Energy and entropy balance of ATP synthesis

Are size and mitochondrial power of cells inter-determined?

Mitochondria are the central hub of ATP production in most eukaryotic cells. Cellular power (energy per unit time), which is primarily generated in these organelles, is crucial to our understanding of cell function in health and disease. We investigated the relation between a mitochondrion's power (metabolic rate) and host cell size by combining metabolic theory with the analysis of two recent databases, one covering 109 protists and the other 63 species including protists, metazoans, microalgae, and vascular plants. We uncovered an interesting statistical regularity: in well-fed protists, relatively elevated values of mitochondrion power cluster around the smallest cell sizes and the medium-large cell sizes. In contrast, in starved protists and metazoans, the relation between mitochondrion power and cell size is inconclusive, and in microalgae and plants, mitochondrion power seems to increase from smaller cells to larger ones (where this investigation includes plant cells of volume up to ca. 2.18 × 105 μm3). Using these results, estimates are provided of the number of active ATP synthase molecules and basal uncouplers.

Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii

Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0 '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αβ)2 tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.

On the power per mitochondrion and the number of associated active ATP synthases

Recent experiments and thermodynamic arguments suggest that mitochondrial temperatures are higher than those of the cytoplasm. A "hot mitochondrion" calls for a closer examination of the energy balance that endows it with these claimed elevated temperatures. As a first step in this effort, we present here a semi-quantitative bookkeeping whereby, in one stroke, a formula is proposed that yields the rate of heat production in a typical mitochondrion and a formula for estimating the number of "active" ATP synthase molecules per mitochondrion. The number of active ATP synthase molecules is the equivalent number of ATP synthases operating at 100% capacity to maintain the rate of mitochondrial heat generation. Scaling laws are shown to determine the number of active ATP synthase molecules in a mitochondrion and mitochondrial rate of heat production, whereby both appear to scale with cell volume. Four heterotrophic protozoan cell types are considered in this study. The studied cells, selected to cover a wide range of sizes (volumes) fromca.100μm³to 1 millionμm³, are estimated to exhibit a power per mitochondrion ranging fromca.1 pW to 0.03 pW. In these cells, the corresponding number of active ATP synthases per mitochondrion ranges from 5000 to just about a hundred. The absolute total number of ATP synthase molecules per mitochondrion, regardless of their activity status, can be up to two orders of magnitudes higher.

Using a Multi-compartmental Metabolic Model to Predict Carbon Allocation in Arabidopsis thaliana

The molecular mechanism of loading/unloading of sucrose into/from the phloem plays an important role in sucrose translocation among plant tissues. Perturbation of this mechanism results in growth phenotypes of a plant. In order to better understand the coupling of sucrose translocation with metabolic processes a multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized with respect to biomass growth, both in light and in dark conditions. The model can be used to perform flux balance analysis of metabolic fluxes through the central carbon metabolism and catabolic and anabolic pathways. Balances and turnover of energy (ATP/ADP) and redox metabolites (NAD(P)H/NAD(P)) as well as proton concentrations in different compartments can be estimated. Importantly, the model can be used to quantify the translocation of sucrose from source to sink tissues through phloem in association with an integral balance of protons, which in turn is defined by the operational modes of the energy metabolism (light and dark conditions). This chapter describes how a multi-compartmental model to predict carbon allocation is constructed and used.

Nonequilibrium Energetics of Molecular Motor Kinesin

Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum of the dissipation and work did not amount to the input free energy change, indicating large hidden dissipation exists. Possible sources of the hidden dissipation were explored by analyzing the Langevin dynamics of the probe, which incorporates the two-state Markov stepper as a kinesin model. We conclude that internal dissipation is dominant.

