High pressure reveals that the stability of interdimeric contacts in the R- and T-state of HbA is influenced by allosteric effectors: Insights from computational simulations.

The molecular details of the mechanism of action of allosteric effectors on hemoglobin oxygen affinity are not clearly understood. The global allostery model proposed by Yonetani et al. suggests that the binding of allosteric effectors can take place both in the R and T states and that they influence oxygen affinity through inducing global tertiary changes in the subunits. Recently published high pressure studies yielded dissociation constants at atmospheric pressure that showed a stabilizing effect of heterotropic allosteric effectors on the dimer interface in the R state, and a more pronounced destabilizing effect in a T state model. In the present work, we report on computational modeling used to interpret the high pressure experimental data. We show structural changes in the hemoglobin interdimeric interfaces, indicative of a global tertiary structural change induced by the binding of allosteric effectors. We also show that the number of water molecules bound at the interface is significantly influenced by binding effectors in the T state in accordance with the experimental data. Our results suggest that the binding of effectors at definite sites leads to tertiary changes that propagate to the interfaces and results in overall structural re-organizations.

Flash photolysis study of ligand binding by modified myoglobins at low temperatures.

The CO-binding kinetics of myoglobin containing proto-, meso- and deutero-hemes were studied by flash photolysis over the temperature range 50-300 K. Results recorded over a large dynamic range of time (microseconds to many seconds) reveal processes that are non-exponential in time and multiphasic. The data are explained by a model in which the CO molecule must surmount four barriers in migrating from the solvent to the heme iron. At least two of these barriers have heights that vary from one molecule to another. Varying the nature of the heme group affects mainly the innermost of these barriers and, to a lesser degree, the second-outermost barrier.

Resonance Raman spectra of cytochrome oxidase. Evidence for photoreduction by laser photons in resonance with the Soret band.

Resonance Raman spectra of cytochrome oxidase solubilized in Tween 20 and sodium cholate, and excited at 413.1 nm have been recorded. Differences in the resonance Raman spectra of the two preparations are minimal indicating that the local environment of the hemes is similar in the two preparations. As in the work of Salmeen, et al. (1973) (Biochem. Biophys. Res. Commun. 52, 1100) the strongest band appears at 1358 cm-1. Some of the other bands differ slightly in their band shapes and frequencies when compared to their spectra; these differences can be accounted for by differences in resonance enhancement of the various bands wnen exciting at 441.6 and 413.1 nm. A study of the region from 1350 to 1380 cm-1 as a function of laser intensity (10--130 mW on sample) indicate that the doublet reported by Salmeen, et al. at 1358 and 1372 cm-1 is a result of photoreduction of the preparations. In samples to which potassium ferricyanide had been added, broad luminescence bands appear at 476 and 641 nm from which it is inferred that catalytic amounts of flavin in the preparations are photoreduced providing reducing equivalents to cytochrome oxidase.

Study of cytochrome oxidase co-binding site using low-temperature flash photolysis.

Flash photolysis has been used to study the kinetics of CO-binding to the heme alpha isolated cytochrome oxidase. Experiments performed over the range 185-295 degrees K with various CO concentrations have revealed significant deviations from the Arrhenius relationship between rate and temperature. These findings can be explained by a model in which the heme site is considered to have three regions between which CO can move; only from the innermost one can binding to the heme iron take place. The relative enthalpies and entropies of the three regions are calculated.

Low-temperature flash photolysis studies of cytochrome oxidase and its environment.

The CO-binding kinetics of cytochrome a3, in isolated, detergent-solubilized cytochrome oxidase have been studied by flash photolysis over wide ranges of CO concentration and temperature. The results strongly suggest that CO has an intermediate bound state in its path to the final bound state at the heme iron. In the temperture range 230-273 K in frozen aqueous solutions, the recombination rates depend upon CO concentration; at low CO concentrations the kinetics are biphasic. The rate of the faster process depends upon the detergent concentration, that of the slower process upon the salt concentration. In addition, the faster process depends upon the amount of CO photodissociated. It is concluded that the cytochrome oxidase molecules are aggregated in regions that contain detergent and possibly some lipids. The regions retain considerable fluid character well below the macroscopic freezing point of the solution. The faster phase of the recombination is interpreted as the rebinding of CO molecules that remain in the fluid region after photodissociation. The slower phase would then be due to the migration of some dissociated CO out into surrounding frozen solvent. The non-Arrhenius behavior of both phase probably represents partial melting of the medium; preliminary NMR measurements of mobile protons support this hypothesis. Many of the kinetic features described here are also seen in mitochondria; thus the detergent-solubilized cytochrome oxidase may be a useful model system for the ligand-binding behavior of the enzyme in the mitochondrial membrane.

