Directional electron transfer in ruthenium-modified horse heart cytochrome c

Transition metal complexes as mediator-titrants in protein redox potentiometry

A selection of nine macrocyclic Fe(III/II) and Co(III/II) transition metal complexes has been chosen to serve as a universal set of mediator-titrants in redox potentiometry of protein samples. The potential range spanned by these mediators is approximately from +300 to -700 mV vs the normal hydrogen electrode, which covers the range of most protein redox potentials accessible in aqueous solution. The complexes employed exhibit stability in both their oxidized and their reduced forms as well as pH-independent redox potentials within the range 6 < pH < 9. The mediators were also chosen on the basis of their very weak visible absorption maxima in both oxidation states, which will enable (for the first time) optical redox potentiometric titrations of proteins with relatively low extinction coefficients. This has previously been impractical with organic mediators, such as indoles, viologens and quinones, whose optical spectra interfere strongly with those of the protein.

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.

Conformational gating of long distance electron transfer through wire-like bridges in donor-bridge-acceptor molecules

A series of five donor-bridge-acceptor (DBA) molecules in which the donor is tetracene, the acceptor is pyromellitimide, and the bridge molecules are oligo-p-phenylenevinylenes (OPV) of increasing length has been shown to undergo electron transfer (ET) by means of two mechanisms. When the bridge is short, strongly distance dependent superexchange dynamics dominates, whereas when the bridge is longer, bridge-assisted hopping dynamics prevails. The latter mechanism results in relatively soft distance dependence for ET in which the OPV oligomers act effectively as molecular wires. We now report studies on the critical influence that bridge dynamics have on electron transfer through these oligomers. The temperature dependence of the charge separation (CS) rates in all five molecules does not appear to obey the predictions of standard ET theories based upon the Condon approximation. All five molecules show behavior consistent with CS being "gated" by torsional motion between the tetracene donor and the first bridge phenyl ring. This is based on the near equivalence of the CS activation energies measured for all five molecules with the frequency of a known vibrational mode in 5-phenyltetracene. In the molecule containing a trans-stilbene bridge, a competition occurs between the tetracene-phenyl torsional motion and one that occurs between the vinyl group and the phenyls linked to it. This results in complex temperature-dependent CS that exhibits both activated and negatively activated regimes. The charge recombination (CR) reactions within the molecules which have the two shortest bridges, namely phenyl and trans-stilbene, show a weaker dependence on these molecular motions. The three molecules with the longest bridges all display complex temperature dependencies in both their rates of CS and CR, most likely because of the complex torsional motions, which arise from the multiple phenyl-vinyl linkages. The data show that long-distance electron transfer and therefore wire-like behavior within conjugated bridge molecules depend critically on these low-frequency torsional motions. Molecular device designs that utilize such bridges will need to address these issues.

Conformational gating of the electron transfer reaction QA-.QB --> QAQB-. in bacterial reaction centers of Rhodobacter sphaeroides determined by a driving force assay

The mechanism of the electron transfer reaction, QA-.QB --> QAQB-., was studied in isolated reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides by replacing the native Q10 in the QA binding site with quinones having different redox potentials. These substitutions are expected to change the intrinsic electron transfer rate by changing the redox free energy (i.e., driving force) for electron transfer without affecting other events that may be associated with the electron transfer (e.g., protein dynamics or protonation). The electron transfer from QA-. to QB was measured by three independent methods: a functional assay involving cytochrome c2 to measure the rate of QA-. oxidation, optical kinetic spectroscopy to measure changes in semiquinone absorption, and kinetic near-IR spectroscopy to measure electrochromic shifts that occur in response to electron transfer. The results show that the rate of the observed electron transfer from QA-. to QB does not change as the redox free energy for electron transfer is varied over a range of 150 meV. The strong temperature dependence of the observed rate rules out the possibility that the reaction is activationless. We conclude, therefore, that the independence of the observed rate on the driving force for electron transfer is due to conformational gating, that is, the rate limiting step is a conformational change required before electron transfer. This change is proposed to be the movement, controlled kinetically either by protein dynamics or intermolecular interactions, of QB by approximately 5 A as observed in the x-ray studies of Stowell et al. [Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E. & Feher, G. (1997) Science 276, 812-816].

