Water and cytochrome oxidation-reduction reactions

Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection

Despite certain quantum concepts, such as superposition states, entanglement, 'spooky action at a distance' and tunnelling through insulating walls, being somewhat counterintuitive, they are no doubt extremely useful constructs in theoretical and experimental physics. More uncertain, however, is whether or not these concepts are fundamental to biology and living processes. Of course, at the fundamental level all things are quantum, because all things are built from the quantized states and rules that govern atoms. But when does the quantum mechanical toolkit become the best tool for the job? This review looks at four areas of 'quantum effects in biology'. These are biosystems that are very diverse in detail but possess some commonality. They are all (i) effects in biology: rates of a signal (or information) that can be calculated from a form of the 'golden rule' and (ii) they are all protein-pigment (or ligand) complex systems. It is shown, beginning with the rate equation, that all these systems may contain some degree of quantumeffect, and where experimental evidence is available, it is explored to determine how the quantum analysis aids in understanding of the process.

Isotope effect on electron transfer in reaction centers from Rhodopseudomonas sphaeroides

Previous ENDOR studies on reaction centers from Rhodopseudomonas sphaeroides have shown the presence of two hydrogen-bonded protons associated with the primary, ubiquinone, acceptor Q(A). These protons exchange with deuterons from solvent (2)H(2)O. The effect of this deuterium substitution on the charge-recombination kinetics (BChl)(2) (+)Q(A) (-) --> (BChl)(2)Q(A) has been studied with a sensitive kinetic difference technique. The electron-transfer rate was found to increase with deuterium exchange up to a maximum Deltak/k of 5.7 +/- 0.3%. The change in rate was found to have an exchange time of 2 hr, which matched the disappearance of the ENDOR lines due to the exchangeable protons. These results indicate that these protons play a role in the vibronic coupling associated with electron transfer. A simple model for the isotope effect on electron transfer predicts a maximum rate increase of 20%, which is consistent with the experimental results.

Tunneling in Chromatium chromatophores: Detection of a Hopfield charge-transfer band

We have observed a weak charge-transfer band in the cytochrome c-P(870) electron-transfer reaction in Chromatium vinosum chromatophores at 10 K and at 85 K. First, the intermediate acceptor, I, was trapped in the reduced state by lowering the redox potential at room temperature, then illuminating with white light at low temperature for 20 min. Next, illumination by broadband infrared (1-3 mum, 6.5 kW/m(2)) for 4 hr at 10 K decreased the I(-) electron spin resonance signal by 30%. One-hour infrared illumination at 85 K decreased the cytochrome c Soret band shift by 10%. The effect of infrared was to promote the system from the ground vibrational state with the electron on P(870) to an excited vibrational state with the electron on cytochrome c. The absorption band peak is near 2 mum, and the integrated cross section is approximately 6 x 10(-3) eV.M(-1).cm(-1). These values are consistent with small (0.02 nm) nuclear motion and with electron-transfer rates measured in the dark.

A phenomenological model of dynamical arrest of electron transfer in solvents in the glass-transition region

A phenomenological model of electron transfer reactions in solvents undergoing glass transition is discussed. The reaction constant cuts off slow polarization modes from the spectrum of nuclear thermal motions active on the observation time scale. The arrest of nuclear solvation in turn affects the reaction activation barrier making it dependent on the rate. The resultant rate constant is sought from a self-consistent equation. The model describes well the sharp change in the solvent Stokes shift of optical lines in the glass-transition region. It is also applied to describe the temperature dependence of primary charge separation and reduction of primary pair in photosynthetic reaction centers. The model shows that a weak dependence of the primary charge separation rate on temperature can be explained by dynamical arrest of nuclear solvation on the picosecond time scale of electron transfer. For reduction of primary pair by cytochrome, the model yields a sharp turnover of the reaction kinetics at the transition temperature when nuclear solvation freezes in.

