Electron self-exchange in Pseudomonas cytochromes

Heme crevice disorder after sixth ligand displacement in the cytochrome c-551 family

1H NMR and visible absorption spectroscopy were used to monitor sixth ligand methionine displacement reactions in four members of the ferricytochrome c-551 family from Pseudomonas aeruginosa, Pseudomonas stutzeri, Pseudomonas stutzeri substrain ZoBell, and Nitrosomonas europae. Potassium cyanide displaces the methionine ligand with very modest changes in the visible spectra, but profound changes in the NMR spectra. The initial product formed kinetically, designated complex I, changes with time and/or heating to a more thermodynamically favored product termed complex II. Spectra indicate that both I and II are actually a family of closely related conformational isomers. Low temperature NMR spectra of complex II indicate that some of the isomers are in chemical exchange on the NMR time scale. High pH also displaces the methionine ligand in a manner similar to the well-known alkaline transition of mitochondrial cytochrome c. However, the reaction occurs at higher pH values and over a narrower pH range for the c-551 family, and the transition pH range is different for the different proteins studied. The final alkaline forms also show peak widths and a number of peaks indicative of multiple conformational isomers.

Active-site structure and electron-transfer reactivity of plastocyanins

The active-site structures of Cu(II) plastocyanins (PCu's) from a higher plant (parsley), a seedless vascular plant (fern, Dryopteris crassirhizoma), a green alga (Ulva pertusa), and cyanobacteria (Anabaena variabilis and Synechococcus) have been investigated by paramagnetic (1)H NMR spectroscopy. In all cases the spectra are similar, indicating that the structures of the cupric sites, and the spin density distributions onto the ligands, do not differ greatly between the proteins. The active-site structure of PCu has remained unaltered during the evolutionary process. The electron transfer (et) reactivity of these PCu's is compared utilizing the electron self-exchange (ESE) reaction. At moderate ionic strength (0.10 M) the ESE rate constant is dictated by the distribution of charged amino acid residues on the surface of the PCu's. Most higher plant and the seedless vascular plant PCu's, which have a large number of acidic residues close to the hydrophobic patch surrounding the exposed His87 ligand (the proposed recognition patch for the self-exchange process), have ESE rate constants of approximately 10(3) M(-)(1) s(-)(1). Removal of some of these acidic residues, as in the parsley and green algal PCu's, results in more favorable protein-protein association and an ESE rate constant of approximately 10(4) M(-)(1) s(-)(1). Complete removal of the acidic patch, as in the cyanobacterial PCu's, leads to ESE rate constants of approximately 10(5)-10(6) M(-)(1) s(-)(1). The ESE rate constants of the PCu's with an acidic patch also tend toward approximately 10(5)-10(6) M(-)(1) s(-)(1) at higher ionic strength, thus indicating that once the influence of charged residues has been minimized the et capabilities of the PCu's are comparable. The cytochromes and Fe-S proteins, two other classes of redox metalloproteins, also possess ESE rate constants of approximately 10(5)-10(6) M(-)(1) s(-)(1) at high ionic strength. The effect of the protonation of the His87 ligand in PCu(I) on the ESE reactivity has been investigated. When the influence of the acidic patch is minimized, the ESE rate constant decreases at high [H(+)].

Solution Conformation of the Met 61 to His 61 Mutant of Pseudomonas stutzeri ZoBell Ferrocytochrome c-551

The gene encoding for bacterial cytochrome c-551 from Pseudomonas stutzeri substrain ZoBell has been mutated to convert the invariant sixth ligand methionine residue into histidine, creating the site-specific mutant M61H. Proton NMR resonance assignments were made for all main-chain and most-side chain protons in the diamagnetic, reduced form at pH 9.2 and 333 K by two-dimensional NMR techniques. Distance constraints (1074) were determined from nuclear Overhauser enhancements and main-chain torsion-angle constraints (72) from scalar coupling estimates. Solution conformations for the protein were computed by the simulated annealing approach. For 28 computed structures, the root mean squared displacement from the average structure excluding the terminal residues 1, 2, 81, and 82 was 0.52 A (sigma = 0.096) for backbone atoms and 0.90 A (sigma = 0.122) for all heavy atoms. The global folding of the mutant protein is the same as for wild type. The biggest changes are localized in a peptide span over residues 60-65. The most striking behavior of the mutant protein is that at room temperature and neutral pH it exists in a state similar to the molten globular state that has been described for several proteins under mild denaturing conditions, but the mutant converts to a more ordered state at high pH and temperature.

