Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.     

Environmental control of primary photochemistry in a mutant bacterial reaction center

The core structure of the photosynthetic reaction center is quasisymmetric with two potential pathways (called A and B) for transmembrane electron transfer. Both the pathway and products of light-induced charge separation depend on local electrostatic interactions and the nature of the excited states generated at early times in reaction centers isolated from Rhodobacter sphaeroides. Here transient absorbance measurements were recorded following specific excitation of the Q(y)() transitions of P (the special pair of bacteriochlorophylls), the monomer bacteriochlorophylls (B(A) and B(B)), or the bacteriopheophytins (H(A) and H(B)) as a function of both buffer pH and detergent in a reaction center mutant with the mutations L168 His to Glu and L170 Asn to Asp in the vicinity of P and B(B). At a low pH in any detergent, or at any pH in a nonionic detergent (Triton X-100), the photochemistry of this mutant is faster than, but similar to, wild type (i.e. electron transfer occurs along the A-side, 390 nm excitation is capable of producing short-lived B-side charge separation (B(B)(+)H(B)(-)) but no long-lived B(B)(+)H(B)(-) is observed). Certain buffering conditions result in the stabilization of the B-side charge separated state B(B)(+)H(B)(-), including high pH in the zwitterionic detergent LDAO, even following excitation with low energy photons (800 or 740 nm). The most striking result is that conditions giving rise to stable B-side charge separation result in a lack of A-side charge separation, even when P is directly excited. The mechanism that links B(B)(+)H(B)(-) stabilization to this change in the photochemistry of P in the mutant is not understood, but clearly these two processes are linked and highly sensitive to the local electrostatic environment produced by buffering conditions (pH and detergent).     

Temperature dependence of electron transfer to the M-side bacteriopheophytin in rhodobacter capsulatus reaction centers

Subpicosecond time-resolved absorption measurements at 77 K on two reaction center (RC) mutants of Rhodobacter capsulatus are reported. In the D(LL) mutant the D helix of the M subunit has been substituted with the D helix from the L subunit, and in the D(LL)-FY(L)F(M) mutant, three additional mutations are incorporated that facilitate electron transfer to the M side of the RC. In both cases the helix swap has been shown to yield isolated RCs that are devoid of the native bacteriopheophytin electron carrier HL (Chuang, J. I.; Boxer, S. G.; Holten, D.; Kirmaier, C. Biochemistry 2006, 45, 3845-3851). For D(LL), depending whether the detergent Deriphat 160-C or N-lauryl-N,N-dimethylamine-N-oxide (LDAO) is used to suspend the RCs, the excited state of the primary electron donor (P*) decays to the ground state with an average lifetime at 77 K of 330 or 170 ps, respectively; however, in both cases the time constant obtained from single-exponential fits varies markedly as a function of the probe wavelength. These findings on the D(LL) RC are most easily explained in terms of a heterogeneous population of RCs. Similarly, the complex results for D(LL)-FY(L)F(M) in Deriphat-glycerol glass at 77 K are most simply explained using a model that involves (minimally) two distinct populations of RCs with very different photochemistry. Within this framework, in 50% of the D(LL)-FY(L)F(M) RCs in Deriphat-glycerol glass at 77 K, P* deactivates to the ground state with a time constant of approximately 400 ps, similar to the deactivation of P* in the D(LL) mutant at 77 K. In the other 50% of D(LL)-FY(L)F(M) RCs, P* has a 35 ps lifetime and decays via electron transfer to the M branch, giving P+HM- in high yield (> or =80%). This result indicates that P* --> P(+)H(M)(-) is roughly a factor of 2 faster at 77 K than at 295 K. In alternative homogeneous models the rate of this M-side electron-transfer process is the same or up to 2-fold slower at low temperature. A 2-fold increase in rate with a reduction in temperature is the same behavior found for the overall L-side process P* --> P(+)H(L)(-) in wild-type RCs. Our results suggest that, as for electron transfer on the L side, the M-side electron-transfer reaction P* --> P(+)H(M)(-) is an activationless process.     

