Environmental effects on H-bond potentials: A SCRF MO CNDO/2 study of some model systems

The self-consistent reaction field (SCRF) theory of solvent effects upon dipolar species has been applied to the study of H-bonded systems. A model to represent the enzyme core medium is discussed. It is shown, albeit heuristically, that this type of environment may be represented with the combined effect of a reaction field and an inhomogeneous external electric field acting over the site system, this latter being provided by the main chain dipolar peptide residues. The generalization of the reaction field concept attained within the SCRF theory allowed for this extention to be operationally implemented.The model systems considered are: a formaldehyde-water, acetone-water, a water dimer and a tetrahedrally arranged water trimer. The interest has been focuzed on the study of the dependance upon the site-surrounding coupling strength of the intermolecular potentials and interactions related to the H-bond. The orientational and intermolecular distance dependance of the pair potential and the proton potentials have been considered.The perturbing effect of the enzyme core medium is manifested through the drastic variation of many (but not all) of the H-bond potentials. The changes showed by the orientational component of the intermolecular potential together with that of the proton potential shape illustrate this point. As far as the proton and charge relay mechanisms are concerned, the results reported, while confirming our previous ones, shed a new light upon these matters. The sensitization of the H-bridge towards an external electric field is made possible by the presence of the reaction field, in absence of this latter, the external field effect is not significant.     

The inside pH determines rates of electron and proton transfer in vesicle-reconstituted cytochrome c oxidase

Cytochrome c oxidase is the terminal enzyme in the respiratory chains of mitochondria and many bacteria where it translocates protons across a membrane thereby maintaining an electrochemical proton gradient. Results from earlier studies on detergent-solubilized cytochrome c oxidase have shown that individual reaction steps associated with proton pumping display pH-dependent kinetics. Here, we investigated the effect of pH on the kinetics of these reaction steps with membrane-reconstituted cytochrome c oxidase such that the pH was adjusted to different values on the inside and outside of the membrane. The results show that the pH on the inside of the membrane fully determines the kinetics of internal electron transfers that are linked to proton pumping. Thus, even though proton release is rate limiting for these reaction steps (Salomonsson et al., Proc. Natl. Acad. Sci. USA, 2005, 102, 17624), the transition kinetics is insensitive to the outside pH (in the range 6-9.5).     

Potential generation in bilayer lipid membranes in the NADH-flavin mononucleotide-ubiquinone-6-O2 system

Membrane conductance and generation of transmembrane potential by the NADH oxidation reactions in the NADH-flavin mononucleotide-ubiquinone-6-O₂ system have been studied. It has been shown that in solutions of a relatively low buffer capacity at pH 5.8 in the presence of a proton carrier, a potential is generated, the value of which depends on the concentration of the reducer and amounts to 40–60 mV. In the absence of a proton carrier at pH 8, a potential arises, which suggests a transmembrane negative charge transfer. Bilayer lipid membranes have been shown to possess proton selectivity if the reaction is run at pH 3.7. At a pH higher than 5.8 the proton selectivity disappears. Schemes of potential generation in lipid bilayers in different conditions are suggested and discussed.     

Stimulation of ATP synthesis in Halobacterium halobium R1 by light-induced or artificially created proton electrochemical potential gradients across the cell membrane

The relationship between proton movement and phosphorylation in Halobacterium halobium R₁ has been investigated under anaerobic conditions. The light-induced changes in the bacteriorhodopsin are accompanied by proton movements across the cell membrane which result in pH changes in the suspending medium. The initial alkaline shift is shown to be closely paralleled by (and hence correlated with) ATP synthesis. Acidification of the medium in the presence of valinomycin, under conditions of low external potassium, brings about ATP synthesis in the dark.     

Effect of a low-frequencey magnetic field on esterase activity and change in pH in wheat germ during swelling of wehat seeds