Electron transfer properties of iron-sulfur proteins

The details of most electron transfer reactions involving iron-sulfur proteins have remained undisclosed because of the lack of experimental methods suitable to measure precisely the relevant rates. Nuclear magnetic resonance (NMR) provides a powerful means to overcome these problems, at least with selected proteins. A combination of NMR studies and site-directed mutagenesis experiments has been instrumental in defining both the site of interaction and the main trends of the intracomplex electron transfer in the case of rubredoxin electron self-exchange. Analysis of the NMR data obtained for mixtures of different redox levels of several 2[4Fe-4S] ferredoxins provided both first-order, for intramolecular, and second-order, for intermolecular, rate constants. Their dependence as a function of structural changes gave insight into the mechanism of electron transfer in this type of protein. Contrary to some expectations, the high-spin [4Fe-4Se]+ clusters assembled in isopotential ferredoxins do not change the intramolecular electron transfer rate as compared to low-spin [4Fe-4S]+ homologs. In combination with activity measurements, the kinetic data have been used to model the electron transfer competent complexes between Clostridium pasteurianum ferredoxin and the main enzymes acting as redox partners in vivo.

Solution conformation of ferricytochrome c-551 from Pseudomonas stutzeri substrain ZoBell

The main chain protons and the majority of side chain protons have been assigned for the ferric form of Pseudomonas stutzeri substrain ZoBell (American Type Culture Collection 14405) cytochrome c-551. The chemical shifts were compared to those for the ferrous protein to determine the pseudocontact shift contribution. These observed values were compared to contributions calculated from the atomic coordinates of the ferrous cytochrome and an optimized effective room temperature g-tensor centered on the paramagnetic ferric iron. The agreement between observed and calculated values indicates that the conformations of the two forms are highly similar.

Primary sequence and solution conformation of ferrocytochrome c-552 from Nitrosomonas europaea

Cytochrome c-552 from Nitrosomonas europaea is a 9.1-kDa monoheme protein that is a member of the bacterial cytochrome c-551 family. The gene encoding for c-552 has been cloned and sequenced and the primary sequence of the product deduced. Proton resonance assignments were made for all main-chain and most side-chain protons in the diamagnetic, reduced form by two-dimensional NMR techniques. Distance constraints (1056) were determined from nuclear Overhauser enhancements, and torsion angle constraints (88) were determined from scalar coupling estimates. Solution conformations for the protein were computed by the hybrid distance geometry-simulated annealing approach. For 20 computed structures, the root mean squared deviation from the average position of equivalent atoms was 0.84 A (sigma = 0.12) for backbone atoms over all residues. Analysis by residue revealed there were three regions clearly less well defined than the rest of the protein: the first two residues at the N-terminus, the last two at the C-terminus, and a loop region from residues 34 to 40. Omitting these regions from the comparison, the root mean squared deviation was 0.61 A (sigma = 0.13) for backbone atoms, 0.86 A (sigma = 0.12) for all associated heavy atoms, and 0. 43 A (sigma = 0.17) for the heme group. The global folding of the protein is consistent with others in the c-551 family. A deletion at the N-terminus relative to other family members had no impact on the global folding, whereas an insertion at residue 65 did affect the way the polypeptide packs against the methionine-ligated side of the heme. The effects of specific substitutions will be discussed. The structure of c-552 serves to delineate essential features of the c-551 family.