Differences in thermal stability between reduced and oxidized cytochrome b562 from Escherichia coli

The thermal stabilities of ferri- and ferrocytochrome b562 were examined. Thermally induced spectral changes, monitored by absorption and second-derivative spectroscopies, followed the dissociation of the heme moiety and the increased solvation of tyrosine residue(s) located in close proximity to the heme binding site. All observed thermal transitions were independent of the rate of temperature increase (0.5-2 degrees C/min), and the denatured protein exhibited partial to near-complete reversibility upon return to ambient temperature. The extent of renaturation of cytochrome b562 is dependent on the amount of time the unfolded conformer is exposed to temperatures above the transition temperature, Tm. All thermally induced spectra changes fit a simple two-state model, and the thermal transition was assumed to be reversible. The thermal transition for ferrocytochrome b562 yielded Tm and van't Hoff enthalpy (delta HvH) values of 81.0 degrees C and 137 kcal/mol, respectively. In contrast, Tm and delta HvH values obtained for the ferricytochrome were 66.7 degrees C and 110 kcal/mol, respectively. The estimated increase in the stabilization free energy at the Tm of ferricytochrome b562 following the one-electron reduction to the ferrous form, where delta delta G = delta Tm delta Sm [delta Sm = 324 cal/(K.mol), delta Tm = 14.3 degrees C] [Becktel, W. J., & Schellman, J. A. (1987) Biopolymers 26, 1859-1877], is 4.6 kcal/mol.

Structural microheterogeneity of a tryptophan residue required for efficient biological electron transfer between putidaredoxin and cytochrome P-450cam

The carboxy-terminal tryptophan of putidaredoxin, the Fe2S2.Cys4 iron-sulfur physiological redox partner of cytochrome P-450cam, is essential for maximal biological activity [Davies, M. D., Qin, L., Beck, J. L., Suslick, K. S., Koga, H., Horiuchi, T., & Sligar, S. G. (1990) J. Am. Chem. Soc. 112, 7396-7398]. This single tryptophan-containing protein thus represents an excellent system for studying the solution dynamics of a residue directly implicated in an electron-transfer pathway. Steady-state and time-resolved measurements of the tryptophan fluorescence have been conducted across the emission spectrum as a function of redox state to probe potential structural changes which might be candidates for structural gating phenomena. The steady-state emission spectrum (lambda max = 358 nm) and anisotropy (alpha = 0.04) suggest that Trp-106 is very solvent-exposed and rotating partially free of global protein constraints. The time-resolved fluorescence kinetics for both oxidized and reduced putidaredoxin are fit best with three discrete components of approximately 5, 2, and 0.3 ns. The lifetime components were assigned to physical species with iodide ion quenching experiments, where differential quenching of the longer components was observed (k tau = 2 = 5.9 X 10(8) M-1 s-1, k tau = 5 = 1.3 X 10(8) M-1 s-1). These findings suggest that the multiexponential fluorescence decay results from ground-state conformational microheterogeneity and thus demonstrate that the essential tryptophan exists in at least two distinguishable conformations. Small differences in the relative proportions of the components between redox states were observed but not cleanly resolved.(ABSTRACT TRUNCATED AT 250 WORDS)

Substrate specificity of solvent viscosity effects in carboxypeptidase A catalyzed peptide hydrolysis

We have investigated the viscosity of carboxypeptidase A catalyzed Bz-Gly-Phe hydrolysis at pH 7.5 (Tris) and 0.5 mol.l-1 NaCl over the range 10-100 mp, varied by addition of glycerol or sucrose. In contrast to previous reports of strong viscosity effects on the corresponding Cbz-Ala-Ala-Ala hydrolysis, both the catalytic constant and the Michaelis constant are virtually independent of viscosity over the 10-fold range investigated. Furthermore, the CD spectra of carboxypeptidase A in the high-viscosity media point to no change in the alpha-helix and beta-sheet structure in these media. The data are compatible either with a compacter, more rigid enzyme-substrate structure or with a more prominent role of intramolecular nuclear reorganization compared to protein reorganization for Bz-Gly-Phe than for Cbz-Ala-Ala-Ala. These views can be given a preciser frame in terms of stochastic chemical rate theory.