The role of nonsteady phenomena determined by a low velocity of ion movements in a weak external field is considered in relation to their possible nonlinear effects on processes occurring in boundary layers near the membrane, particularly, on the release of membrane-bound proteins and pH value. It is shown that a short-term treatment of wheat seeds with low-frequency magnetic field at the stage of esterase activation during seed swelling enhances the activation of esterases; the effect observed at final stages of activation depends on the time after the treatment with electromagnetic field. Treatment of seeds with electromagnetic field at this stage changed qualitatively the time course of the release of reaction products into the medium: the reaction rate increased initially and then decreased below the control level. At earlier stages of swelling in treated seeds and at all stages in control seeds, the time course of the product release was linear. The retardation of the release of the reaction products at terminal stages of esterase activation is presumably related to the release of proteins and their complexes under the action of electromagnetic field and the resulting restoration of the barrier properties of membranes. Treatment with electromagnetic field also caused a noticeable acceleration of proton flow form the medium, which was judged from pH changes in the bulk medium and in the vicinity of germ surface. The difference between the treated and control samples after 23-24 h of imbibition became statistically significant and was as high as 0.4 pH units. By taking into account the nonsteady phenomena occurring upon action of low-frequency electromagnetic field, it is possible to explain unusual dependences of biological effects on the amplitude of the electromagnetic field, including the atypical enhancement of these effects by the action of weak low-frequency fields.     

Proton transfer during the reaction between fully reduced cytochrome c oxidase and dioxygen: pH and deuterium isotope effects.

The pH dependence of proton uptake and electron transfers during the reaction between fully reduced cytochrome c oxidase and oxygen has been studied using the flow-flash method. Proton uptake was monitored using different pH indicators. We have also investigated the effect of D2O on the electron-transfer reactions. Proton uptake was biphasic throughout the pH range studied (6.3-9.3), and the decrease of the observed rate constants at increasing pH could be described by titration curves with pKa values of 8-8.5. Of the four phases resolved in the redox reaction, the rate constants for the first two were independent of pH, whereas that of the third decreased at increasing pH with a pKa of 7.9. All phases except the first were slower in D2O than in H2O. The values obtained for kH/kD were 1.0 for the first phase, 1.4 for the second and third phases, and 2.5 for the fourth phase. We suggest from these results that the fast phase of proton uptake is initiated by the second phase of the redox reaction and that this step includes a partially rate-limiting internal proton transfer. The third and fourth phases of the redox reaction are suggested to be rate limited by proton uptake from the medium. The pH dependencies of the proton uptake reactions are consistent with the participation of a titrable group in the protein in proton transfer from the medium to the oxygen-binding site.     

\vec H^ + /2\bar e Stoichiometry of the NADH:Ubiquinone Reductase Reaction Catalyzed by Submitochondrial Particles

Mitochondrial NADH:ubiquinone-reductase (Complex I) catalyzes proton translocation into inside-out submitochondrial particles. Here we describe a method for determining the stoichiometric ratio (n) for the coupled reaction of NADH oxidation by the quinone acceptors. Comparison of the initial rates of NADH oxidation and alkalinization of the surrounding medium after addition of small amounts of NADH to coupled particles in the presence of Q₁ gives the value of n = 4. Thermally induced deactivation of Complex I [1,2] results in complete inhibition of the NADH oxidase reaction but only partial inhibition of the NADH:Q₁-reductase reaction. N-Ethylmaleimide (NEM) prevents reactivation and thus completely blocks the thermally deactivated enzyme. The residual NADH:Q₁-reductase activity of the deactivated, NEM-treated enzyme is shown to be coupled with the transmembraneous proton translocation (n = 4). Thus, thermally induced deactivation of Complex I as well as specific inhibitors of the endogenous ubiquinone reduction (rotenone, piericidin A) do not inhibit the proton translocating activity of the enzyme.     

Kinetics of luminescence in the 10−6–10−4-s range in Chlorella

The decay of luminescence in the 6–600-μs range following a microsecond flash has been studied in Chlorella. The decay is highly polyphasic; three kinetic components are outlined, in confirmation of the results of K. L. Zankel (1971, Biochim. Biophys. Acta 245, 373–385).Extrapolation of the decay to zero dark time suggests that a unique metastable species C^?₊, resulting from photochemical charge separation in the System II reaction center, is the substrate of the recombination reaction which gives rise to luminescence.The fast (5–10 μs) and medium (50–70 μs) phases of the decay denote different stabilization steps, preceding relaxation of the centers by electron and proton transduction to the photosynthetic chain.NH₂OH specifically inhibits the fast phase and enhances the medium phase. This effect is explained by assuming that the fast phase results from electron transfer from the water splitting system Z to the oxidized primary donor Y.3-(3,4-Dichlorophenyl)-1,1-dimethylurea (DCMU), in the presence of NH₂OH elicits another fast phase. It is believed that DCMU affords a parasitic stabilization of C^?₊ by forming a complex with Q^?.     