IDENTIFICATION OF THE PROTON ACCEPTOR OF SCHIFF BASE DEPROTONATION IN BACTERIORHODOPSIN: A FOURIER-TRANSFORM-INFRARED STUDY OF THE MUTANT ASP85 → GLU IN ITS NATURAL LIPID ENVIRONMENT

Abstract— In order to assign the proton acceptor for Schiff base deprotonation in bacteriorhodopsin to a specific Asp residue, the photoreaction of the Asp85 → Glu mutant, as expressed in Halobacterium sp . GRB, was investigated by static low-temperature and time-resolved infrared difference spec-troscopy. Measurements were also performed on the mutant protein labeled with [4-¹³C]Asp which allowed discrimination between Asp and Glu residues. 14,15-di¹³C-retinal was incorporated to distinguish amide-II absorbance changes from changes of the ethylenic mode of the chromophore. In agreement with earlier UV-VIS measurements, our data show that from both the 540 and 610 nm species present in a pH-dependent equilibrium, intermediates similar to K and L can be formed. The 14 ms time-resolved spectrum of the 540 nm species shows that a glutamic acid becomes protonated in the M-like intermediate, whereas the comparable difference spectrum of the 610 nm species demonstrates that in the initial state a glutamic acid is already protonated. In conjunction with earlier observations of protonation of an Asp residue in wild-type M, the data provide direct evidence that the proton acceptor in the deprotonation reaction of the Schiff base is Asp85.     

Electron transfer kinetics in photosynthetic reaction centers embedded in polyvinyl alcohol films

The coupling between electron transfer and protein dynamics has been studied at room temperature in isolated reaction centers (RCs) from the photosynthetic bacterium Rhodobacter sphaeroides by incorporating the protein in polyvinyl alcohol (PVA) films of different water/RC ratios. The kinetic analysis of charge recombination shows that dehydration of RC-containing PVA films causes reversible, inhomogeneous inhibition of electron transfer from the reduced primary quinone acceptor (Q(A)(-)) to the secondary quinone Q(B). A more extensive dehydration of solid PVA matrices accelerates electron transfer from Q(A)(-) to the primary photooxidized electron donor P(+). These effects indicate that incorporation of RCs into dehydrated PVA films hinders the conformational dynamics gating Q(A)(-) to Q(B) electron transfer at room temperature and slows down protein relaxation which stabilizes the primary charge-separated state P(+)Q(A)(-). A comparison with analogous effects observed in trehalose-coated RCs suggests that protein motions are less severely reduced in PVA films than in trehalose matrices at comparable water/RC ratios.     

Electron self-exchange in the solid-state: cocrystals of hydroquinone and bipyridyl triazole.