Steady-state kinetics of yeast cytochrome c peroxidase catalyzed oxidation of inorganic reductants by hydrogen peroxide.

Rates of yeast cytochrome c peroxidase (ferrocytochrome c:hydrogen-peroxide oxidoreductase, EC 1.11.1.5) catalyzed oxidation of bis(tripyridine)cobalt(II) ion, penta(amine)pyridineruthenium(II) ion and ferrocyanide ion by hydrogen peroxide have been found to obey the empirical equation: (formula; see text) in the pH range 5 to 8, and at saturating H2O2 concentrations. [( S] and [CcP] are the concentrations of the reductant and the enzyme, respectively.) Values of k2 were found to be independent of the reductant. The term k0[S] is only significant with the cobalt and ruthenium complexes at high pH. The mechanism proposed to account for this rate equation differs significantly from previous mechanistic proposals. In particular, the rate data require the assignment of the rate-limiting step at high substrate concentrations to a slow electron-transfer within the enzyme, and not, as previously suggested, to saturation of substrate binding to the enzyme. Also, the term k0[S] implies that the reactive substrates, including the natural substrate (yeast cytochrome c), react with the hydrogen peroxide-heme complex and not with the radical species formed by reaction with hydrogen peroxide in the absence of reductants.

Mössbauer spectroscopic study of compound ES of cytochrome c peroxidase.

Mössbauer spectra of Compound ES of cytochrome c peroxidase have been observed over a range of temperature and applied magnetic field. These have been interpreted in terms of a crystal field model of the iron site in which the iron is assumed to be in the Fe(IV) state with unpaired spin S = 1. Detailed least-squares fitting of the spectra fitting of the spectra indicates that both the electric field gradient choice of a single parameter, the axial crystal field, the magnetic properties are well reproduced. The model also provides the observed positive sign for the electric field gradient interaction, but overestimates its magnitude. This apparent discrepnancy may be caused by the presence of significant electronic charge in filled bonding orbitals, a feature which is in keeping with expected covalent charge compensation of the extreme oxidation state. There is no evidence in the Mössbauer spectra of interaction between the iron and the ESR-visible free radical. This suggests they are well separated.

The oxidation of cytochrome c peroxidase by hydrogen peroxide. Characterization of products.

H2O2 reacts with cytochrome c peroxidase in a variety of ways. The initial reaction produces cytochrome c peroxidase Compound I. If more than a 10-fold excess of H2O2 is added to the enzyme, a portion of the H2O2 will react with Compound I to produce molecular oxygen. The remainder oxidizes the heme group and various amino acid residues in the protein. If less than a 10-fold excess of H2O2 is added to the enzyme, essentially all the H2O2 is utilized by oxidation of amino acid residues in the protein. The oxidation of the amino acid residues by H2O2 substantially modifies the reactivity of cytochrome c peroxidase. The modification of reactivity could be the direct result of amino acid oxidation or an indirect result caused by a perturbation of the protein structure at the active site. The products oxidized at pH 8 lose their ability to react with H2O2. The products oxidized at pH4 react with H2O2 but their reactivity toward Fe(CN)4-6 is substantially reduced.

A kinetic study of the endogenous reduction of the oxidized sites in the primary cytochrome c peroxidase-hydrogen peroxide compound.

The primatry compound formed in the reaction between H2O2 and cytochrome c peroxidase is oxidized two equivalents above the native enzyme. The two oxidized sites are thought to be an Fe(IV) and an amino acid radical. In the absence of oxidizable substrate, the Fe(IV) and radical sites decay by apparent first-order processes but at different rates. It is likely that the decay involves both intra- and intermolecular electron-transfer reactions. The reduction of the Fe(IV) site depends upon the pH with a minimum reduction rate of 2.9-10(-5)s(-1) at pH 6. At pH 4 and 6, the reduction of the Fe(IV) site is facilitated by prior oxidation of amino acid residues in the protein.

Low temperature photodissociation studies of ferrous hemoglobin and myoglobin complexes by Mössbauer spectroscopy.