Sequential 1H NMR assignments of iron(II) cytochrome c551 from Pseudomonas aeruginosa

Sequence-specific 1H NMR resonance assignments for all but the C-terminal Lys 82 are reported for iron(II) cytochrome c551 from Pseudomonas aeruginosa at 25 degrees C and pH = 6.8. Spin systems were identified by using TOCSY and DQF-COSY spectra in 2H2O and 1H2O. Sequential assignments were made by using NOESY connectivities between adjacent amide, alpha, and beta protons. Resonances from several amino acids including His 16, Gly 24, Ile 48, and Met 61 experience strong ring-current shifts due to their placement near the heme. All heme protons, including the previously unassigned propionates, have been identified. Preliminary analysis of sequential and medium-range NOEs provides evidence for substantial amounts of helix in the solution structure. Long-range NOEs indicate that the folds in solution and crystal structures are similar. For one aromatic side chain (Tyr 27) that is close to the heme group we found a transition from hindered ring rotation at low temperature to rapid rotation at high temperature.

Long-range electron exchange measured in proteins by quenching of tryptophan phosphorescence

Ten proteins that span a wide range of phosphorescence lifetimes were examined for sensitivity to quenching by four agents of disparate chemical nature. The results show that quenching efficiency is relatively independent of the quencher and is highly correlated with depth of burial of the phosphorescent tryptophan. The bimolecular quenching rate constants (kq) measured for the different proteins, spanning 5 orders of magnitude in kq, are found to decrease exponentially with the distance (r) of the tryptophan in angstroms from the protein surface--i.e., kq = Aexp(-r/rho), where A contains a geometrical factor dependent on tryptophan burial and surface geometry [corrected]. Theoretical analysis shows that this behavior can be expected for an electron-exchange reaction between the buried tryptophans and quenchers in solution in the rapid diffusion limit. Therefore, the results obtained provide evidence for an exponential dependence of electron-transfer rate on distance in a protein environment and evaluate the distance parameter, rho, for electron transfer through the general protein matrix at 1.0 A. For a unimolecular donor-acceptor pair with ket = koexp(-r/rho), ko approximately 10(9) sec-1.

Photoinduced electron-transfer kinetics of singly labeled ruthenium bis(bipyridine) dicarboxybipyridine cytochrome c derivatives

Cytochrome c derivatives labeled at specific lysine amino groups with ruthenium bis(bipyridine) dicarboxybipyridine [RuII(bpy)2(dcbpy)] were prepared by using the procedure described previously [Pan, L. P., Durham, B., Wolinska, J., & Millett, F. (1988) Biochemistry 27, 7180-7184]. Four additional singly labeled derivatives were purified, bringing the total number to 10. These derivatives have a strong luminescence emission centered at 662 nm arising from the excited state, RuII*. Transient absorption spectroscopy was used to directly measure the rate constants for the photoinduced electron-transfer reaction from RuII* to the ferric heme group (k1) and for the thermal back-reaction from the ferrous heme group to RuIII (k2). The rate constants were found to be k1 = 14 X 10(6) s-1 and k2 = 24 X 10(6) s-1 for the derivative modified at lysine 72, which has a distance of 8-16 A between the ruthenium and heme groups. Similar rate constants were found for the derivatives modified at lysines 13 and 27, which have distances of 6-12 A separating the ruthenium and heme groups. The rate constants were significantly slower for the derivatives modified at lysine 25 (k1 = 1 X 10(6) s-1, k2 = 1.5 X 10(6) s-1) and lysine 7 (k1 = 0.3 X 10(6) s-1, k2 = 0.5 X 10(6) s-1), which have distances of 9-16 A. Transients due to photoinduced electron transfer could not be detected for the remaining derivatives, which have larger distances between the ruthenium and heme groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Long-range intramolecular electron transfer in azurins