Solid-state voltammetry, spectroscopy, and microscopy studies have been used to probe the proton and electron conductivity within a self-assembled cocrystal, HQBpt. This crystallographically defined material contains 3,5-bis(pyridin-2-yl)-1,2,4-triazole, HBpt, dimers that are pi-stacked and hydrogen bonded to 1,4-hydroquinone, H(2)Q, in a herringbone arrangement. When deposited onto platinum microelectrodes, the cocrystal exhibits a well-defined voltammetric response corresponding to oxidation of H(2)Q to the quinone, Q, across a wide range of voltammetric time scales, electrolyte compositions, and pH values. Scanning electron microscopy reveals that redox cycling in aqueous perchlorate solutions in which the pH is systematically varied from 1 to 7 triggers electrocrystallization and the extensive formation of rodlike crystals. Fast scan rate voltammetry reveals that the homogeneous charge transport diffusion coefficient, D(app), is independent of the perchlorate concentration for 0.1 < [ClO(4)(-)] < 1.0 M (pH 6.6) at 3.14 +/- 0.11 x 10(-)(9) cm(2) s(-)(1). Moreover, D(app) is independent of the perchloric acid concentration for concentrations greater than approximately 2.0 M, maintaining a value of 4.81 +/- 0.07 x 10(-)(8) cm(2) s(-)(1). The observation that D(app) is independent of the supporting electrolyte suggests that the rate-determining step for homogeneous charge transport is not the availability of charge-compensating counterions or protons, but the dynamics of electron self-exchange between H(2)Q and Q. We have used the Dahms-Ruff formalism to determine electron self-exchange rate constants which are 2.84 +/- 0.22 x 10(9) and 9.69 +/- 0.73 x 10(10) M(-)(1) s(-)(1) for pH values greater than approximately 2.0 and less than -0.3, respectively. Significantly, these values are more than 2 orders of magnitude larger that those found for benzoquinone self-exchange reactions in aqueous solution. These results indicate that hydrogen bonds play an important role in supporting rapid electron transfer. The increase in D(app) between pH 1.0 and -0.3 is associated with protonation of the HBpt moieties, which triggers a reversible change in the material's structure.     

Effect of D2O and cryosolvents on the redox properties of bacteriochlorophyll dimer and electron transfer processes in Rhodobacter sphaeroides reaction centers

Effects of environmental changes on the reaction pattern of excitation energy trapping and transformation into the "stable" radical pair P+Q(A)-, have been analyzed in isolated reaction centers of the anoxygenic purple bacterium Rhodobacter sphaeroides. The following results were obtained: (a) replacement of exchangeable protons by deuterons significantly retarded the electron transfer steps of primary charge separation, leading to the radical pair P+I- and of the subsequent reoxidation of I- by the quinone acceptor Q(A) but has virtually no effect on the midpoint potential of P/P+ that was found to be 430+/-20 mV; (b) addition of 70% (v/v) glycerol causes a shift of Em by about 30 mV towards higher values whereas the kinetics of the electron transfer reactions remain almost unaffected; (c) in the presence of the cryoprotectant DMSO, a combined effect arises, i.e. a retardation of the electron transfer kinetics comparable to that induced by H/D exchange and simultaneously an upshift of the Em value to 475+/-20 mV, resembling the action of glycerol. These results are discussed within the framework of effects on the midpoint potential due to the dielectric constant of the medium and changes of the charge distribution in the vicinity of the redox groups and the influence of relaxation processes on electron transfer reactions.     

A facile and sensitive chemiluminescence detection of amino acids in biological samples after capillary electrophoretic separation

It was found that native amino acids enhanced the chemiluminescence (CL) reaction between luminol and BrO(-) in an alkaline aqueous solution. This has led to the development of a facile and highly sensitive CL detection scheme for the determination of amino acids in biological samples after capillary electrophoretic (CE) separation. The CE-CL conditions were optimized. An electrophoretic buffer of 2.5 x 10(-2) M sodium borate (pH 9.4) containing 1 x 10(-4) M luminol was used. The oxidizer solution of 8 x 10(-4) M NaBrO in 0.1 M sodium carbonate buffer solution (pH 12.5) was introduced post-column. Under the optimal conditions, the detection limits were 1.0 x 10(-7) M for glutamic acid (Glu) and 1.3 x 10(-7) M (S/N = 3) for aspartic acid (Asp). The relative standard deviations (RSDs) of peak area and migration time were in the ranges of 3.8-4.3% and 1.4-1.6%, respectively. The present method was applied to the determination of excitatory amino acids (i.e., Asp and Glu) in rat brain tissue and monkey plasma. The levels of these major excitatory amino acids in monkey plasma were quantified for the first time and found to be 1.17 +/- 0.17 x 10(-5) M (mean +/- SD, n = 6) for Glu and 1.64 +/- 0.19 x 10(-6) M for Asp, which were comparable with the levels in human plasma.     