Mechanical transduction via a single soft polymer

Molecular machines from biology and nanotechnology often depend on soft structures to perform mechanical functions, but the underlying mechanisms and advantages or disadvantages over rigid structures are not fully understood. We report here a rigorous study of mechanical transduction along a single soft polymer based on exact solutions to the realistic three-dimensional wormlike-chain model and augmented with analytical relations derived from simpler polymer models. The results reveal surprisingly that a soft polymer with vanishingly small persistence length below a single chemical bond still transduces biased displacement and mechanical work up to practically significant amounts. This "soft" approach possesses unique advantages over the conventional wisdom of rigidity-based transduction, and potentially leads to a unified mechanism for effective allosterylike transduction and relay of mechanical actions, information, control, and molecules from one position to another in molecular devices and motors. This study also identifies an entropy limit unique to the soft transduction, and thereby suggests a possibility of detecting higher efficiency for kinesin motor and mutants in future experiments.

Thermodynamics of Bioreactions

Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.

Standard Gibbs energy of metabolic reactions: II. Glucose-6-phosphatase reaction and ATP hydrolysis

ATP (adenosine triphosphate) is a key reaction for metabolism. Tools from systems biology require standard reaction data in order to predict metabolic pathways accurately. However, literature values for standard Gibbs energy of ATP hydrolysis are highly uncertain and differ strongly from each other. Further, such data usually neglect the activity coefficients of reacting agents, and published data like this is apparent (condition-dependent) data instead of activity-based standard data. In this work a consistent value for the standard Gibbs energy of ATP hydrolysis was determined. The activity coefficients of reacting agents were modeled with electrolyte Perturbed-Chain Statistical Associating Fluid Theory (ePC-SAFT). The Gibbs energy of ATP hydrolysis was calculated by combining the standard Gibbs energies of hexokinase reaction and of glucose-6-phosphate hydrolysis. While the standard Gibbs energy of hexokinase reaction was taken from previous work, standard Gibbs energy of glucose-6-phosphate hydrolysis reaction was determined in this work. For this purpose, reaction equilibrium molalities of reacting agents were measured at pH7 and pH8 at 298.15K at varying initial reacting agent molalities. The corresponding activity coefficients at experimental equilibrium molalities were predicted with ePC-SAFT yielding the Gibbs energy of glucose-6-phosphate hydrolysis of -13.72±0.75kJ·mol^-1. Combined with the value for hexokinase, the standard Gibbs energy of ATP hydrolysis was finally found to be -31.55±1.27kJ·mol^-1. For both, ATP hydrolysis and glucose-6-phosphate hydrolysis, a good agreement with own and literature values were obtained when influences of pH, temperature, and activity coefficients were explicitly taken into account in order to calculate standard Gibbs energy at pH7, 298.15K and standard state.

Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation

BACKGROUND

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families). To better understand regulation of sucrose export from source tissues and sucrose import into sink tissues, there is a need for a metabolic model that takes in account the tissue organisation of Arabidopsis thaliana with corresponding metabolic specificities of respective tissues in terms of sucrose and proton production/utilization. An ability of the model to operate under different light modes ('light' and 'dark') and correspondingly in different energy producing modes is particularly important in understanding regulatory modules.

RESULTS

Here, we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO₂ under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue dependent on sucrose supply from the mesophyll compartment. In total, the model includes 413 balanced compounds interconnected by 400 transformers. The structured metabolic model accounts for central carbon metabolism, photosynthesis, photorespiration, carbohydrate metabolism, energy and redox metabolisms, proton metabolism, biomass growth, nutrients uptake, proton gradient generation and sucrose translocation between tissues. Biochemical processes in the model were associated with gene-products (742 ORFs). Flux Balance Analysis (FBA) of the model resulted in balanced carbon, nitrogen, proton, energy and redox states under both light and dark conditions. The main H⁺-fluxes were reconstructed and their directions matched with proton-dependent sucrose translocation from 'source' to 'sink' under any light condition.

CONCLUSIONS

The model quantified the translocation of sucrose between plant tissues in association with an integral balance of protons, which in turn is defined by operational modes of the energy metabolism.