Electron-transfer properties of Pseudomonas aeruginosa [Lys44, Glu64]azurin

In the hydrophobic patch of azurin from Pseudomonas aeruginosa, an electric dipole was created by changing Met44 into Lys and Met64 into Glu. The effect of this dipole on the electron-transfer properties of azurin was investigated. From a spectroscopic characterization (NMR, EPR and ultraviolet-visible) it was found that both the copper site and the overall structure of the [Lys44, Glu64]azurin were not disturbed by the two mutations. A small perturbation of the active site at high pH, similar to that observed for [Lys44]azurin, occurs in the double mutant. At neutral pH the electron-self-exchange rate constant of the double mutant shows a decrease of three orders of magnitude compared with the wild-type value. The possible reasons for this decrease are discussed. Electron transfer with the proposed physiological redox partners cytochrome c551 and nitrite reductase have been investigated and the data analyzed in the Marcus framework. From this analysis it is confirmed that the hydrophobic patch of azurin is the interaction site with both partners, and that cytochrome c551 uses its hydrophobic patch and nitrite reductase a negatively charged surface area for the electron transfer.

Redox reactivity of the type 1 copper protein amicyanin from Thiobacillus versutus with its physiological partner cytochrome C550 and inter-protein cross-reaction studies

Reduction potentials Eo' for the T. versutus amicyanin couple, AmCuII/I, were determined at pH values in the range 4.4-9.0 by direct measurement using cyclic voltammetry, and from rate constants for the reactions AmCu1 + [Co(terpy)2]3+ and [Co(terpy)2]2+ + AmCuII, using an Eo' for the [Co(terpy)2]2+/3+ couple of 260 mV. At pH > 7.5 the value obtained is 236 mV, which increases with decreasing pH in keeping with proton inactivation of AmCuI. Together with previously determined Eo' values for the T. versutus cytochrome C550 FeIII/FeII couple, it is concluded that the physiologically relevant reaction AmCuI + cyt C550FeIII (kf) is thermodynamically favourable at pH > 6.25, but that the back reaction cyt C550FeII + AmCuII (kb) is favourable at pH < 6.25. Values of kf (25 degrees C) at pH > 6.25 were determined directly by the stopped-flow method, I = 0.100 M (NaCl). At pH < 6.25 kf values were obtained indirectly from the measured kb and equilibrium constants from delta Eo'. The combined kf variations with pH give an acid dissociation pKa for AmCuIH+ of 6.6. In further studies (25 degrees C) rate constants/M-1 S-1 (pH 6.0-8.6) were determined for the cross-reactions of AmCuI with P. aeruginosa azurin AzCuII, and AmCuI with P. aeruginosa cyt C550FeIII, and are 11.0 x 10(5) and 6.4 x 10(5) M-1 S-1 respectively at pH 8.6. Using the Marcus equations corresponding electron self-exchange rate constants (kese/M-1 S-1) of 1.3 x 10(5) and 0.6 x 10(5) M-1 S-1 were calculated for the exchange of AmCuII with unprotonated AmCuI, in good agreement with the value 1.2 x 10(5) M-1 S-1 determined by NMR at pH 8.6. Information was also obtained as to the effect of pH on these kese values.

Possible Role of the Iron Coordination Sphere in Hemoprotein Electron Transfer Self-Exchange: (1)H NMR Study of the Cytochrome c-PMe(3) Complex

The rates of self-exchange electron transfer in the trimethylphosphine complex of cytochrome c have been measured by an NMR technique over a large range of ionic strengths. The rate constant is 1.56 x 10(4) M(-)(1) s(-)(1) at 23 degrees C (&mgr; = 0.34 M) at pH 6.9. Dependence on ionic strength of the rate constant is treated by van Leeuwen theory. Extrapolation of the rate constant to infinite ionic strength gives a rate constant of 3.9 x 10(5) M(-)(1) s(-)(1). This rate constant is compared with others reported for myoglobin and cytochrome b(5)(). The values for these systems range over 2 orders of magnitude with myoglobin-PMe(3) << cytochrome b(5)() < cytochrome c-PMe(3) < cytochrome c. Analysis of the data in terms of Marcus theory gives a reorganization energy, lambda, for self-exchange of 0.75 eV mol(-)(1) for cytochrome c-PMe(3). Substitution of Met-80 by PMe(3) appears to influence only weakly the rearrangement barrier to electron transfer.