Light- and redox-dependent thermal stability of the reaction center of the photosynthetic Bacterium rhodobacter sphaeroides

Irreversible loss of the photochemical activity and damage of the pigments (bacteriochlorophyll [Bchl] monomer, Bchl dimer [P] and bacteriopheophytin) by combined treatment with intense and continuous visible light and elevated temperature have been studied in a deoxygenated solution of reaction center (RC) protein from the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Both the fraction of RC in the charge-separated redox state (P+Q-, where Q is a quinone electron acceptor) and the degradation of the pigments showed saturation as a function of increasing light intensity up to 400 mW cm(-2) (488/515 nm) or 1100 microE m(-2) s(-1) (white light). The thermal denaturation curves of the RC in the P+Q- redox state demonstrated broadening and 10-20 degrees C shift to lower temperature (after 30-90 min heat treatment) compared with those in the PQ redox state. Similar but less striking behavior was seen for RC of other redox states (P+Q and PQ-) generated either by light or by electrochemical treatment in the dark. These experiments suggest that it is not the intense light per se but the changes in the redox state of the protein that are responsible for the increased sensitivity to photo- and heat damage. The RC with a charge pair (P+Q-) is more vulnerable to elevated temperature than the RC with (P+Q or PQ-) or without (PQ) a single charge. To reveal both the thermodynamic and kinetic aspects of the denaturation, a simple three-state model of coupled reversible thermal and irreversible kinetic transitions is presented. These effects may have relevance to the heat stability of other redox proteins in bioenergetics.     

EPR and optical spectroscopic studies of Met80X mutants of yeast ferricytochrome c. Models for intermediates in the alkaline transition

The ferric forms of Met80X mutants of yeast iso-1-cytochrome c (X = Ala, Ser, Asp, and Glu) display EPR and optical spectra that are strongly pH dependent. At low pH values (pH approximately 5) the sixth coordination sites are filled by H(2)O that, on elevating the pH, is replaced by OH(-) in the cases of Met80Ala and -Ser (pK approximately 5.6 and 5.9, respectively) and by a lysine amino group in the cases of Met80Asp and -Glu (pK approximately 9.3 and 11.6, respectively). The ligand sets and the pK values of the transitions are rationalized in terms of the structure of the heme pocket, and a possible mechanism of the "trigger" in the alkaline transition of the native protein is suggested.     

Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state

The mechanism of action of inosine-uridine nucleoside hydrolase has been investigated by long-term molecular dynamics (MD) simulation in TIP3P water using stochastic boundary conditions. Five MD studies have been performed with enzyme substrate complex (E.S), enzyme substrate complex with protonated His241 (EH.S), enzyme transition state complex (E.TS), enzyme transition state complex with protonated His241 (EH.TS), and His241Ala transition state complex E(H241A).TS. Special attention has been given to the role of His241, which has been considered as the general acid catalyst to assist departure of the leaving nucleobase on the basis of its location in the active site in the X-ray crystal structure (). Yet on the basis of the location in the active site, Tyr229 is closer to the aniline ring of pAPIR as compared to His241. On initiation of MD simulations, His241 does not approach the nucleobase in the structures of EH.S, E.S, EH.TS, and E.TS. In the solvated enzyme, Tyr229, which is a member of the hydrogen bonding network inosine O2'.Asp14.His241.Tyr229.inosine N7, serves as a proton source to the leaving nucleobase. The loss of significant activity of His241Ala mutant is shown to be related to the disruption of the above hydrogen bonded network and the distancing of Tyr229 from inosine N7. The structures of the enzyme complexes with substrate or TS are not visibly altered on protonation of His241, a most unusual outcome. The bell-shaped pH dependence upon pK(app)'s of 7.1 and 9.1 may be attributed to the necessity of the dissociation of Asp10 or Asp15 and the acid form of Tyr229, respectively. In TS, the residue Ile81 migrated closer, whereas Arg233 moved away from the nucleobase. The probability of ribooxocarbenium ion stabilization by Asn168 and Asp14 is discussed. The Asp14-CO(2)(-) is hydrogen bonded to the ribose 2'-OH for 96% of the MD simulation time. Nucleophilic addition of water138 to ribooxocarbenium ion is suggested to be assisted by the proton shuttle from water138 --> Asp10 --> Asp15 --> water pool. An anticorrelation motion between Tyr229-OH and Asn168-OD1 in EH.S and E.S is observed. The relationship of this anticorrelated motion to mechanism, if any, deserves further exploration, perhaps the formation of a near attack conformation.     