On the inactivity of thiol-subtilisin. The role of the intramolecular electric field

Based on computed proton affinities for several model systems, the energetics of proton transfer and the acidity of the catalytic triads Cys-His-Asn (papain). Cys-His-Asp (thiol-subtilisin) and Ser-His-Asp (subtilisin) are discussed. It is shown that in papain the ion-pair Cys--HisH+ exists owing to the intramolecular electric field, and that a similar situation is found in thiol-subtilisin. but not in subtilisin. Assuming similar reaction mechanisms for papain and thiol-subtilisin - i.e. proton transfer from HisH+ to the NH group of the scissile peptide bond - the inactivity of thil-subtilisin towards proteins is explained by the much greater basicity of His in the complex His-Asp- than in His-Asn. In order for this explanation to be consistent, it is tentatively concluded that the catalytic mechanism of the serine proteases is different from that of the cystein proteases, and involves direct transfer of the serine proton to the leaving group in the acylation step.     

Reaction mechanism of gramicidin S synthetase 1, phenylalanine racemase, of Bacillus brevis

We have demonstrated that gramicidin S synthetase 1 (GS 1), phenylalanine racemase [EC 5.1.1.11], of Bacillus brevis catalyzes the exchange between a proton in the medium and alpha-hydrogen of phenylalanine in the course of the racemase reaction by using tritiated water or L-phenyl[2,3-3H]alanine. GS 1 from some gramicidin S non-producing mutants of B. brevis lacking phenylalanine racemase activity did not catalyze the tritium exchange reaction. The proton exchange between phenylalanine bound as thioester on the GS 1-phenylalanine complex and water in the medium was detected, but 5,5'-dithiobis(2-nitrobenzoic acid)-modified complex lacked both the proton exchange and phenylalanine racemase activity. It is suggested that a base group, probably a sulfhydryl group, on the enzyme functions as proton donor and acceptor during the phenylalanine racemase reaction.     

Energy conservation by Rhodothermus marinus respiratory complex I

A sodium ion efflux, together with a proton influx and an inside-positive ΔΨ, was observed during NADH-respiration by Rhodothermus marinus membrane vesicles. Proton translocation was monitored by fluorescence spectroscopy and sodium ion transport by ²³Na-NMR spectroscopy. Specific inhibitors of complex I (rotenone) and of the dioxygen reductase (KCN) inhibited the proton and the sodium ion transport, but the KCN effect was totally reverted by the addition of menaquinone analogues, indicating that both transports were catalyzed by complex I. We concluded that the coupling ion of the system is the proton and that neither the catalytic reaction nor the establishment of the delta-pH are dependent on sodium, but the presence of sodium increases proton transport. Moreover, studies of NADH oxidation at different sodium concentrations and of proton and sodium transport activities allowed us to propose a model for the mechanism of complex I in which the presence of two different energy coupling sites is suggested.     

The medium reorganization energy for the charge transfer reactions in proteins

A low static dielectric permittivity of proteins causes the low reorganization energies for the charge transfer reactions inside them. This reorganization energy does not depend on the pre-existing intraprotein electric field. The charge transferred inside the protein interacts with its aqueous surroundings; for many globular proteins, the effect of this surroundings on the reorganization energy is comparable with the effect of reorganization of the protein itself while for the charge transfer in the middle of membrane the aqueous phase plays a minor role. Reorganization energy depends strongly on the system considered, and hence there is no sense to speak on the "protein reorganization energy" as some permanent characteristic parameter. We employed a simple algorithm for calculation of the medium reorganization energy using the numerical solution of the Poisson-Boltzmann equation. Namely, the reaction field energy was computed in two versions - all media having optical dielectric permittivity, and all the media with the static one; the difference of these two quantities gives the reorganization energy. We have calculated reorganization energies for electron transfer in cytochrome c, various ammine-ruthenated cytochromes c, azurin, ferredoxin, cytochrome c oxidase, complex of methylamine dehydrogenase with amicyanin, and for proton transfer in α-chymotrypsin. It is shown that calculation of the medium reorganization energy can be a useful tool in analysis of the mechanisms of the charge transfer reactions in proteins.     