Effects of charged amino acid mutations on the bimolecular kinetics of reduction of yeast iso-1-ferricytochrome c by bovine ferrocytochrome b5

The reduction of wild-type yeast iso-1-ferricytochrome c (ycytc) and several mutants by trypsin-solubilized bovine liver ferrocytochrome b5 (cytb5) has been studied under conditions in which the electron-transfer reaction is bimolecular. The effect of electrostatic charge modifications and steric changes on the kinetics has been determined by experimental and theoretical observations of the electron-transfer rates of ycytc mutants K79A, K'72A, K79A/K'72A, and R38A (K' is used to signify trimethyllysine (Tml)). A structurally robust Brownian dynamics (BD) method simulating diffusional docking and electron transfer was employed to predict the mutation effect on the rate constants. A realistic model of the electron-transfer event embodied in an intrinsic unimolecular rate constant is used which varies exponentially with donor-acceptor distance. The BD method quantitatively predicts rate constants over a considerable range of ionic strengths. Semiquantitative agreement is obtained in predicting the perturbing influence of the mutations on the rate constants. Both the experimentally observed rate constants and those predicted by BD descend in the following order: native ycytc > K79A > K'72A > K79A/K'72A. Variant R38A was studied at a different ionic strength than this series of mutations, and the theory agreed with experiment in predicting a smaller rate constant for the mutant. In all cases the predicted effect of mutation was in the correct direction, but not as large as that observed. The BD simulations predict that the two proteins dock through essentially a single domain, with a distance of closest approach of the two heme groups in rigid body docking typically around 12 A. Two predominant classes of complexes were calculated, the most frequent involving the quartet of cytb5/ycytc interactions, Glu48-Arg13, Glu56-Lys87, Asp60-Lys86, and heme-Tml72, having an average electrostatic energy of -13.0 kcal/mol. The second most important complexes were of the type previously postulated (Salemme, 1976; Mauk et al., 1986; Rodgers et al., 1988) with interactions Glu44-Lys27, Glu48-Arg13, Asp60-Tml72, and heme-Lys79 and having an energy of -6.4 kcal/mol. The ionic strength dependence of the bimolecular reaction rate was well reproduced using a discontinuous dielectric model, but poorly so for a uniform dielectric model.

Electron-transfer self-exchange kinetics of trimethylphosphine horse-heart myoglobin

Electron self-exchange has been measured by an NMR technique for horse-heart myoglobin. The rate is 3.1 x 10(3) M-1 s-1 at 23 degrees in 0.1 M phosphate at pH 6.9. The rate was weakly dependent on ionic strength up to 0.7 M in added KCl (3.9 x 10(3) M-1 s-1). The enthalpy of activation was 12.1 +/- 0.5 kcal mol-1, and the entropy of activation was -1.2 +/- 0.5 cal mol-1 deg-1. Analysis of the data in terms of the Marcus theory gives a reorganization energy, lambda, for self-exchange of 1.6 eV mol-1.

Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome C551 and nitrite reductase

The electron-transfer reactions of site-specific mutants of the blue copper protein azurin from Pseudomonas aeruginosa with its presumed physiological redox partners cytochrome c551 and nitrite reductase were investigated by temperature-jump and stopped-flow experiments. In the hydrophobic patch of azurin Met44 was replaced by Lys, and in the His35 patch His35 was replaced by Phe, Leu and Gln. Both patches were previously thought to be involved in electron transfer. 1H-NMR spectroscopy revealed only minor changes in the three-dimensional structure of the mutants compared to wild-type azurin. Observed changes in midpoint potentials could be attributed to electrostatic effects. The slow relaxation phase observed in temperature-jump experiments carried out on equilibrium mixtures of wild-type azurin and cytochrome c551 was definitively shown to be due to a conformational relaxation involving His35. Analysis of the kinetic data demonstrated the involvement of the hydrophobic but not the His35 patch of azurin in the electron transfer reactions with both cytochrome c551 and nitrite reductase.