Intricate role of water in proton transport through cytochrome c oxidase

Cytochrome c oxidase (CytcO), the final electron acceptor in the respiratory chain, catalyzes the reduction of O(2) to H(2)O while simultaneously pumping protons across the inner mitochondrial or bacterial membrane to maintain a transmembrane electrochemical gradient that drives, for example, ATP synthesis. In this work mutations that were predicted to alter proton translocation and enzyme activity in preliminary computational studies are characterized with extensive experimental and computational analysis. The mutations were introduced in the D pathway, one of two proton-uptake pathways, in CytcO from Rhodobacter sphaeroides . Serine residues 200 and 201, which are hydrogen-bonded to crystallographically resolved water molecules halfway up the D pathway, were replaced by more bulky hydrophobic residues (Ser200Ile, Ser200Val/Ser201Val, and Ser200Val/Ser201Tyr) to query the effects of changing the local structure on enzyme activity as well as proton uptake, release, and intermediate transitions. In addition, the effects of these mutations on internal proton transfer were investigated by blocking proton uptake at the pathway entrance (Asp132Asn replacement in addition to the above-mentioned mutations). Even though the overall activities of all mutant CytcO's were lowered, both the Ser200Ile and Ser200Val/Ser201Val variants maintained the ability to pump protons. The lowered activities were shown to be due to slowed oxidation kinetics during the P(R) → F and F → O transitions (P(R) is the "peroxy" intermediate formed at the catalytic site upon reaction of the four-electron-reduced CytcO with O(2), F is the oxoferryl intermediate, and O is the fully oxidized CytcO). Furthermore, the P(R) → F transition is shown to be essentially pH independent up to pH 12 (i.e., the apparent pK(a) of Glu286 is increased from 9.4 by at least 3 pK(a) units) in the Ser200Val/Ser201Val mutant. Explicit simulations of proton transport in the mutated enzymes revealed that the solvation dynamics can cause intriguing energetic consequences and hence provide mechanistic insights that would never be detected in static structures or simulations of the system with fixed protonation states (i.e., lacking explicit proton transport). The results are discussed in terms of the proton-pumping mechanism of CytcO.     

Attenuated total reflection Fourier transform infrared spectroscopy of redox transitions in photosynthetic reaction centers: comparison of perfusion- and light-induced difference spectra

Chemically induced Fourier transform infrared difference spectra associated with redox transitions of several primary electron donors and acceptors in photosynthetic reaction centers (RCs) have been compared with the light-induced FTIR difference spectra involving the same cofactors. The RCs are deposited on an attenuated total reflection (ATR) prism and form a film that is enclosed in a flow cell. Redox transitions in the film of RCs can be repetitively induced either by perfusion of buffers poised at different redox potentials or by illumination. The perfusion-induced ATR-FTIR difference spectra for the oxidation of the primary electron donor P in the RCs of the purple bacteria Rb. sphaeroides and Rp. viridis and P700 in the photosystem 1 of Synechocystis 6803, as well as the Q(A)/Q(A) transition of the quinone acceptor (Q(A)) in Rb. sphaeroides RCs are reported for the first time. They are compared with the light-induced ATR-FTIR difference spectra P+Q(A)/PQ(A) for the RCs of Rb. sphaeroides and P700+/P700 for photosystem 1. It is shown that the perfusion-induced and light-induced ATR-FTIR difference spectra recorded on the same RC film display identical signal to noise ratios when they are measured under comparable conditions. The ATR-FTIR difference spectra are very similar to the equivalent FTIR difference spectra previously recorded upon photochemical or electrochemical excitation of these RCs in the more conventional transmission mode. The ATR-FTIR technique requires a smaller amount of sample compared with transmission FTIR and allows precise control of the aqueous environment of the RC films.     

Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin

The potential energy change during the M --> N process in bacteriorhodopsin has been evaluated by ab initio quantum chemical and advanced quantum chemical calculations following molecular dynamics (MD) simulations. Many previous experimental studies have suggested that the proton transfer from Asp96 to the Schiff base occurs under the following two conditions: (1) the hydrogen bond between Thr46 and Asp96 breaks and Thr46 is detached from Asp96 and (2) a stable chain of four water molecules spans an area from Asp96 --> Schiff base. In this work, we successfully reproduced the proton-transfer process occurring under these two conditions by molecular dynamics and quantum chemical calculations. The quantum chemical computation revealed that the proton transfer from Asp96 to Shiff base occurs in two-step reactions via an intermediate in which an H(3)O(+) appears around Ala215. The activation energy for the proton transfer in the first reaction was calculated to be 9.7 kcal/mol, which enables fast and efficient proton pump action. Further QM/MM (quantum mechanical/molecular mechanical) and FMO (fragment molecular orbital) calculations revealed that the potential energy change during the proton transfer is tightly regulated by the composition and the geometry of the surrounding amino acid residues of bacteriorhodopsin. Here, we report in detail the Asp96 --> Schiff base proton translocation mechanism of bacteriorhodopsin. Additionally, we discuss the effectiveness of combining quantum chemical calculations with truncated cluster models followed by advanced quantum chemical calculations applied to a whole protein to elucidate its reaction mechanism.     

Water Activity Regulates the Q(A)(-) to Q(B) electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides

We report on the effects of water activity and surrounding viscosity on electron transfer reactions taking place within a membrane protein: the reaction center (RC) from the photosynthetic bacterium Rhodobacter sphaeroides. We measured the kinetics of charge recombination between the primary photoxidized donor (P(+)) and the reduced quinone acceptors. Water activity (aW) and viscosity (eta) have been tuned by changing the concentration of cosolutes (trehalose, sucrose, glucose, and glycerol) and the temperature. The temperature dependence of the rate of charge recombination between the reduced primary quinone, Q(A)(-), and P(+) was found to be unaffected by the presence of cosolutes. At variance, the kinetics of charge recombination between the reduced secondary quinone (Q(B)(-)) and P(+) was found to be severely influenced by the presence of cosolutes and by the temperature. Results collected over a wide eta-range (2 orders of magnitude) demonstrate that the rate of P(+)Q(B)(-) recombination is uncorrelated to the solution viscosity. The kinetics of P(+)Q(B)(-) recombination depends on the P(+)Q(A)(-)Q(B) <--> P(+)Q(A)Q(B)(-) equilibrium constant. Accordingly, the dependence of the interquinone electron transfer equilibrium constant on T and aW has been explained by assuming that the transfer of one electron from Q(A)(-) to Q(B) is associated with the release of about three water molecules by the RC. This implies that the interquinone electron transfer involves at least two RC substates differing in the stoichiometry of interacting water molecules.     