Thermodynamics of proton transport coupled ATP synthesis

The thermodynamic H(+)/ATP ratio of the H(+)-ATP synthase from chloroplasts was measured in proteoliposomes after energization of the membrane by an acid base transition (Turina et al. 2003 [13], 418-422). The method is discussed, and all published data obtained with this system are combined and analyzed as a single dataset. This meta-analysis led to the following results. 1) At equilibrium, the transmembrane ΔpH is energetically equivalent to the transmembrane electric potential difference. 2) The standard free energy for ATP synthesis (reference reaction) is ΔG°(ref)=33.8±1.3kJ/mol. 3) The thermodynamic H(+)/ATP ratio, as obtained from the shift of the ATP synthesis equilibrium induced by changing the transmembrane ΔpH (varying either pH(in) or pH(out)) is 4.0±0.1. The structural H(+)/ATP ratio, calculated from the ratio of proton binding sites on the c-subunit-ring in F(0) to the catalytic nucleotide binding sites on the β-subunits in F(1), is c/β=14/3=4.7. We infer that the energy of 0.7 protons per ATP that flow through the enzyme, but do not contribute to shifting the ATP/(ADP·Pi) ratio, is used for additional processes within the enzyme, such as activation, and/or energy dissipation, due e.g. to internal uncoupling. The ratio between the thermodynamic and the structural H(+)/ATP values is 0.85, and we conclude that this value represents the efficiency of the chemiosmotic energy conversion within the chloroplast H(+)-ATP synthase.

Estimating the rotation rate in the vacuolar proton-ATPase in native yeast vacuolar membranes

The rate of rotation of the rotor in the yeast vacuolar proton-ATPase (V-ATPase), relative to the stator or steady parts of the enzyme, is estimated in native vacuolar membrane vesicles from Saccharomyces cerevisiae under standardised conditions. Membrane vesicles are formed spontaneously after exposing purified yeast vacuoles to osmotic shock. The fraction of total ATPase activity originating from the V-ATPase is determined by using the potent and specific inhibitor of the enzyme, concanamycin A. Inorganic phosphate liberated from ATP in the vacuolar membrane vesicle system, during ten min of ATPase activity at 20 °C, is assayed spectrophotometrically for different concanamycin A concentrations. A fit of the quadratic binding equation, assuming a single concanamycin A binding site on a monomeric V-ATPase (our data are incompatible with models assuming multiple binding sites), to the inhibitor titration curve determines the concentration of the enzyme. Combining this with the known ATP/rotation stoichiometry of the V-ATPase and the assayed concentration of inorganic phosphate liberated by the V-ATPase, leads to an average rate of ~10 Hz for full 360° rotation (and a range of 6-32 Hz, considering the ± standard deviation of the enzyme concentration), which, from the time-dependence of the activity, extrapolates to ~14 Hz (8-48 Hz) at the beginning of the reaction. These are lower-limit estimates. To our knowledge, this is the first report of the rotation rate in a V-ATPase that is not subjected to genetic or chemical modification and is not fixed to a solid support; instead it is functioning in its native membrane environment.

Comparison of the H+/ATP ratios of the H+-ATP synthases from yeast and from chloroplast

F(0)F(1)-ATP synthases use the free energy derived from a transmembrane proton transport to synthesize ATP from ADP and inorganic phosphate. The number of protons translocated per ATP (H(+)/ATP ratio) is an important parameter for the mechanism of the enzyme and for energy transduction in cells. Current models of rotational catalysis predict that the H(+)/ATP ratio is identical to the stoichiometric ratio of c-subunits to β-subunits. We measured in parallel the H(+)/ATP ratios at equilibrium of purified F(0)F(1)s from yeast mitochondria (c/β = 3.3) and from spinach chloroplasts (c/β = 4.7). The isolated enzymes were reconstituted into liposomes and, after energization of the proteoliposomes with acid-base transitions, the initial rates of ATP synthesis and hydrolysis were measured as a function of ΔpH. The equilibrium ΔpH was obtained by interpolation, and from its dependency on the stoichiometric ratio, [ATP]/([ADP]·[P(i)]), finally the thermodynamic H(+)/ATP ratios were obtained: 2.9 ± 0.2 for the mitochondrial enzyme and 3.9 ± 0.3 for the chloroplast enzyme. The data show that the thermodynamic H(+)/ATP ratio depends on the stoichiometry of the c-subunit, although it is not identical to the c/β ratio.

