Effects of pH and light on the membrane conductance measured in the acid and basic zones ofChara

Summary The area-specific coductance of the membrane in the acid and basic zones (denoted byG _A andG _B , respectively) ofChara cells was measured in flowing solutions, containing 5mm zwitterionic buffer, as a function of the external pH(denoted by pH⁰). During illuminationG _A was 1 S/m² for pH⁰ in the range 5 to 8.5, and increased markedly to 3 to 6 S/m² at higher pH₀.G _B , however, was always larger thanG _A during illumination with a typical magnitude of 5 to 15 S/m² for pH⁰ 6 to 12. Thus under many experimental conditions it is possible that there is no single correct value for the membrane area-specific conductance. A flow of current in the external medium between the acid and basic regions was found to be associated with pH banding, and also withG _B exceedingG _A . This current could be present in flowing solutions without added HCO ₃ ^– over a wide range of pH⁰ and at high (25mm) buffer concentration. Combining measurements ofG _A andG _B with measurements of the currents in the acid and basic zones (denoted byJ _A andJ _B , respectively), it was estimated that the resting (i.e. in the absence of net current flow) potential difference (PD) across the membranes within the individual zones (denoted byU _A andU _B ) was –265±20 and –183±5 mV, respectively, during illumination. Upon the removal of illumination at pH⁰-7.5,G _A ,G _B andJ _B were found to decrease rapidly during the initial few hundred seconds. During this period (U _B –V _m ) remained relatively constant. A transient hyperpolarization ofV _m often occurred, the magnitude of which was correlated with the magnitude ofJ _B prior to the removal of illumination. After some 0.5 to 1 ksec of darkness,G _A andG _B had both decreased considerably and nowG _A G _B andU _A U _B V _m . Eventually, after 2 to 8 ksec of darkness, the membrane conductance was effectively homogeneous with a much smaller magnitude (typically<0.2S/m²) andV _m was depolarized by typically 5 to 15 mV.     

The sequence of electron carriers in the reaction of cytochromec oxidase with oxygen

Kinetic studies of the electron transfer processes performed by cytochrome oxidase have assigned rates of electron transfer between the metal centers involved in the oxidation of ferrocytochromec by molecular oxygen. Transient-state studies of the reaction with oxygen have led to the proposal of a sequence of carriers from cytochromec, to Cu_A, to cytochromea, and then to the binuclear (i.e., cytochromea ₃-Cu_B) center. Electron exchange rates between these centers agree with relative center-to-center distances as follows; cytochromec to Cu_A 5–7 Å, cytochromec to cytochromea 20–25 Å, Cu_A to cytochromea 14–16 Å and cytochromea to cytochrome a₃-Cu_B 8–10 Å. It is proposed that the step from cytochromea to the binuclear center is the key control point in the reaction and that this step is one of the major points of energy transduction in the reaction cycle.     

Role of cooperative H(+)/e(-) linkage (redox bohr effect) at heme a/Cu(A) and heme a(3)/Cu(B) in the proton pump of cytochrome c oxidase

It is a pleasure to contribute to the special issue published in honor of Vladimir Skulachev, a distinguished scientist who greatly contributes to maintain a high standard of biochemical research in Russia. A more particular reason can be found in his work (Artzabanov, V. Y., Konstantinov, A. A., and Skulachev, V. P. (1978) FEBS Lett., 87, 180–185), where observations anticipating some ideas presented in my article were reported. Cytochrome c oxidase exhibits protonmotive, redox linked allosteric cooperativity. Experimental observations on soluble bovine cytochrome c oxidase are presented showing that oxido-reduction of heme a/Cu_A and heme a ₃/Cu_B is linked to deprotonation/protonation of two clusters of protolytic groups, A₁ and A₂, respectively. This cooperative linkage (redox Bohr effect) results in the translocation of 1 H⁺/oxidase molecule upon oxido-reduction of heme a/Cu_A and heme a ₃/Cu_B, respectively. Results on liposome-reconstituted oxidase show that upon oxidation of heme a/Cu_A and heme a ₃/Cu_B protons from A₁ and A₂ are released in the outer aqueous phase. A₁ but not A₂ appears to take up protons from the inner aqueous space upon reduction of the respective redox center. A cooperative model is presented in which the A₁ and A₂ clusters, operating in close sequence, constitute together the gate of the proton pump in cytochrome c oxidase.Translated from Biokhimiya, Vol. 70, No. 2, 2005, pp. 220–230.Original Russian Text Copyright © 2005 by Papa.This revised version was published online in April 2005 with corrections to the post codes.     