Systematic approach to the quantitative voltammetric analysis of the FeIII/FeII component of the [alpha2-Fe(OH2)P2W17O61]7-/8- reduction process in buffered and unbuffered aqueous media

The one-electron reduction of [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-) at a glassy carbon electrode was investigated using cyclic and rotating-disk-electrode voltammetry in buffered and unbuffered aqueous solutions over the pH range 3.45-7.50 with an ionic strength of approximately 0.6 M maintained. The behavior is well-described by a square-scheme mechanism P + e(-) <--> Q (E(1)(0/) = -0.275 V, k(1)(0/) = 0.008 cm s(-1), and alpha(1) = 1/2), PH(+) + e(-) <--> QH(+) (E(2)(0/) = -0.036 V, k(2)(0/) = 0.014 cm s(-1), and alpha(2) = 1/2), PH(+) <--> P + H(+) (K(P) = 3.02 x 10(-6) M), and QH(+) <--> Q + H(+) (K(Q) = 2.35 x 10(-10) M), where P, Q, PH(+), and QH(+) correspond to [alpha(2)-Fe(III)(OH)P(2)W(17)O(61)](8-), [alpha(2)-Fe(II)(OH)P(2)W(17)O(61)](9-), [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-), and [alpha(2)-Fe(II)(OH(2))P(2)W(17)O(61)](8-), respectively; E(1)(0)' and E(2)(0)' are the formal potentials, k(1)(0)' and k(2)(0)' are the formal (standard) rate constants, and K(P) and K(Q) are the acid dissociation constants for the relevant reactions. The analysis for the buffered media is based on the approach of Laviron who demonstrated that a square scheme with fully reversible protonations, reversible or quasi reversible electron transfers with the assumption that alpha(1) = alpha(2), can be well-described by the behavior of a simple redox couple, ox + e(-) <--> red, whose formal potential, E(app)(0)', and standard rate constant, k(app)(0)', are straightforwardly derived functions of pH, as are the values of E(1)(0)', k(1)(0)', E(2)(0)', k(2)(0)', and K(P) (only three of the four thermodynamic parameters in a square scheme can be specified). It was assumed that alpha(app) = 1/2, and the simulation program DigiSim was used to determine the values of E(app)(0)' and k(app)(0)', which are required to describe the cyclic voltammograms obtained in buffered media in the pH range from 3.45 to 7.52 (buffer-related reactions which effect general acid-base catalysis are included in the simulations). DigiSim simulations of cyclic voltammograms obtained in unbuffered media yielded the values of E(1)(0)' and k(1)(0)'; K(Q) was then directly computed from thermodynamic constraints. These simulations included additional reactions between the redox species and H(2)O. The value of the diffusion coefficient of the [alpha(2)-Fe(III)(OH(2))P(2)W(17)O(61)](7-), 2.92 x 10(-6) cm(2) s(-1), was determined using DigiSim simulations of voltammograms at a rotating disk electrode in buffered and unbuffered media at pH 3.45. The diffusion coefficients of all redox species were assumed to be identical. When the pH is greater than 6, instability of P (i.e., [alpha(2)-Fe(III)(OH)P(2)W(17)O(61)](8-)) led to the loss of the reactant and precluded lengthy experimentation.     

Influence of cardiolipin on the functionality of the Q(a) site of the photosynthetic bacterial reaction center

The effect of cardiolipin on the functionality of the Q(A) site of a photosynthetic reaction center (RC) was studied in RCs from the purple non-sulfur bacterium Rhodobacter sphaeroides by means of time-resolved absorbance measurements. The binding of the ubiquinone-10 to the Q(A) site of the RC embedded in cardiolipin or lecithin liposomes has been followed at different temperatures and phospholipid loading. A global fit of the experimental data allowed us to get quite reliable values of the thermodynamic parameters joined to the binding process. The presence of cardiolipin does not affect the affinity of the Q(A) site for ubiquinone but has a marked influence on the rate of P+QA(-) --> PQA electron transfer. The P+QA(-) charge recombination kinetics has been examined in liposomes made of cardiolipin/lecithin mixtures and in detergent (DDAO) micelles doped with cardiolipin. The electron-transfer rate constant increases upon cardiolipin loading. It appears that the main effect of cardiolipin on the electron transfer can be ascribed to a destabilization of the charge-separated state. Results obtained in micelles and vesicles follow the same titration curve when cardiolipin concentration evaluated with respect to the apolar phase is used as a relevant variable. The dependence of the P+QA(-) recombination rate on cardiolipin loading suggests two classes of binding sites. In addition to a high-affinity site (compatible with previous crystallographic studies), a cooperative binding, involving about four cardiolipin molecules, takes place at high cardiolipin loading.     