Dual Role for the Tyrosine Decarboxylation Pathway in Enterococcus faecium E17: Response to an Acid Challenge and Generation of a Proton Motive Force

In this work we investigated the role of the tyrosine decarboxylation pathway in the response of Enterococcus faecium E17 cells to an acid challenge. It was found that 91% of the cells were able to remain viable in the presence of tyrosine when they were incubated for 3 h in a complex medium at pH 2.5. This effect was shown to be related to the tyrosine decarboxylation pathway. Therefore, the role of tyrosine decarboxylation in pH homeostasis was studied. The membrane potential and pH gradient, the parameters that compose the proton motive force (PMF), were measured at different pHs (pH 4.5 to 7). We obtained evidence showing that the tyrosine decarboxylation pathway generates a PMF composed of a pH gradient formed due to proton consumption in the decarboxylation reaction and by a membrane potential which results from electrogenic transport of tyrosine in exchange for the corresponding biogenic amine tyramine. The properties of the tyrosine transporter were also studied in this work by using whole cells and right-side-out vesicles. The results showed that the transporter catalyzes homologous tyrosine/tyrosine antiport, as well as electrogenic heterologous tyrosine-tyramine exchange. The tyrosine transporter had properties of a typical precursor-product exchanger operating in a proton motive decarboxylation pathway. Therefore, the tyrosine decarboxylation pathway contributes to an acid response mechanism in E. faecium E17. This decarboxylation pathway gives the strain a competitive advantage in nutrient-depleted conditions, as well as in harsh acidic environments, and a better chance of survival, which contributes to higher cell counts in food fermentation products.     

Study of ring influence and electronic response to proton transfer reactions. Reaction electronic flux analysis

In this article, a theoretical study of 1–5 proton transfers is presented. Two model systems which represent 1–5 proton transfer, 3-hidroxy-2-propenimine and salicyldenaniline have been studied as shown in Fig. 1. For this purpose, a DFT/B3LYP/6-311+G**, reaction force and reaction electronic flux analysis is made. The obtained results indicate that both proton transfers exhibit energetic and electronic differences emphasizing the role of the neighbor ring and the impact of conjugation on electronic properties.     

The inside pH determines rates of electron and proton transfer in vesicle-reconstituted cytochrome c oxidase

Cytochrome c oxidase is the terminal enzyme in the respiratory chains of mitochondria and many bacteria where it translocates protons across a membrane thereby maintaining an electrochemical proton gradient. Results from earlier studies on detergent-solubilized cytochrome c oxidase have shown that individual reaction steps associated with proton pumping display pH-dependent kinetics. Here, we investigated the effect of pH on the kinetics of these reaction steps with membrane-reconstituted cytochrome c oxidase such that the pH was adjusted to different values on the inside and outside of the membrane. The results show that the pH on the inside of the membrane fully determines the kinetics of internal electron transfers that are linked to proton pumping. Thus, even though proton release is rate limiting for these reaction steps (Salomonsson et al., Proc. Natl. Acad. Sci. USA, 2005, 102, 17624), the transition kinetics is insensitive to the outside pH (in the range 6-9.5).     

Reversibility of energy-dependent Ca2+ accumulation in mitochondria

Ca2+ accumulation in energized rat liver mitochondria has been studied after the blockage of mitochondrial permeability transition pore (MPTP) by cyclosporin A. It is shown that Ca2+ transport is coupled to the countertransport of protons: from the matrix of mitochondria in the medium in the course of Ca2+ accumulation, and, on the contrary, from the medium to mitochondrial matrix after membrane depolarization. In standard incubation medium containing K+, Cl-, oxidation substrate (glutamate) and inorganic phosphate (H2PO4(-)) the observed stoichiometry of the exchange is 1Ca2+ : 1H+. In accordance with this exchange ratio, proton, as well as cation, transport follows the same first-order kinetics, which is characterized in both cases by very close values of reaction half-times and rate constants. It is shown that reversion of Ca2+ -uniporter, sensitive to ruthenium red, is necessary for Ca2+ - efflux from the matrix ofdeenergized mitochondria when MPTP is blocked by cyclosporin A. It is also shown that Ca2+ -uniporter reversion takes place only after membrane depolarization and permeabilization by protonophore CCCP. Calcium release from mitochondria in the presence of CCCP is accompanied by proton flow into the matrix. Both calcium and proton fluxes are sensitive to Ca2+ uniporter blocker, ruthenium red, which gives the evidence of the identity of Ca2+ -efflux and influx pathways. The data obtained lead to the conclusion that calcium-proton exchange is necessary for Ca2+ -uniporter reversion and the reversibility of energy-dependent Ca2+ -uptake in mitochondria.     