A numerical experiment on the determination of kinetic rate constants in the presence of diffusion

Two chemicals,A andB, are allowed to diffuse together and a reaction described by $$A + B\mathop \rightleftharpoons \limits_{K_{ - 1} }^{K_1 } C$$ is allowed to proceed. This system is described mathematically by a system of partial differential equations. A numerical procedure is presented to find the rate constants ofK ₁ andK _?1. A systematic analysis of the effects of errors is also presented.     

Kinetics of ultrafiltration hemodialysis

The expressions of Wolfet al. (1951) and Renkin (1956) for the kinetics of artificial kidneys are generalized to include the effects of filtration. IfB is the bath volume,b the relevant volume of distribution,f the filtration rate,t the time, andA ₀,B ₀,b ₀ representA, B, andb at timet=0, then the plasma concentrationA is given by

$$\frac{A}{{A_0 }} = \frac{{B_0 }}{{B_0 + b_0 }}e^{ - \frac{{\left( {B_0 + b_0 } \right)}}{{B_0 }}\frac{{D_f }}{{b_0 }}K\left( {ft} \right)t} + \frac{{b_0 }}{{B_0 + b_0 }}$$     

Resolution and reconstitution of complex V of the mitochondrial oxidative phosphorylation system: properties and composition of the membrane sector

The antigenic properties of purified glycinin subunits were studied using antibodies prepared against them. Antisera against native glycinin did not react with the isolated subunits, and antibodies prepared against the purified subunits were not active against native glycinin. When native glycinin -was denatured, the antiglycinin immunoglobulins lost their ability to react with it, although the denatured complex was then recognized by antibodies against the purified subunits. Substantial structural rearrangement apparently occurred when the native complex was denatured and disaggregated. Acidic polypeptides A_1a, A_1b, and A₂ had similar determinants as judged by their reactions against A_1a and A_1a antisera. The reaction of the A₃ polypeptides with these antibodies was of lower intensity and in each case clear spurs of cross-reactivity were visible. No cross-reaction was detected between polypeptide A₄ and either anti-A_1a or A₂. Anti-A₃ antibodies reacted with each of the acidic polypeptides of glycinin, and distinct spurs of cross-reactivity were observed between A₃ vs A_1a, A₃ vs A₂, and A₃ vs A₄. B₁ Antisera developed a reaction of identity between basic polypeptides B₁ and B₂, but reacted very weakly with B₃ and B₄. The acidic and basic polypeptides of glycinin were immunologically unrelated. The results demonstrated that immunological tests would successfully differentiate some members of the family of acidic subunits, and other immunoglobulins would discriminate between members of the family of basic subunits.     

Studies in imitative behavior: A generalization of the rashevsky model; Its mathematical properties