Length, time, and energy scales of photosystems

The design of photosynthetic systems reflects the length scales of the fundamental physical processes. Energy transfer is rapid at the few angstrom scale and continues to be rapid even at the 50-A scale of the membrane thickness. Electron tunneling is nearly as rapid at the shortest distances, but becomes physiologically too slow well before 20 A. Diffusion, which starts out at a relatively slow nanosecond time scale, has the most modest slowing with distance and is physiologically competent at all biologically relevant distances. Proton transfer always operates on the shortest angstrom scale. The structural consequences of these distance dependencies are that energy transfer networks can extend over large, multisubunit and multicomplex distances and take leaps of 20 A before entering the domain of charge separating centers. Electron transfer systems are effectively limited to individual distances of 15 A or less and span the 50 A dimensions of the bioenergetic membrane by use of redox chains. Diffusion processes are generally used to cover the intercomplex electron transfer distances of 50 A and greater and tend to compensate for the lack of directionality by restricting the diffusional space to the membrane or the membrane surface, and by multiplying the diffusing species through the use of pools. Proton transfer reactions act over distances larger than a few angstroms through the use of clusters or relays, which sometimes rely on water molecules and which may only be dynamically assembled. Proteins appear to place a premium on robustness of design, which is relatively easily achieved in the long-distance physical processes of energy transfer and electron tunneling. By placing cofactors close enough, the physical process is relatively rapid compared to decay processes. Thus suboptimal conditions such as cofactor orientation, energy level, or redox potential level can be tolerated and generally do not have to be finely tuned. The most fragile regions of design tend to come in areas of complex formation and catalysis involving proton management, where relatively small changes in distance or mutations can lead to a dramatic decrease in turnover, which may already be limiting the overall speed of energy conversion in these proteins. Light-activated systems also face a challenge to robust function from the ever-present dangers of high redox potential chemistry. This can turn the protein matrix and wandering oxygen molecules into unintentional redox partners, which in the case of PSII requires the frequent, costly replacement of protein subunits.

Purification, redox and spectroscopic properties of the tetraheme cytochrome c isolated from Rubrivivax gelatinosus

The tetraheme cytochrome c subunit of the Rubrivivax gelatinosus reaction center was isolated in the presence of octyl beta-D-thioglucoside by ammonium sulfate precipitation and solubilization at pH 9 in a solution of Deriphat 160. Several biochemical properties of this purified cytochrome were characterized. In particular, it forms small oligomers and its N-terminal amino acid is blocked. In the presence or absence of diaminodurene, ascorbate and dithionite, different oxidation/reduction states of the isolated cytochrome were studied by absorption, EPR and resonance Raman spectroscopies. All the data show two hemes quickly reduced by ascorbate, one heme slowly reduced by ascorbate and one heme only reduced by dithionite. The quickly ascorbate-reduced hemes have paramagnetic properties very similar to those of the two low-potential hemes of the reaction center-bound cytochrome (gz = 3.34), but their alpha band is split with two components peaking at 552 nm and 554 nm in the reduced state. Their axial ligands did not change, being His/Met and His/His, as indicated by the resonance Raman spectra. The slowly ascorbate-reduced heme and the dithionite-reduced heme are assigned to the two high-potential hemes of the bound cytochrome. Their alpha band was blue-shifted at 551 nm and the gz values decreased to 2.96, although the axial ligations (His/Met) were conserved. It was concluded that the estimated 300 mV potential drop of these hemes reflected changes in their solvent accessibility, while the reduction in gz indicates an increased symmetry of their cooordination spheres. These structural modifications impaired the cytochrome's essential function as the electron donor to the photooxidized bacteriochlorophyll dimer of the reaction center. In contrast to its native state, the isolated cytochrome was unable to reduce efficiently the reaction center purified from a Rubrivivax gelatinosus mutant in which the tetraheme was absent. Despite the conformational changes of the cytochrome, its four hemes are still divided into two groups with a pair of low-potential hemes and a pair of high-potential hemes.