Nonequilibrium energetics of a single F1-ATPase molecule

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against an external load is almost equal to the free energy change per a single ATP hydrolysis under various conditions. This implies that F1-ATPase works at an efficiency of nearly 100% in a thermally fluctuating environment.

The thermodynamic H+/ATP ratios of the H+-ATPsynthases from chloroplasts and Escherichia coli

The H(+)/ATP ratio is an important parameter for the energy balance of all cells and for the coupling mechanism between proton transport and ATP synthesis. A straightforward interpretation of rotational catalysis predicts that the H(+)/ATP coincides with the ratio of the c-subunits to beta-subunits, implying that, for the chloroplast and Escherichia coli ATPsynthases, numbers of 4.7 and 3.3 are expected. Here, the energetics described by the chemiosmotic theory was used to determine the H(+)/ATP ratio for the two enzymes. The isolated complexes were reconstituted into liposomes, and parallel measurements were performed under identical conditions. The internal phase of the liposomes was equilibrated with the acidic medium during reconstitution, allowing to measure the internal pH with a glass electrode. An acid-base transition was carried out and the initial rates of ATP synthesis or ATP hydrolysis were measured with luciferin/luciferase as a function of DeltapH at constant Q = [ATP]/([ADP][P(i)]). From the shift of the equilibrium DeltapH as a function of Q the standard Gibbs free energy for phosphorylation, DeltaG(p)(0)'; and the H(+)/ATP ratio were determined. It resulted DeltaG(p)(0)' = 38 +/- 3 kJ.mol(-1) and H(+)/ATP = 4.0 +/- 0.2 for the chloroplast and H(+)/ATP = 4.0 +/- 0.3 for the E. coli enzyme, indicating that the thermodynamic H(+)/ATP ratio is the same for both enzymes and that it is different from the subunit stoichiometric ratio.

Monitoring cytosolic pH of carboxysome-deficient cells of Synechocystis sp. PCC 6803 using fluorescence analysis

Disruption of the ccmM gene in the cyanobacterium Synechocystis sp. PCC 6803 causes a deficiency of carboxysomes and impairs growth in ambient CO2. The effect of this gene defect on cellular metabolism was investigated using electron microscopy, biochemical and fluorescence analysis. Mutant cells were devoid of the characteristic dense polyhedral bodies called carboxysomes. The photosynthetic oxygen evolution was considerably lower in mutant cells compared to wild type, while Rubisco activity in cell extracts was similar. During photosynthetic CO2-dependent oxygen evolution, Rubisco Vmax dropped from 142 micromol mg-1 chlorophyll h-1 (WT) to 77 micromol mg-1 chlorophyll h-1 in the mutant cells, and the Km for Ci (inorganic carbon) increased from 0.5 mM (WT) to 40 mM. The fluorescent indicator, acridine yellow, was used for non-invasive measurements of cytoplasmic pH changes in whole cells induced by addition of Ci, making use of the decrease in fluorescence yield that accompanies cytoplasmic acidification. The experimental results indicate that control of the cytoplasmic pH is linked to the internal carbon pool (Ci). Both wild-type and ccmM-deficient cells showed a linear response of acridine yellow fluorescence quenching and, thus, of internal acidification, with respect to externally added inorganic carbon. However, the fluorescence analysis of mutant (carboxysome-free) cells indicated slower kinetics of Ci accumulation.