The Cu(II) sites of azurins, the blue single copper proteins, isolated from Pseudomonas aeruginosa and Alcaligenes spp. (Iwasaki) are reduced by CO2- radicals, produced by pulse radiolysis, in two distinct reaction steps: (i) a fast bimolecular phase, at the rates (5.0 +/- 0.8) x 10(8) M-1.s-1 (P. aeruginosa) and (6.0 +/- 1.0) x 10(8) M-1.s-1 (Alcaligenes); (ii) a slow unimolecular phase with specific rates of 44 +/- 7 s-1 in the former and 8.5 +/- 1.5 s-1 for the latter (all at 298 K, 0.1 M ionic strength). Concomitant with the fast reduction of Cu(II), the single disulfide bridge linking cysteine-3 to -26 in these proteins is reduced to the RSSR- radical ion as evidenced by its characteristic absorption band centered at 410 nm. This radical ion decays in a unimolecular process with a rate identical to that of the slow Cu(II) reduction phase in the respective protein, thus clearly suggesting that a long-range intramolecular electron transfer occurs between the RSSR- radicals and the Cu(II) site. The temperature dependence of the internal electron transfer process in both proteins was measured over the 4 degrees C to 42 degrees C range. The activation parameters derived are delta H* = 47.5 +/- 4.0 and 16.7 +/- 1.5 kJ.mol-1; and delta S not equal to = -56.5 +/- 7.0 and -171 +/- 18 J.K-1.mol-1, respectively. Using the Marcus theory, we found that the intramolecular electron transfer rates and their activation parameters observed for the two azurins correlate well with the distances between the reactive sites, their redox potential, and the nature of the separating medium. Thus, azurins with distinct structural and reactivity characteristics isolated from different bacteria or modified by site-directed mutagenesis can be used in comparing long-range electron transfer process between their conserved disulfide bridge and the Cu(II) sites.

Photochemical generation and reactions of heme cation radicals in heme proteins

A novel approach is described for generating reactive oxidizing centers in heme proteins, with zinc hemoglobin (Zn Hb) and zinc cytochrome c (Zn cyt c) used as examples. The reaction of 3Zn* Hb with [CoIII(NH3)5 Cl]2+, and of 3Zn* cyt c with methyl viologen are described. In the case of Zn Hb the cation radical produced decays with a rate constant of k3 = 2400s-1. Using this value the rate of the reaction (formula; see text) can be calculated to be 4500s-1.

Temperature dependence of intramolecular electron transfer as a probe for predenaturational changes in lysozyme

Intramolecular electron transfer in hen egg-white lysozyme between tryptophan and tyrosine units was investigated by means of pulse radiolysis in the temperature range 288-333 K. An Arrhenius plot for the kinetics of this process shows a sharp break at approximately 303 K (30 degrees C) compatible with the trend noted earlier (cf P. Jolles, et al. BBA, 491, 354, (1977)) on the Arrhenius plot for kinetics of bacterial substrate digestion by lysozyme. The departure from linearity of the Arrhenius plot for intramolecular electron transfer is interpreted in terms of local intralobe fluctuations of the native structure of lysozyme. It is suggested that such an approach can be useful for probing predenaturational changes in proteins.

Photoexcitation of the methionine-iron bond in iron(III) cytochrome c: bimolecular reaction with NADH

When iron(III) cytochrome c aqueous solutions containing NADH are irradiated with polychromatic light (wavelength greater than 280 nm), iron(II) cytochrome c and NAD+ in the stoichiometric ratio 2/1 are observed to be the principal reaction products, independently of the presence of oxygen; in addition, a minor process due to direct photodegradation of the nucleotide is observed. The selection of monochromatic 290 nm irradiation light (at which NADH has an absorbance minimum) and an adequate reactant concentration allowed parallel reactions to be minimized and new information to be obtained on the mechanism of the photoredox process. The experimental results are consistent with a reaction mechanism whereby NADH donates one electron to a "reactive intermediate" of the hemoprotein formed from the light-induced methionine-to-iron charge transfer excited state. In this process an NAD. radical is formed which, in deaerated solution, immediately reduces another molecule of the hemoprotein, and is itself oxidized to NAD+. In aerated solution, the NAD. radical rapidly reacts with oxygen to give NAD+ and superoxide O2- anion radical which, in turn, reduces the second iron(III) cytochrome c molecule.

Redox reactivity of bacterial and mammalian ferritin: is reductant entry into the ferritin interior a necessary step for iron release?