Low-temperature electron transfer from cytochrome to the special pair in Rhodopseudomonas viridis: role of the L162 residue

Electron transfer from the tetraheme cytochrome c to the special pair of bacteriochlorophylls (P) has been studied by flash absorption spectroscopy in reaction centers isolated from seven strains of the photosynthetic purple bacterium Rhodopseudomonas viridis, where the residue L162, located between the proximal heme c-559 and P, is Y (wild type), F, W, G, M, T, or L. Measurements were performed between 294 K and 8 K, under redox conditions in which the two high-potential hemes of the cytochrome were chemically reduced. At room temperature, the kinetics of P+ reduction include two phases in all of the strains: a dominant very fast phase (VF), and a minor fast phase (F). The VF phase has the following t(1/2): 90 ns (M), 130 ns (W), 135 ns (F), 189 ns (Y; wild type), 200 ns (G), 390 ns (L), and 430 ns (T). These data show that electron transfer is fast whatever the nature of the amino acid at position L162. The amplitudes of both phases decrease suddenly around 200 K in Y, F, and W. The effect of temperature on the extent of fast phases is different in mutants G, M, L, and T, in which electron transfer from c-559 to P+ takes place at cryogenic temperatures in a substantial fraction of the reaction centers (T, 48%; G, 38%; L, 23%, at 40 K; and M, 28%, at 60 K), producing a stable charge separated state. In these nonaromatic mutants the rate of VF electron transfer from cytochrome to P+ is nearly temperature-independent between 294 K and 8 K, remaining very fast at very low temperatures (123 ns at 60 K for M; 251 ns at 40 K for L; 190 ns at 8 K for G, and 458 ns at 8 K for T). In all cases, a decrease in amplitudes of the fast phases is paralleled by an increase in very slow reduction of P+, presumably by back-reaction with Q(A)-. The significance of these results is discussed in relation to electron transfer theories and to freezing at low temperatures of cytochrome structural reorganization.

Interaction between cytochrome c and the photosynthetic reaction center of purple bacteria: behaviour at low temperature

In purple photosynthetic bacteria the electron donor to the special pair, after its oxidation by a light-induced reaction, is a c-type cytochrome: either a soluble monoheme cytochrome which forms a transitory complex with the reaction center, or a tetraheme cytochrome which remains permanently bound to the reaction center. The effects of low temperatures on electron transfer in the complex are presented and discussed. They provide estimates for the reorganization energy. The most prominent effect of low temperature is that a dominant fast phase of electron transfer becomes impossible at a temperature of around 250 K (monoheme cytochrome) or located between 250 K and 80 K according to the redox state (tetraheme cytochrome). This inhibition is attributed to a freezing-like transition of pools of water molecules which blocks structural changes of the protein which are normally associated with the cytochrome oxidation.

Electron transfer within xanthine oxidase: a solvent kinetic isotope effect study

Solvent kinetic isotope effect studies of electron transfer within xanthine oxidase have been performed, using a stopped-flow pH-jump technique to perturb the distribution of reducing equivalents within partially reduced enzyme and follow the kinetics of reequilibration spectrophotometrically. It is found that the rate constant for electron transfer between the flavin and one of the iron-sulfur centers of the enzyme observed when the pH is jumped from 10 to 6 decreases from 173 to 25 s-1 on going from H2O to D2O, giving an observed solvent kinetic isotope effect of 6.9. An effect of comparable magnitude is observed for the pH jump in the opposite direction, the rate constant decreasing from 395 to 56 s-1. The solvent kinetic isotope effect on kobs is found to be directly proportional to the mole fraction of D2O in the reaction mix for the pH jump in each direction, consistent with the effect arising from a single exchangeable proton. Calculations of the microscopic rate constants for electron transfer between the flavin and the iron-sulfur center indicate that the intrinsic solvent kinetic isotope effect for electron transfer from the neutral flavin semiquinone to the iron-sulfur center designated Fe/S I is substantially greater than for electron transfer in the opposite direction and that the observed solvent kinetic isotope effect is a weighted averaged of the intrinsic isotope effects for the forward and reverse microscopic electron-transfer steps.(ABSTRACT TRUNCATED AT 250 WORDS)

Quantum simulation of ferrocytochrome c

The dramatic progress in the understanding of the dynamics of biomolecules has been largely fuelled by computer simulations based on the law of classical mechanics. However in some respects biomolecules are at the borders of the domain of applicability of classical mechanics. The role of quantum mechanical effects in biomolecular structure and function is therefore worth investigating. Here we present preliminary results from a quantum simulation of a protein and contrast them with results from full classical simulations. The most significant differences are found in motions of high frequency, such as bond stretching or the torsional oscillation of groups that bear hydrogen atoms. The amplitudes of such motions are significantly increased by the penetration of atoms into classically forbidden regions. These differences will directly influence the rates of such processes as proton and electron transfer.