Isolation and characterization of cytochrome c550 from the methylamine-oxidizing electron-transport chain of Thiobacillus versutus

The isolation and purification of cytochrome c550 from the methylamine-oxidizing electron-transport chain in Thiobacillus versutus is reported. The cytochrome is a single-heme-containing type I cytochrome c with a relative molecular mass of 16 +/- 1 kDa, an isoelectric point of 4.6 +/- 0.1, a midpoint potential of 272 +/- 3 mV at pH less than 4 and 255 +/- 5 mV at pH = 7.0, and an axial coordination of the Fe by a methionine and a histidine. The midpoint potential decreases with increasing pH due to the deprotonation of a group tentatively identified as a propionate (pKa = 6.5 +/- 0.1 and 6.7 +/- 0.1 in the oxidized and reduced protein, respectively) and a change in the Fe coordination at pH greater than 10. The electron-self-exchange rate appears to depend strongly on the ionic strength of the solution and is relatively insensitive to changes in pH. At 313 K and pH 5.2 the electron-exchange rate amounts to 0.7 x 10(2) M-1 s-1 and 5.3 x 10(2) M-1 s-1 at I = 40 mM and I = 200 mM, respectively. Amino acid composition and molar absorption coefficients at various wavelengths are reported. Resonances of heme protons and the epsilon H3 group of the ligand methionine of the Fe have been identified in the 1H-NMR spectrum of the reduced as well as the oxidized cytochrome.

NMR comparison of prokaryotic and eukaryotic cytochromes c

1H NMR spectroscopy has been used to examine ferrocytochrome c-551 from Pseudomonas aeruginosa (ATCC 19429) over the pH range 3.5-10.6 and the temperature range 4-60 degrees C. Resonance assignments are proposed for main-chain and side-chain protons. Comparison of results for cytochrome c-551 to recently assigned spectra for horse cytochrome c (Wand et al. (1989) Biochemistry 28, 186-194) and mutants of yeast iso-1 cytochrome (Pielak et al. (1988) Eur. J. Biochem. 177, 167-177) reveals some unique resonances with unusual chemical shifts in all cytochromes that may serve as markers for the heme region. Results for cytochrome c-551 indicate that in the smaller prokaryotic cytochrome, all benzoid side chains are rapidly flipping on the NMR time scale. In contrast, in eukaryotic cytochromes there are some rings flipping slowly on the NMR time scale. The ferrocytochrome c-551 undergoes a transition linked to pH with a pK around 7. The pH behavior of assigned resonances provides evidence that the site of protonation is the inner or buried 17-propionic acid heme substituent (IUPAC-IUB porphyrin nomenclature). Conformational heterogeneity has been observed for segments near the inner heme propionate substituent.

Electrostatic and steric control of electron self-exchange in cytochromes c, c551, and b5

The ionic strength dependence of the electron self-exchange rate constants of cytochromes c, c551, and b5 has been analyzed in terms of a monopole-dipole formalism (van Leeuwen, J.W. 1983. Biochim. Biophys. Acta. 743:408-421). The dipole moments of the reduced and oxidized forms of Ps. aeruginosa cytochrome c551 are 190 and 210 D, respectively (calculated from the crystal structure). The projections of these on the vector from the center of mass through the exposed heme edge are 120 and 150 D. For cytochrome b5, the dipole moments calculated from the crystal structure are 500 and 460 D for the reduced and oxidized protein; the projections of these dipole moments through the exposed heme edge are -330 and -280 D. A fit of the ionic strength dependence of the electron self-exchange rate constants gives -280 (reduced) and -250 (oxidized) D for the center of mass to heme edge vector. The self-exchange rate constants extrapolated to infinite ionic strength of cytochrome c, c551, and b5 are 5.1 x 10(5), 2 x 10(7), and 3.7 x 10(5) M-1 s-1, respectively. The extension of the monopole-dipole approach to other cytochrome-cytochrome electron transfer reactions is discussed. The control of electron transfer by the size and shape of the protein is investigated using a model which accounts for the distance of the heme from each of the surface atoms of the protein. These calculations indicate that the difference between the electrostatically corrected self-exchange rate constants of cytochromes c and c551 is due only in part to the different sizes and heme exposures of the two proteins.