57Fe-enriched complexes of hemoglobin and myoglobin with CO and O2 were photodissociated at 4.2 degrees K, and the resulting spectra were compared with those of the deoxy forms. Differences in both quadrupole splitting and isomer shift were noted for each protein, the photoproducts having smaller isomer shift and larger quadrupole splitting than the deoxy forms. The photoproducts of HbCO and HbO2 had narrow absorption lines, indicating a well-defined iron environment. The corresponding myoglobin species had broader absorption lines, as did both deoxy forms. The weak absorption lines of photodissociated NO complexes appeared to be wide, possibly indicating magnetic interaction with the unpaired electron of the nearby NO.

Electron paramagnetic resonance and spectrophotometric studies of the peroxide compounds of manganese-substituted horseradish peroxidase, cytochrome-c peroxidase and manganese-porphyrin model complexes.

Peroxide compounds of manganese protoporphyrin IX and its complexes with apo-horseradish peroxidase and apocytochrome-c peroxidase were characterized by electronic absorption and electron paramagnetic resonance spectroscopies. An intermediate formed upon titration of Mn(III)-horseradish peroxidase with hydrogen peroxide exhibited a new electron paramagnetic resonance absorption at g = 5.23 with a definite six-lined 55Mn hyperfine (AMn = 8.2 mT). Neither a porphyrin pi-cation radical nor any other radical in the apoprotein moiety could be observed. The reduced form of Mn-horseradish peroxidase, Mn(II)-horseradish peroxidase, reacted with a stoichiometric amount of hydrogen peroxide to form a peroxide compound whose electronic absorption spectrum was identical with that formed from Mn(III)-horseradish peroxidase. The electronic state of the peroxide compound of manganese horseradish peroxidase was thus concluded to be Mn(IV), S = 3/2. Mn(III)-cytochrome-c peroxidase reacted with stoichiometry quantities of hydrogen peroxide to form a catalytically active intermediate. The electronic absorption spectrum was very similar to that of a higher oxidation state of manganese porphyrin, Mn(V). Since the peroxide compound of manganese cytochrome-c peroxidase retained two oxidizing equivalents per mol of the enzyme (Yonetani, T. and Asakura, T. (1969) J. Biol. Chem. 244, 4580-4588), this peroxide compound might contain an Mn(V) center.

Oxygenation and EPR spectral properties of Aplysia myoglobins containing cobaltous porphyrins.

Cobalt myoglobins (Aplysia) have been reconstituted from apo-myoglobin (Aplysia) and proto-, meso-, and deutero-cobalt porphyrins. Each of them showed the 30--60 times lower oxygen affinity than those of the corresponding cobalt myoglobins (Sperm whale). Kinetic investigation of their oxygenation by the temperature-junp relaxation technique showed that the low oxygen affinity of cobalt myoglobin (Aplysia) is due to a large dissociation rate constant. the electron paramagnetic resonance (EPR) spectrum of oxy cobalt myoglobin (Aplysia) is affected by the replacement of H2O with D2O, suggesting a possible interaction between the bound oxygen and the neighboring hydrogen atom. A low temperature photodissociation study showed that the product of photolysis of oxy cobalt myoglobin (Aplysia) gives an EPR spectrum different from that of the deoxy-cobalt myoglobin (Aplysia) and from that of the photolysed form of oxy-cobalt myogloin (Sperm whale). These observations suggest that in oxy-cobalt myoglobin (Aplysia) the bound oxygen might interact with amino acid adjacent to it, but the interaction is weaker than that in oxy cobalt myoglobin (Sperm whale).

Enzyme behaviour and molecular environment. The effects of ionic strength, detergents, linear polyanions and phospholipids on the pH profile of soluble cytochrome oxidase.