Rate enhancement of the internal electron transfer in cytochrome c oxidase by the formation of a peroxide complex; its implication on the reaction mechanism of cytochrome c oxidase

The oxidation of reduced cytochrome c oxidase by hydrogen peroxide was investigated with stopped-flow methods. It was reported by us previously (A.C.F. Gorren, H. Dekker and R. Wever (1986) Biochim. Biophys. Acta 852, 81-92) that at low H2O2 concentrations cytochrome a is oxidised simultaneously with cytochrome a3, but that at higher H2O2 concentrations the oxidation of cytochrome a is slower than that of cytochrome a3. We now report that for high peroxide concentrations (10-45 mM) the oxidation rate of cytochrome a increased linearly with the concentration of H2O2 (k = 700 M-1.S-1). Upon extrapolation to zero H2O2 concentration an intercept with a value of 16 s-1 (at 20 degrees C and pH 7.4) was found. A reaction sequence is described to explain these results; according to this model the rate constant (16 S-1) at zero H2O2 concentration represents the true value of the rate of electron transfer from cytochrome a to cytochrome a3 when the a3-CuB site is oxidised and unligated. However, when a complex of hydrogen peroxide with oxidised cytochrome a3 is formed, this rate is strongly enhanced. The slope (700 M-1.S-1) would then represent the rate of cytochrome a3(3+)-H2O2 complex formation. From experiments in which the pH was varied, we conclude that the reaction of H2O2 with cytochrome a3(2+) is independent of pH, whereas the electron-transfer rate from cytochrome a to cytochrome a3 gradually decreases with increasing pH. From the temperature dependence we could calculate values of 23 kJ.mol-1 and 45 kJ.mol-1 for the activation energies of the oxidations by H2O2 of cytochrome a3(2+) and cytochrome a2+, respectively. The similarity of the values that were obtained for cytochrome a oxidation both with H2O2 and with O2 as the electron acceptor suggests that the reactions share the same mechanism. In 2H2O the reactions studied decreased in rate. For the reaction of 2H2O2 with reduced cytochrome a3 in 2H2O, a small effect was found (15% decrease in rate constant). However, the internal electron-transfer rate from cytochrome a to cytochrome a3 decreased by 50%, Our results suggest that the internal electron transfer is associated with proton translocation.

The effect of pH and ionic strength on the pre-steady-state reaction of cytochrome c and cytochrome aa3

(1) In the pH range between 5.0 and 8.0, the rate constants for the reaction of ferrocytochrome c with both the high- and low-affinity sites on the cytochrome aa3 increased by a factor of approx. 2 per pH unit. (2) The pre-steady-state reaction between ferrocytochrome c and cytochrome aa3 did nt cause a change in the pH of an unbuffered medium. Furthermore, it was found that this reaction and the steady-state reaction are equally fast in H2O and 2H2O. From these results it was concluded that no protons are directly involved in a rate-determining reaction step. (3) Arrhenius plots show that the reaction between ferrocytochrome c and cytochrome aa3 requires a higher enthalpy of activation at temperatures below 20 degrees C (15--16 kcal/mol) as compared to that at higher temperature (9 kcal/mol). We found no effect of ionic strength on the activation enthalpy of the pre-steady-state reaction, nor on that of the steady-state reaction. This suggests that ionic strength does not change the character of these reactions, but merely affects the electrostatic interaction between both cytochromes.