Conformational control of the Q(A) to Q(B) electron transfer in bacterial reaction centers: evidence for a frozen conformational landscape below -25 degrees C

The competition between the P(+)Q(A)(-) --> PQ(A) charge recombination (P, bacteriochlorophyll pair acting as primary photochemical electron donor) and the electron transfer to the secondary quinone acceptor Q(A)(-)Q(B) --> Q(A)Q(B)(-) (Q(A) and Q(B), primary and secondary electron accepting quinones) was investigated in chromatophores of Rb. capsulatus, varying the temperature down to -65 degrees C. The analysis of the flash-induced pattern for the formation of P(+)Q(A)Q(B)(-) shows that the diminished yield, when lowering the temperature, is not due to a homogeneous slowing of the rate constant k(AB) of the Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron transfer but to a distribution of conformations that modulate the electron transfer rate over more than 3 orders of magnitude. This distribution appears "frozen", as no dynamic redistribution was observed over time ranges > 10 s (below -25 degrees C). The kinetic pattern was analyzed to estimate the shape of the distribution of k(AB), showing a bell-shaped band on the high rate side and a fraction of "blocked" reaction centers (RCs) with very slow k(AB). When the temperature is lowered, the high rate band moves to slower rate regions and the fraction of blocked RCs increases at the expense of the high rate band. The RCs that recombine from the P(+)Q(A)Q(B)(-) state appear temporarily converted to a state with rapid k(AB), indicating that the stabilized state described by Kleinfeld et al. (Biochemistry 1984, 23, 5780-5786) is still accessible at -60 degrees C.     

Mechanistic implications of proton transfer coupled to electron transfer.

The kinetics of electron transfer for the reactions cis-[Ru(IV)(bpy)2(py)(O)]2+ + H+ + [Os(II)(bpy)3]2+ <==> cis-[Ru(III)(bpy)2(py)(OH)]2+ + [Os(III)(bpy)3]3+ and cis-[Ru(III)(bpy)2(py)(OH)]2+ + H+ + [Os(II)(bpy)3]2+ <==> cis-[Ru(II)(bpy)2(py)(H2O)]2+ + [Os(III)(bpy)3]3+ have been studied in both directions by varying the pH from 1 to 8. The kinetics are complex but can be fit to a double "square scheme" involving stepwise electron and proton transfer by including the disproportionation equilibrium, 2cis-[Ru(III)(bpy)2(py)(OH)]2+ <==> (3 x 10(3) M(-1) x s(-1) forward, 2.1 x 10(5) M(-1) x s(-1) reverse) cis-[Ru(IV)(bpy)2(py)(O)]2+ + cis-[Ru(II)(bpy)2(py)(H2O)]2+. Electron transfer is outer-sphere and uncoupled from proton transfer. The kinetic study has revealed (1) pH-dependent reactions where the pH dependence arises from the distribution between acid and base forms and not from variations in the driving force; (2) competing pathways involving initial electron transfer or initial proton transfer whose relative importance depends on pH; (3) a significant inhibition to outer-sphere electron transfer for the Ru(IV)=O2+/Ru(III)-OH2+ couple because of the large difference in pK(a) values between Ru(IV)=OH3+ (pK(a) < 0) and Ru(III)-OH2+ (pK(a) > 14); and (4) regions where proton loss from cis-[Ru(II)(bpy)2(py)(H2O)]2+ or cis-[Ru(III)(bpy)2(py)(OH)]2+ is rate limiting. The difference in pK(a) values favors more complex pathways such as proton-coupled electron transfer.