Both mammalian and bacterial ferritin undergo rapid reaction with small-molecule reductants, in the absence of Fe2+ chelators, to form ferritins with reduced (Fe2+) mineral cores. Large, low-potential reductants (flavoproteins and ferredoxins) similarly react anaerobically with both ferritin types to quantitatively produce Fe2+ in the ferritin cores. The oxidation of Fe2+ ferritin by large protein oxidants [cytochrome c and Cu(II) proteins] also occurs readily, yielding reduced heme and Cu(I) proteins and ferritins with Fe3+ in their cores. These latter oxidants also convert enthetically added Fe2+, bound in mammalian or bacterial apo- or holoferritin, to the corresponding Fe3+ state in the core of each ferritin type. Because the protein reductants and oxidants are much larger than the channels leading into the mineral core attached to the ferritin interior, we conclude that redox reactions involving the Fe2+/Fe3+ components of the ferritin core can occur without direct interaction of the redox reagent at the mineral core surface. Our results also suggest that the oxo, hydroxy species of the core, composed essentially of Fe(O)OH, arise exclusively from solvent deprotonation. The long-distance ferritin-protein electron transfer observed in this study may occur by electron tunneling.

Preparation and characterization of singly labeled ruthenium polypyridine cytochrome c derivatives

A novel two-step procedure has been developed to prepare cytochrome c derivatives labeled at specific lysine amino groups with ruthenium bis(bipyridine) dicarboxybipyridine [RuII(bpy)2(dcbpy)]. In the first step, cytochrome c was treated with the mono-N-hydroxysuccinimide ester of 4,4'-dicarboxy-2,2'-bipyridine (dcbpy) to convert positively charged lysine amino groups to negatively charged dcbpy-lysine groups. Singly labeled dcbpy-cytochrome c derivatives were then separated and purified by ion-exchange chromatography. In the second step, the individual dcbpy-cytochrome c derivatives were treated with RuII(bpy)2CO3 to form singly labeled RuII(bpy)2(dcbpy-cytochrome c) derivatives. The specific lysine labeled in each derivative was determined by reverse-phase chromatography of a tryptic digest. All of the derivatives had a strong luminescence emission centered at 662 nm, but the luminescence decay rates were increased relative to that of a non-heme protein control, RuII(bpy)2(dcbpy-lysozyme), which was 1.8 X 10(6) s-1. The luminescence decay rates were found to be 21, 16, 7.2, 5.7, 4.3, 4.3, and 3.5 X 10(6) s-1 for derivatives singly labeled at lysines 13, 72, 25, 7, 39, 86, and 87, respectively. There was an inverse relationship between the luminescence decay rates and the distances between the ruthenium labels and the heme group. The increased luminescence decay rates observed in the cytochrome c derivatives might be due to electron transfer from the excited triplet state of ruthenium to the ferric heme group. However, it is also possible that an energy-transfer mechanism might contribute to the luminescence quenching.(ABSTRACT TRUNCATED AT 250 WORDS)

Energy coupling and Hill cycles in enzymatic processes

We review how Hill's work on enzyme catalysis has nurtured our understanding of the mechanism by which enzymes can couple downhill processes to uphill processes. More specifically, we discuss the following questions: (i) Does it make sense to distinguish the chemical potential of the bound ligand from that of the binding enzyme? (ii) To what extent can free-energy transduction be localized at some crucial step in the catalytic cycle? (iii) Need enzymes be optimized so as to even out the profile of basic free energy along the catalytic cycle? (iv) How do continuous models of conformational transitions relate to discrete state diagrams and their kinetic elaborations? We conclude that (1) only in very special cases is it useful to designate a portion of the free energy of the enzyme-ligand complex as the free energy of the bound ligand; (2) only for some mechanisms can free-energy transduction be localized within a part of the catalytic cycle; (3) only in special cases should one expect enzymes to be "optimized" so as to have smooth basic free-energy profiles; and (4) transition rate constants can often be related to conformational diffusion constants, although in certain situations the kinetic description of an enzyme as if jumping between discrete states is impracticable; a diffusion-type description may then be preferable.

The azurin gene from Pseudomonas aeruginosa codes for a pre-protein with a signal peptide. Cloning and sequencing of the azurin gene

The azurin gene from Pseudomonas aeruginosa is located on a 1.3 kb long PstI DNA fragment. Its nucleotide sequence has been determined. It appears that the gene codes for a pre-protein with a 19 amino acid long signal sequence which possibly assists in the transport of the azurin over the periplasmic membrane.