The activity vs. pH profile for the oxidation of ferrocytochrome c by purified cytochrome oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) was investigated as a function of ionic strength (from 10 to 200 mM) in the absence and in the presence of various perturbants: Tween 20, linear polyanions (RNA, heparin, polyglutamic acid) and phospholipids (asolectin, phosphatidylcholine, phosphatidic acid and cardiolipin). The activation induced by Tween 20 and "zero net charge" phospholipid liposomes was not pH dependent. On the other hand, linear polyanions and polyanionic liposomes strongly perturbed the pH profile, mostly at low ionic strength, by shifting the pH optimum about 1.7 pH units towards alkaline pH values. This effect was reversed by increasing ionic strength. These observations are interpreted in the light of polyelectrolyte theory. Since these results show striking with membrane-bound enzyme, it is concluded that in vivo cytochrome oxidase is located within polyanionic sites of the micochondrial membrane. The activation broght about by phospholipids may result from two posible processes: creation of a hydrophobic environment by the non-polar tails, preventing autoaggregation; and creation of a suitable polyelectrolytic environment by the polar heads (of non zero net charge), increasing the intrinsic reaction rate.

Mössbauer investigation of deoxymyoglobin in a high magnetic field. Orientation of the electric field gradient and magnetic tensors.

We have examined the Mössbauer spectra of deosymyoglobin in a 6 T magnetic field in the temperature range 4.2-195 K. Spectra were fitted by the least-squares method using a phenomenological model in which the internal magnetic hyperfine field was assumed to be related to the applied field by a temperature dependent tensor õmega. The results indicate that õmega has axial symmetry and a principal axis system aligned with that of the electric field gradient (efg). The principal component of the latter is negative and lies on the symmetry axis of õmega. Our fits indicate that of efg asymmetry parameter is eta = 0.7, with no appreciable temperature dependence. Both axial and transverse components of õmega have the expected 1/T temperature dependence for T greater than 20 K. Our experimentally determined value of eta, combined with published single crystal zero-field measurements, constrains the efg-heme relative orientation to two possibilities. In neither of these is an efg principal axis near to the heme normal.

The formation of ES of cytochrome-c peroxidase: a comparison with lactoperoxidase and horseradish peroxidase.

The activation energy for the formation of the first red compound, ES, for cytochrome-c peroxidase (ferrocytochrome-c: hydrogen-peroxide oxidoreductase, EC 1.11.1.5) by i-propyl hydroperoxide and the rate constants for the formation of ES with various hydroperoxides have been determined. Multivariate data analysis by the partial least-squares model in latent variables has been used to compare the rate constants with the corresponding rate constants for the formation of compound I from lactoperoxidase and two isoenzymes of horseradish peroxidase. The results show that the rate of formation of ES from cytochrome-c peroxidase is highly correlated with the pKa of the hydroperoxides. The activation energy for the formation of ES with i-propyl hydroperoxide is close to the corresponding value for hydrogen peroxide.

Light absorption, electron paramagnetic resonance and resonance Raman characteristics of nitridochromium(V) protoporphyrin-IX and its reconstituted hemoproteins.

A surprisingly stable complex of the photolyzed product of azidochromium(III)protoporphyrin-IX was prepared and examined by light absorption, electron paramagnetic resonance (EPR) and resonance Raman spectroscopies. The characteristic EPR spectrum for this complex was consistent with a nitridochromium(V)-porphyrin complex which was two oxidation equivalents above the resting Cr(III) complex. The Cr(V)-N stretching mode was observed at 1010 cm-1 by resonance Raman spectroscopy. A simple diatomic harmonic oscillation model gave a force constant of 6.7 mdyn/A for the Cr(V)-N bond, in the region characteristic for the metal-nitrogen triple bond. Nitridochromium(V) protoporphyrin-IX reconstituted myoglobin and cytochrome c peroxidase were prepared for the first time. The nitridochromium(V)-porphyrins in these apo-proteins were unstable in contrast with the protein-free chromium(V)porphyrin. Upon irradiation of the azide complexes of the chromium(III) protoporphyrin-IX reconstituted myoglobin and cytochrome c peroxidase with ultraviolet light aerobically at room temperature, the characteristic optical and EPR spectra for nitridochromium(V) derivatives were observed. The optical spectra of these photo-induced products were different from those of the nitridochromium(V) protoporphyrin-IX reconstituted hemoproteins. The electrochemical structures of the unusual metalloporphyrin seemed to be modulated by the heme surrounding amino acid residues.

High magnetic field Mössbauer studies of deoxymyoglobin, deoxyhemoglobin, and synthetic analogues.