This paper is based on N. Rashevsky's theory of imitative behavior, the underlying idea being that performance of one reaction by a given individual produces an increased stimulation (or tendency) toward the same reaction in other individuals. For simplicity, consideration is limited to cases in which each individual may choose only between two (or two main categories of) reactions, denoted byA andB in the following. However, upon suggestion from Dr. Rashevsky and certainly in better agreement with actual facts, the strength of imitative interaction is assumed to vary from individual to individual. More precisely, if Ψ_i denotes the additional excitation caused by imitation in theith individual,PA_i the probability for performance of reactionA, andPB_i the probability for performance of reactionB by theith individual, we postulate that where the constants α _ik ^′ and β _ik ^′ (coefficients of imitative interaction) measure the amount of imitative influence exerted by thekth individual upon theith,N being the total number of individuals in the population. The term — α_i Ψ_i accounts for the spontaneous decay of excitation, and the quantities α _ik ^′ and α _ik ^′ are assumed to benon-negative. The expressions forPA_i andPB_i are obtained from H. D. Landahl's theory of conflicting stimuli; they depend non-linearly on the values Ψ_i. It is implicit in this formulation that the theory can only be applied if the frequency of contacts between individuals is not too small. Some further shortcomings and limitations of the model are outlined, and the discussion includes suggestions for reinterpretation and improvement of the theory. If all the quantities α _ik ^′ and α _ik ^′ have the same value, sayA, we return to the case treated by Rashevsky (and Landau, 1950); these authors, however, replace the sums in the equation above by integrals, which automatically restricts the validity of their results to very large values ofN. Their work may therefore be characterized by the assumption of uniform interaction in large populations. Our equations, on the other hand, are applicable even to very small groups, and therein lies one of their main advantages. In this paper the mathematical properties of the non-linear system of equations above are studied with particular reference to the existence and stability of steady states [dΨ_i/dt ≡ 0;, i = 1 , 2, . . . N]. A sufficient condition for the existence of only one stable steady state is derived. It may be formulated roughly by stating that all the coefficients of interaction should be sufficiently small. It that is not the case, there may exist a greater number of stationary states. In particular, two of them (called “extremal”) have the following properties: they arestable and such that the average number of individuals in the group performing one or the other reaction is the largest (or smallest) possible as compared with the other steady states. Hence the situation is qualitatively similar to that found by Rashevsky and Landau.Quantitatively, however, important differences may arise, depending on the nature of the matrix specifying the interaction. A stable state may be approached through damped oscillations, but this effect is important only if the damping is sufficiently small for the oscillations to become practically observable. Little information could be obtained on this point, due to mathematical difficulties. As mentioned above, the most interesting applications of this theory will be with respect to small populations or to populations partitioned into subgroups with varying amounts of imitative interaction within as well as between groups.     

Polymorphism and Expression of cDNAs Encoding Glycinin Subunits

The nucleotide sequence of cDNA encoding the glycinin A₂B_1a subunit from var. Shirotsurunoko was determined and compared with that in the case of var. Bonminori. The comparison showed six nucleotide substitutions in the coding sequence, one of which results in one amino acid replacement, and three in the 3'-noncoding region. These differences indicate the occurrence of polymorphism of the glycinin A₂B_1a subunit gene between the cultivars. The present data together with the previous results indicating the polymorphism of the A_1aB_1b subunit gene [(Utsumi et al., J. Agric. Food Chem., 35, 210 (1987)] suggest that the polymorphism is a general property of glycinin subunit genes. The expression of cDNAs encoding the A₂B_1a and A_1aB_1b subunits was examined. The results obtained in both in vivo- and in vitro-expression experiments indicate that the resultant products were readily degraded.     

The mathematical theory of group selection. I. Full solution of a nonlinear Levins E = E(x) model

The first complete overtime solution is obtained for a group selection model of Levins E = E(x) type with recolonization but no other gene flow between islands. Assuming a subdivided population at carrying capacity, the model describes selection at a biallelic locus (A, a) where a is opposed by Mendelian selection but is favored by a lower rate of extinction of demes having high a frequency. By contrast to the linear diffusion equations encountered in classical mathematical genetics, the PDE governing the dynamics is now nonlinear in the metapopulation gene frequency distribution φ(x, t); furthermore, the initial conditions now heavily influence the equilibrium distribution φ_∞(x). A fully explicit formula (20) expressing this dependence is derived. The results indicate that a fixation is never reached, but (A, a) polymorphism in the metapopulation will result if , where s 1 parametrizes the strength of Mendelian selection, E(x) is the Levins extinction operator, h (typically in the open interval (0, 1)) is the dominance of a, and B is a parameter measuring the flatness of the initial distribution f(x) in the x → 1 limit.     

Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers

Soybean mutant lines that differ in 11S glycinin and 7S β-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A₄ null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A_1aB₂, A₂B_1a, A_1b B_1b, and A₃B₄ subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A₄ peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A₄ (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection.     