A possible new mechanism of temperature dependence of electron transfer in photosynthetic systems

A new theory for the electron transfer by the non-adiabatic process is formulated taking into account the origin shift and the frequency change of the vibration. The resultant formulas are quite similar to those of Jortner (Jortner, J. (1976) J. Chem. Phys. 64, 4860-4867) except that the free energy gap delta G is used instead of the energy gap delta E. By applying this theory to the photosynthetic electron transfer, the role of the remarkable temperature dependence of the electron transfer from cytochrome to P+ in Chromatium vinosum and the experimental data were reproduced very well using a small value of the coupling strength in contrast with the previous theory. This implies that proteins play a role to exclude many of the solvent molecules from the region of the electron transfer reaction between the donor and acceptor molecules. The negative activation process in the back electron transfer from QA- to P+, the very slow back electron transfer from I- to P+ and the solvent isotope effect on the cytochrome oxidation are also successfully explained by this new theory. It is shown that even a qualitative conclusion as to the molecular parameters obtained from the temperature dependence of the electron transfer is different between the present theory and that of Jortner.

Possible role of protein in photosynthetic electron transfer

Photosynthetic electron transfer is discussed from a theoretical viewpoint. Theoretical description of electron transfer including the effect of low-frequency mode of protein is first discussed briefly. Then typical electron transfers in the primary photosynthesis are discussed as examples for the comparison between the theory and experiments. Attention is focussed on the fact that the photosynthetic system organizes a variety of electron transfers in a systematic manner to achieve a vary efficient energy conversion, and it is suggested that the protein environment plays an important role in controlling the rate of electron transfer and maximizing the efficiency of the primary reaction. We emphasize that not only the electronic but also vibrational interactions are important for the regulation of electron transfer. Some novel processes such as activationless and negative activation transfers are shown to be connected with the significance of vibrational factor.

Rates of reduced cytochrome c-ferricyanide binding and electron transfer

The oxidation of reduced cytochrome c by ferricyanide has been studied over a wide range of ferricyanide concentrations using a continuous-flow apparatus. The formation of a ferrocytochrome c-ferricyanide complex has been demonstrated and the binding and electron transfer processes separated to give both the oxidation electron transfer rate and the binding rate parameters. The electron transfer rate has been found to be 1.86 . 10(3) s-1 in H2O buffer and 1.36 . 10(3) s-1 in 2H2O demonstrating that a deuterium isotope effect of similar magnitude (R = 1.37) to that found in the cytochrome reactions in photosynthetic bacteria [18] is also found in the reaction studied here. The binding association rate parameters also show a similar deuterium isotope effect suggesting that water rotation may be involved in both the binding of ferricyanide to reduced cytochrome c and the subsequent oxidation electron transfer.

Cytochrome c-cytochrome oxidase interaction at subzero temperatures

Cytochrome oxidase forms two distinctive compounds with oxygen at --105 and --90 degrees C, one appears to be oxycytochrome oxidase (Compound A) and the other peroxycytochrome oxidase (Compound B). The functional role of compound B in the oxidation of cytochrome c has been examined in a variety of mitochondrial preparations. The rate and the extent of the reaction have been found to be dependent upon the presence of a fluid phase in the vicinity of the site of the reaction of cytochrome c and cytochrome oxidase. The kinetics of cytochrome c oxidation and of the slowly reacting component of cytochrome oxidase are found to be linked to one another even in cytochrome c depleted preparations, but under appropriate conditions, especially low temperatures, the oxidation of cytochrome c precedes that of this component of cytochrome oxidase. Based upon the identification of the slowly reacting components of cytochrome oxidase with cytochrome c, various mechanisms are considered which allow cytochrome c to be oxidized without the intervention of cytochrome a at very low temperatures, and tunneling seems an appropriate mechanism.

H/2H isotope effect in redox reactions of cytochrome c

The rate of reaction of ferro- and ferricytochrome c (C(II) and C(III) with ferri- and ferrocyanide and of C(III) with 02- and CO2- was determined in H2O and in 2H2O in the temperature range 5-35 degrees C. No isotope effect was evident in any of the reductions of C(III); the apparent energy of activation was identical in H2O and 2H2O. An isotope effect with kH2O/k2H2O = 1.25 to 1.85, depending on pH for instance was observed in the oxidation of C(II), in the slow phase of oxidation which involves conformational changes. An interpretation (supported by evidence from previous work) involving water molecules in the close vicinity of the reaction site on the protein is discussed.