Mössbauer spectra of deoxymyoglobin, deoxyhemoglobin, and the synthetic analogues, iron (II) 2-methylimidazole meso-tetraphenylporphyrin, and iron (II) 1,2-dimethylimidazole meso-tetraphenylporphyrin have been observed in high magnetic fields and over a wide range of temperature. At temperatures greater than 20 K all materials exhibit remarkably similar spectra, with anisotropic internal magnetic fields decreasing as 1/T. All have negative quadrupole interaction, and both this and the magnetic anisotropy imply that the orbital of the odd electron is prolate in the ground quintet, with little unquenched orbital angular momentum. At 4.2 K the spectra differ, suggesting different detailed structure within the quintet. In contrast to the proteins, the 2-methyl model exhibits spectra at 4.2 K which imply that the lowest spin state has high susceptibility in a single direction.

Studies on Scapharca hemoglobins. Properties of the dimeric protein reconstituted with Fe- or Co-porphyrin.

A native globin from the dimeric hemoglobin, hemoglobin I, of the mollusc Scapharca inaequivalvis has been obtained with the acid-acetone method. The globin has a lower sedimentation coefficient than the native protein at neutral pH; its reconstitution product with natural heme has the same physicochemical and functional properties as the native protein. proto- and meso-cobalt hemoglobin I have been prepared and characterized. proto-Cobalt hemoglobin I binds oxygen reversibly with a lower affinity and a lower cooperativity than native hemoglobin I; thus, the changes in the functional properties brought about by substitution of iron with cobalt are similar to those observed in human hemoglobin A. The EPR spectra of deoxy-proto-cobalt hemoglobin I and of the photolysis product of oxy-meso-cobalt hemoglobin I indicate that two histidine residues are the apical heme ligands. The broad signal at g = 2.38 in deoxy-proto-cobalt hemoglobin I points to a constrained structure of the heme site in this derivative which results from a distorted coordination of the hindered proximal histidine. A similar structure has been proposed previously for the alpha chains in deoxy-cobalt hemoglobin A.

The nature of the copper atoms of cytochrome c oxidase as studied by optical and x-ray absorption edge spectroscopy.

X-ray absorption edge spectroscopy has been used to study the copper of 1--2 mM cytochrome c oxidase in the resting oxidized, mixed-valence, and fully reduced states. A comparison was made of this protein with copper complexes and with natural and artificial copper proteins. Spectra were obtained with synchrotron radiation from the SPEAR storage ring using highly sensitive fluorescence detectors. Temperatures of -80 to -120 degrees C were employed further to improve the stability of the samples and to avoid the possibility of either auto- or photon-induced reduction of the materials, which might have occurred in previous studies. In order to characterize the valence states of the Cu and Fe components, the samples were monitored by infrared and visible spectroscopy before and after irradiation by the X-ray beam. The combination of the optical and X-ray absorption techniques has afforded a deconvolution of the four species of copper in the various states of cytochrome c oxidase and the tentative assignment of Cu alpha, the copper redox coupled to the heme alpha of cytochrome alpha, as a highly covalent type of copper and Cu alpha 3, the copper of cytochrome alpha 3, as a more ionic 'blue' type I copper. The implications of these findings upon the mechanism of action of cytochrome oxidase are briefly outlined.

Transient kinetics of oxygen dissociation from ferrous subunits of iron-cobalt hybrid hemoglobins. The principal reaction controlling the co-operativity.

The oxygen dissociation constants from Fe subunits in the half-ligated intermediate states of Fe-Co hybrid hemoglobins, alpha(Fe-O2)2 beta(Co)2 and alpha(Co)2 beta(Fe-O2)2, have been determined as functions of pH, temperature and inositol hexaphosphate. The oxygen dissociation rates from alpha(Fe-O2)2 beta(Co)2 are estimated to be more than 1300 s-1 for the deoxy quaternary state (T-state) and less than 3 s-1 for the oxy quaternary state (R-state) at 15 degrees C in 50 mM-Tris or Bis-Tris buffer containing 0.1 M-Cl-, while those of alpha(Co)2 beta(Fe-O2)2 are more than 180 s-1 and less than 5 s-1 for the T and R-states, respectively. The pH dependence of the oxygen dissociation rate from Fe subunits is large enough to be accounted for by the R-T transition, and implies that those half-ligated intermediate hybrids mainly exist in the R-state at pH 8.8, and in the T-state at pH 6.6, while other studies indicated that the half-ligated hybrids are essentially in the R-state at pH 7. Large activation energies of the oxygen dissociation process of 19 to 31 kcal/mol determined from the temperature dependence suggest that the process is entropy-driven.