Recovery of photosystem I and II activities during re-hydration of lichen<Emphasis Type="Italic"> Hypogymnia physodes</Emphasis> thalli

Photochemical efficiencies of photosystem I (PSI) and photosystem II (PSII) were studied in dry thalli of the lichen Hypogymnia physodes and during their re-hydration. In dry thalli, PSII reaction centers are photochemically inactive, as evidenced by the absence of variable chlorophyll (Chl) fluorescence, whereas the primary electron donor of PSI, P700, exhibits irreversible oxidation under continuous light. Upon application of multiple- and, particularly, single-turnover pulses in dry lichen, P700 oxidation partially reversed, which indicated recombination between P700⁺ and the reduced acceptor F_X of PSI. Re-wetting of air-dried H. physodes initiated the gradual restoration of reversible light-induced redox reactions in both PSII and PSI, but the recovery was faster in PSI. Two slow components of P700⁺ reduction occurred after irradiation of partially and completely hydrated thalli with strong white light. In contrast, no slow component was found in the kinetics of re-oxidation of Q_A^–, the reduced primary acceptor of PSII, after exposure of such thalli to white light. This finding indicated the inability of PSII in H. physodes to provide the reduction of the plastoquinone pool to significant levels. It is concluded that slow alternative electron transport routes may contribute to the energetics of photosynthesis to a larger extent in H. physodes than in higher plants.Abbreviations A₀ and A₁ Primary acceptor chlorophyll and secondary electron acceptor phylloquinone - Chl a Chlorophyll a - F_m Maximal level of chlorophyll fluorescence when all PSII centers are closed - F_o Minimal level of fluorescence when all PSII centers are open after dark adaptation - FR Far-red - F_v Variable fluorescence (=F_m–F_o) - F_X, F_A, and F_B Iron–sulfur centers - MT pulse Multiple-turnover pulse - PS Photosystem - P700 Reaction center chlorophyll of PSI - Q_A Primary quinone acceptor of PSII - Q_B Secondary quinone acceptor of PSII - ST pulse Single-turnover pulse     

Mycotoxin-producing potential of fungi associated with qat (Catha edulis) leaves in yemen

Forty-four fungal species belonging to 20 genera were isolated from 30 samples of qat leaves. The most frequent genera wereAspergillus, Alternaria, Penicillium, andCladosporium followed byFusarium, Drechslera, Chœtomium, andMucor. The most prevalent species in above genera wereAspergillus niger, A. flavus, A fumigatus, Alternaria alternata, Penicillium chrysogenum, P. citrinum, Cladosporium cladosporioides, andFusarium verticillioides. From these fungi, 17 species (39%) related to 7 genera (35%) proved to be true endophytes. Eleven out of 75 isolates were mycotoxigenic.A. alternata produced alternariol and alternariol monomethyl ether whereasA. flavus produced aflatoxins B₁ and B₂. Ochratoxin A, sterigmatocystin, citrinin and T-2 toxin were produced byA. ochraceus, A. versicolor, P. citrinum andF. oxysporum, respectively. The presence of such toxigenic fungi associated with qat leaves is considered to be a threat to public health.     

The effects of chemicals on the phenotypic expression of aVestigial mutant inDrosophila melanogaster

Several kinds of chemicals were tested to determine their effects on the wings of avestigial mutant inDrosophila melanogaster. Two isogenic strains were used, viz.vg-ms andB; vg-ms, both co-isogenic with the Oregon-isogenic strain. Ammonium lactate was found to have a conspicuous effect in enlarging thevestigial wings. At an appropriate concentration of this agent the wings of thevg-ms- andB;vg-ms-co-isogenic strains were restored almost to wild-type wing at 27°C. This fact indicates that the wings of thevg-ms mutant can be restored to wild type not only by temperature but also by certain chemicals. Ammonium lactate was effective conspicuously on bothBar andvestigial-ms mutants. However, there was found an interaction betweenBar andvestigial-ms when these genes were combined. The manifestation ofB is enhanced byvg-ms, especially under the the condition of feeding in medium containing the chemical, and the manifestation ofvg-ms is reduced byB.This work forms part of a thesis for the doctorate of Kyoto University.     