Reactions of the ferri-ferrocytochrome-c system with superoxide/oxygen and CO2-/CO2 studied by fast pulse radiolysis

The reduction of ferricytochrome c by O2- and CO2- was studied in the pH range 6.6-9.2 and Arrhenius as well as Eyring parameters were derived from the rate constants and their temperature dependence. Ionic effects on the rate indicate that the redox process proceeds through a multiply-positively charged interaction site on cytochrome c. It is shown that the reaction with O2- (and correspondingly with O2 of ferrocytochrome c) is by a factor of approx. 10(3) slower than warranted by factors such as redox potential. Evidence is adduced to support the view that this slowness is connected with the role of water in the interaction between O2-/O2 and ferri-ferrocytochrome c in the positively charged interaction site on cytochrome c in which water molecules are specifically involved in maintaining the local structure of cytochrome c and participate in the process of electron equivalent transfer.

Na+-dependent phosphorylation of the rat brain (Na+ + K+)-ATPase. Possible non-equivalent activation sites for Na+

The steady state levels of Na+-dependent phosphoenzyme (E-P) in the (Na+ + K+)-ATPase (EC 3.6.1.3) of rat brain, obtained from a time course study of phosphoenzyme formation at 4 degrees C, were dependent on the concentration of Na+ in the reaction and were maximal in the presence of 64 mM Na+. The plot of phosphoenzyme vs. Na+ concentration gave a curve which on conversion to a double reciprocal plot (1/E-P vs. 1/Na+) gave a line with two breaks, yielding apparently three linear segments. This may be taken to indicate the presence of multiple Na+ sites for the formation of the phosphoenzyme. To test this hypothesis further, the following approach was taken. By making the assumption that the phosphoenzyme may represent bound Na+, it was possible to subject the data to rigorous multiple-site analysis by utilizing steady-state binding equations described by Klotz and Hunston (1971) (Biochemistry 10, 3065-3069), and by Scatchard (1949) (Ann. N.Y. Acad. Sci. 51, 660-672). The analysis of the data by these methods suggests that there may be three non-equivalent Na+ activation sites for the formation of Na+-dependent phosphoenzyme in the (Na+ + K+)-ATPase. The estimated intrinsic association constants (Ka) for activation by Na+ at each of the three sites were 3.4, 0.295, and 0.025 mM-1, respectively.

Excited states of photosynthetic reaction centers at low recox potentials

In preparations of photochemical reaction centers from Rhodopseudomonas spheroides R-26, lowering the recox potential so as to reduce the primary electron acceptor prevents the photochemical transfer of an electron from bacteriochlorophyll to the acceptor. Measuring absorbance changes under these conditions, we found that a 20-ns actinic flash converts the reaction center to a new state, P-F, which then decays with a half-time that is between 1 and 10 ns at 295 degrees K. At 25 degrees K, the decay half-time is approx. 20 ns. The quantum yield of state P-F appears to be near 1.0, both at 295 and at 15 degrees K. State P-F could be an intermediate in the photochemical electron-transfer reaction which occurs when the acceptor is in the oxidized form. Following the decay of state P-F, we detected another state, P-R, with a decay half-time of 6 mus at 295 degrees K and 120 mus at 15 degrees K. The quantum yield of state P-R is approx. 0.1 at 295 degrees K, but rises to a value nearer 1.0 at 15 degrees K. The kinetics and quantum yields are consistent with the view that state P-R forms from P-F. State P-R seems likely to be a side-product, rather than an intermediate in the electron-transfer process. The decay kinetics indicate that state P-F cannot be identical with the lowest excited singlet state of the reaction center. One of the two states, P-F or P-R, probably is the lowest excited triplet state of the reaction center, but it remains unclear which one.

A proposed hydrogen transfer function for cytochrome c

Outlines of proposed mechanisms for cytochrome c oxidoreduction are presented which differ in detail from those previously published. The mechanisms, while accommodating the fact that cytochrome c is a net electron acceptor and donor in its catalytic cycle, dictate that the enzyme catalyses hydrogen transfer. It is shown that the mechanism of cytochrome c reduction fulfills a recent proposal that the transition state is an analogue of the structure of ferricytochrome c(2). The implications of a hydrogen transfer role of cytochrome c are discussed.