the carbon surface is energetically heterogeneous.A mathematical model that describes the adsorption dynamics, including film-, pore- and concentration-dependent surface diffusion on an energetically and structurally heterogeneous adsorbent, is presented here and fitted to the experimental concentration vs. time curves obtained in the continuously stirred tank adsorber.Structural heterogeneity of the carbon, if not accounted for in the kinetic model, can be responsible for the very strong concentration dependence of the surface diffusion coefficient and for the variation in the parameter D_o with particle size and adsorber porosity as shown in this work.     

Comparative effects of curcuminoids on endothelial heme oxygenase-1 expression: ortho-methoxy groups are essential to enhance heme oxygenase activity and protection

Recently, it has been reported that curcumin, which is known as a potent antioxidant, acts as a non- stressful and non-cytotoxic inducer of the cytoprotective heme oxygenase (HO)-1. In this study, naturally occurring curcuminoids, such as pure curcumin, demethoxycurcumin (DMC) and bis-demethoxycurcumin (BDMC), were compared for their potential ability to modulate HO-1 expression and cytoprotective activity in human endothelial cells. All three curcuminoids could induce HO-1 expression and HO activity with differential levels. The rank order of HO activity was curcumin, DMC and BDMC. In comparison with endothelial protection against H2O2-induced cellular injury, cytoprotective capacity was found to be highest with curcumin, followed by DMC and BDMC. Interestingly, cytoprotective effects afforded by curcuminoids were considerably associated with their abilities to enhance HO activity. Considering that the main difference among the three curcuminoids is the number of methoxy groups (none for BDMC, one for DMC, and two for curcumin), the presence of methoxy groups in the ortho position on the aromatic ring was suggested to be essential to enhance HO-1 expression and cytoprotection in human endothelial cells. Our results may be useful in designing more efficacious HO-1 inducers which could be considered as promising pharmacological agents in the development of therapeutic approaches for the prevention or treatment of endothelial diseases caused by oxidative damages.     

Direct electrochemistry of heme proteins: effect of electrode surface modification by neutral surfactants

Direct electrochemical studies on horse heart myoglobin and horseradish peroxidase (HRP) have been carried out using tin-doped indium oxide (ITO) and surfactant modified glassy carbon working electrodes. These proteins show very slow electron transfer kinetics at metal or untreated electrodes. Moreover, small amounts of surface-active impurity were drastically affects the electrode reaction of these proteins. The results showed that modification of the electrode surface with neutral surfactants significantly improves the electrochemical response of myoglobin as well as of HRP. The electrode response was found to depend on the structure of the surfactants. The amount of surfactant required per unit area of the electrode surface to promote the maximum electron transfer rate constants was found to be constant. This indicated that the surfactant molecules interacted with the electrode surface in a specific manner and anchored the protein molecules to align in the suitable orientation. The hydrophobicity of the surfactants rather than their charge was found to be crucial in promoting the electrode response of these proteins at the glassy carbon electrode.     

Conformational heterogeneity and low-frequency vibrational modes of proteins

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm(-1)) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.