Mathematical biophysics of cellular forms and movements

Rashevsky's equations for describing the joint variation of cell shape and concentration of a metabolite are discussed. Conditions for the existence of non-spherical equilibria and the location of these are obtained and involve only two parametersa andA. Sufficient (but not necessary) conditions for the stability of these equilibria can also be expressed in terms of these parameters alone. Necessary conditions involve in some cases a third parameterB. Quasi-periodic fluctuations about a stable nonspherical equilibrium may occur, but only in caseB lies on a certain finite range which can be defined in terms ofa andA.     

Production of extracellular enzymes and aflatoxins in solid substrate fermentation with aflatoxigenic<Emphasis Type="Italic">Aspergillus</Emphasis> spp.

AflatoxigenicAspergillus flavus andAspergillus parasiticus were subjected to solid substrate fermentation process for 6 days to determine the formation of aflatoxins and production of extracellular enzymes (amyloglucosidase, cellulase, invertase and proteinase). Both organisms produced enzymes which generally increased with fermentation.Aspergillus flavus produced four enzymes whereasA. parasiticus produced three with no proteinase activity.Aspergillus parasiticus produced aflatoxins B₁, B₂ and G₁ but no G₂ andA. flavus produced aflatoxins B₁ and B₂. Invertase showed the highest activity withA. parasiticus and that corresponded with the highest total toxin produced. The enzyme activities were higher withA. parasiticus thanA. flavus although total toxins produced byA. parasiticus were lower than total toxins produced byA. flavus under the same environmental conditions.     

Hemoglobin types in saanen goats and Barbary sheep: Genetic and comparative aspects

By the use of the Immobiline technique at pH ranges 7.0–7.6 and 6.9–7.9, 16 different hemoglobin (Hb) phenotypes were observed in 61 English Saanen goats. They are explained in this breed by a genetic theory of five β-globin genes (A ₄,A ₆,A ₈,E, andD) and two closely linked α-globin loci (′α and ″α) of which the ″α has a variant allele, provisionally called ″α ^X . Family data together with observed and expected Hb frequencies were in agreement with the genetic theory. Among six Barbary sheep there were three Hb phenotypes explained by the occurrence of the β-chain allelesB andC ^na.     

Allosteric modulators of human A2B adenosine receptor

Background

Among adenosine receptors (ARs) the A_2B subtype exhibits low affinity for the endogenous agonist compared with the A₁, A_2A, and A₃ subtypes and is therefore activated when concentrations of adenosine increase to a large extent following tissue damages (e.g. ischemia, inflammation). For this reason, A_2B AR represents an important pharmacological target.

Methods

We evaluated seven 1-benzyl-3-ketoindole derivatives (7–9) for their ability to act as positive or negative allosteric modulators of human A_2B AR through binding and functional assays using CHO cells expressing human A₁, A_2A, A_2B, and A₃ ARs.

Results

The investigated compounds behaved as specific positive or negative allosteric modulators of human A_2B AR depending on small differences in their structures. The positive allosteric modulators 7a,b and 8a increased agonist efficacy without any effect on agonist potency. The negative allosteric modulators 8b,c and 9a,b reduced agonist potency and efficacy.

Conclusions

A number of 1-benzyl-3-ketoindole derivatives were pharmacologically characterized as selective positive (7a,b) or negative (8c, 9a,b) allosteric modulators of human A_2B AR.

General significance

The 1-benzyl-3-ketoindole derivatives 7–9 acting as positive or negative allosteric modulators of human A_2B AR represent new pharmacological tools useful for the development of therapeutic agents to treat pathological conditions related to an altered functionality of A_2B AR.     

Chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence induction kinetics in leaves predicted from a model describing each discrete step of excitation energy and electron transfer associated with Photosystem II