Photo-induced electron transport and water state in Rhodospirillum rubrum chromatophores

It is shown that in bacterial chromatophores the pronounced changes in the free water content with a proton spin-spin relaxation time (T₂) of 10^?3—10^?2 s does not influence the efficiency of electron transfer from the photosynthetic reaction centre to the membrane pool of secondary acceptors. An abrupt inhibition of this process occurs only after the loss of the water with faster proton spin-spin relaxation time (T₂ of 10^?4 s). The process is reversible. The water fraction in question is obviously bound to the chromatophore proteins and forms the primary hydration layer.     

Effects of Ni2+ on proton extrusion, dark CO2 fixation and malate synthesis in maize roots

The presence of Ni²⁺ in the incubation medium of maize root segments ( Zen mays L. cv. Dekalb XL 640) induces an early and significant enhancement of the rate of proton extrusion both in the absence and presence of fusicoccin; with time, an inhibition of proton extrusion and a leakage of K⁺ appear. The inhibition of proton extrusion is accompanied by a decrease in the dark CO₂ fixation and by a decrease in the level of malate in the cells. Ni²⁺ inhibits in vitro phosphoenolpyruvale carboxylase activity of maize roots. The data indicate a correlation between the operativity of the proton pump and that of the malate-pH stat mechanism for the homeostasis of cytoplasmic pH.     

Intact Chloroplasts Show Ca-Gated Switching between Localized and Delocalized Proton Gradient Energy Coupling (ATP Formation)

Intact chloroplasts were compared to isolated thylakoids as to whether storage of the organelle in high KCl medium caused the energy coupling reactions to show a delocalized or a localized proton gradient energy coupling response. With isolated thylakoids, the occurrence of one or the other energy coupling mode can be reversibly controlled by the concentration of mono- and divalent cations used for the thylakoid storage media. Calcium was shown to be the key ion and previous evidence suggested a Ca²⁺-controlled gating of H⁺ fluxes in the thylakoid membrane system (G Chiang, RA Dilley [1987] Biochemistry 26: 4911-4916). Isolated, intact chloroplasts, which retained the outer envelope membranes during the 30 min or longer storage treatments in various concentrations of KCl and CaCl₂ (with sorbitol to maintain iso-osmotic conditions), were osmotically burst in a reaction cuvette and within 3 minutes were assayed for either a localized or a delocalized proton gradient energy coupling (ATP formation) mode. The intact chloroplast system was analogous to isolated thylakoids, with regard to the effects of KCl and CaCl₂ on the energy coupling mode. For example, adding 100 millimolar KCl to the intact organelle storage medium resulted in the subsequent ATP formation assay showing delocalized proton gradient coupling just as with isolated thylakoids. Adding 5 millimolar CaCl₂ to the 100 millimolar KCl storage medium resulted in a localized proton gradient coupling mode. Suspending thylakoids in stromal material previously isolated from intact chloroplast preparations and testing the energy coupling response showed that the stromal milieu has enough Ca²⁺ to cause the localized coupling response even though there was about 80 millimolar K⁺ in the intact chloroplasts used in this study (determined by atomic absorption spectrophotometry). Extrapolating the intact chloroplast data to the whole leaf level, we suggest that proton gradient energy coupling is normally of the localized mode, but under certain conditions it could be either localized or delocalized, depending on factors that affect the putative Ca²⁺-regulated proton flux gating function.     

Some experiments on the primary electron acceptor in reaction centres from Rhodopseudomonas sphaeroides

The bacterial reaction center absorbance change at 450 nm (A-450) assigned to an anionic semiquinone, has been suggested as a candidate for the reduced form of the primary electron acceptor in bacterial photosynthesis. In reaction centers of Rhodopseudomonas sphaeroides we have found kinetic discrepancies between the decay of A-450 and the recovery of photochemical competence. In addition, no proton uptake is measurable on the first turnover, although subsequent ones elicit one proton bound per electron. These results are taken to indicate that the acceptor reaction after a long dark period may be different for the first turnover than for subsequent ones. It is suggested that A-450 is still a likely candidate for the acceptor function but that in reaction centers, additional quinone may act as an adventitious primary acceptor when the “true” primary acceptor is reduced. Alternatively, the primary acceptor may act in a “ping-pong” fashion with respect to subsequent photoelectrons.