Chlorophyll a fluorescence induction (FI) is widely used as a probe for studying photosynthesis. On illumination, fluorescence emission rises from an initial level O to a maximum P through transient steps, termed J and I. FI kinetics reflect the overall performance of photosystem II (PSII). Although FI kinetics are commonly and easily measured, there is a lack of consensus as to what controls the characteristic series of transients, partially because most of the current models of FI focus on subsets of reactions of PSII, but not the whole. Here we present a model of fluorescence induction, which includes all discrete energy and electron transfer steps in and around PSII, avoiding any assumptions about what is critical to obtaining O J I P kinetics. This model successfully simulates the observed kinetics of fluorescence induction including O J I P transients. The fluorescence emission in this model was calculated directly from the amount of excited singlet-state chlorophyll in the core and peripheral antennae of PSII. Electron and energy transfer were simulated by a series of linked differential equations. A variable step numerical integration procedure (ode15s) from MATLAB provided a computationally efficient method of solving these linked equations. This in silico representation of the complete molecular system provides an experimental workbench for testing hypotheses as to the underlying mechanism controlling the O J I P kinetics and fluorescence emission at these points. Simulations based on this model showed that J corresponds to the peak concentrations of Q _A ⁻ Q_B (Q_A and Q_B are the first and second quinone electron acceptor of PSII respectively) and Q _A ⁻ Q _B ⁻ and I to the first shoulder in the increase in concentration of Q _A ⁻ Q _B ²⁻ . The P peak coincides with maximum concentrations of both Q _A ⁻ Q _B ²⁻ and PQH₂. In addition, simulations using this model suggest that different ratios of the peripheral antenna and core antenna lead to differences in fluorescence emission at O without affecting fluorescence emission at J, I and P. An increase in the concentration of Q_B-nonreducing PSII centers leads to higher fluorescence emission at O and correspondingly decreases the variable to maximum fluorescence ratio (F _v/F _m).     

Proteins as potential bacterial growth inhibitors in foods: Suppression of the activity of water by proteins as determined by NMR relaxation methods

Summary Food microbiologists have long known that suppression of the activity of water,a _w, can retard microbial growth in food systems. Traditionally,a _w, suppression has been achieved by addition of salts or humectants to foods. To limit the amount of preservatives added to food products, studies were initiated to assess the feasibility of using proteins to suppressa _w to a practical value for retarding bacterial growth and to determine the optimum environmental condition for maximizing this effect for milk proteins. New expressions were developed relating observed longitudinal and transverse NMR relaxation rates, in the absence of cross-relaxation, to protein hydration , to the protein activity coefficient, _p, and to the correlation time of the bound water, _c. From _p, the second virial coefficient of the protein,B _o, can be found. By use of andB _o,a _w could then be directly evaluated at any protein concentration. Resulting expressions were tested by²H-NMR relaxation measurements made as a function of protein concentration, for: -lactoglobulin A (the major whey protein) under nonassociating (pH 6.0) and associating (pH 4.65) conditions; and for casein (the major milk protein) in the micellar (with added Ca²⁺) and submicellar (without Ca²⁺) forms. Values ofa _w calculated from these²H-NMR data show that casein, at all the concentrations and temperatures examined, suppressesa _w more than does -lactoglobulin A because of a largerB _o. In turn, micellar casein suppressesa _w to a larger extent than does submicellar casein because of a larger . Extrapolation ofa _w at 4°C to a concentration ten times that in normal milk yields a value, ofa _w of less than 0.95, at whichSalmonella and some strains ofClostridium botulinum no longer grow. These results are in agreement with what is known about storageability of condensed milk. Generalizations regarding the types of proteins and cosolutes to be used for suppressinga _w will be discussed. Structural information on these proteins calculated from _c will also be presented.     

Cytochrome oxidase: pathways for electron tunneling and proton transfer

 Electrons from cytochrome c, the substrate of cytochrome oxidase, a redox-linked proton pump, are accepted by Cu_A in subunit II. From there they are transferred to the proton pumping machinery in subunit I, cytochrome a and cytochrome a ₃–Cu_B. The reduction of the latter site, which is the dioxygen reducing unit, is coupled to proton uptake. Dioxygen reduction involves a peroxide and a ferryl ion intermediate, and it is the transition between these and back to the resting oxidized enzyme that are coupled to proton pumping. The X-ray structures suggest electron–transfer pathways that can account for the observed rates provided that the reorganization energies are small. They also reveal two proton-transfer pathways, and mutagenesis experiments have shown that one is used for proton uptake during the initial reduction of cytochrome a ₃–Cu_B, whereas the other mediates transfer of the pumped protons. Received: 23 March 1998 / Accepted: 11 May 1998