Why O2 is required by complex life on habitable planets and the concept of planetary "oxygenation time"

Life is constructed from a limited toolkit: the Periodic Table. The reduction of oxygen provides the largest free energy release per electron transfer, except for the reduction of fluorine and chlorine. However, the bonding of O2 ensures that it is sufficiently stable to accumulate in a planetary atmosphere, whereas the more weakly bonded halogen gases are far too reactive ever to achieve significant abundance. Consequently, an atmosphere rich in O2 provides the largest feasible energy source. This universal uniqueness suggests that abundant O2 is necessary for the high-energy demands of complex life anywhere, i.e., for actively mobile organisms of approximately 10(-1)-10(0) m size scale with specialized, differentiated anatomy comparable to advanced metazoans. On Earth, aerobic metabolism provides about an order of magnitude more energy for a given intake of food than anaerobic metabolism. As a result, anaerobes do not grow beyond the complexity of uniseriate filaments of cells because of prohibitively low growth efficiencies in a food chain. The biomass cumulative number density, n, at a particular mass, m, scales as n (> m) proportional to m(-1) for aquatic aerobes, and we show that for anaerobes the predicted scaling is n proportional to m (-1.5), close to a growth-limited threshold. Even with aerobic metabolism, the partial pressure of atmospheric O2 (P(O2)) must exceed approximately 10(3) Pa to allow organisms that rely on O2 diffusion to evolve to a size approximately 10(3) m x P(O2) in the range approximately 10(3)-10(4) Pa is needed to exceed the threshold of approximately 10(2) m size for complex life with circulatory physiology. In terrestrial life, O(2) also facilitates hundreds of metabolic pathways, including those that make specialized structural molecules found only in animals. The time scale to reach P(O(2)) approximately 10(4) Pa, or "oxygenation time," was long on the Earth (approximately 3.9 billion years), within almost a factor of 2 of the Sun's main sequence lifetime. Consequently, we argue that the oxygenation time is likely to be a key rate-limiting step in the evolution of complex life on other habitable planets. The oxygenation time could preclude complex life on Earth-like planets orbiting short-lived stars that end their main sequence lives before planetary oxygenation takes place. Conversely, Earth-like planets orbiting long-lived stars are potentially favorable habitats for complex life.

The membrane domain of the Na+-motive V-ATPase from Enterococcus hirae contains a heptameric rotor

In F-ATPases, ATP hydrolysis is coupled to translocation of ions through membranes by rotation of a ring of c subunits in the membrane. The ring is attached to a central shaft that penetrates the catalytic domain, which has pseudo-3-fold symmetry. The ion translocation pathway lies between the external circumference of the ring and another hydrophobic protein. The H+ or Na+:ATP ratio depends upon the number of ring protomers, each of which has an essential carboxylate involved directly in ion translocation. This number and the ratio differ according to the source, and 10, 11, and 14 protomers have been found in various enzymes, with corresponding calculated H+ or Na+:ATP ratios of 3.3, 3.7, and 4.7. V-ATPases are related in structure and function to F-ATPases. Oligomers of subunit K from the Na+-motive V-ATPase of Enterococcus hirae also form membrane rings but, as reported here, with 7-fold symmetry. Each protomer has one essential carboxylate. Thus, hydrolysis of one ATP provides energy to extrude 2.3 sodium ions. Symmetry mismatch between the catalytic and membrane domains appears to be an intrinsic feature of both V- and F-ATPases.

Assessing the structure of membrane proteins: combining different methods gives the full picture

The rotor stoichiometry of F-ATPases has been revealed by the combined approaches of X-ray diffraction (XRD), electron crystallography, and atomic force microscopy (AFM). XRD showed the rotor from the yeast mitochondrial F-ATPase to contain 10 subunits. AFM was used to visualize the tetradecameric chloroplast rotors, and electron crystallography and AFM together revealed the rotors from Ilyobacter tartaricus to be composed of 11 subunits. While biochemical methods had determined an approximate stoichiometric value, precise measurements and new insights into a species-dependent rotor stoichiometry became available by applying the three structural tools together. The structures of AQP1, a water channel, and G1pF, a glycerol channel, were determined by electron crystallography and XRD. The combination of both of these structural tools with molecular dynamics simulations gave a differentiated description of the mechanisms determining the selectivity of water and glycerol channels. This illustrates that the combination of different methods in structural biology reveals more than each method alone.

Viscoelastic dynamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme

ATP synthase (F(O)F(1)) operates as two rotary motor/generators coupled by a common shaft. Both portions, F(1) and F(O), are rotary steppers. Their symmetries are mismatched (C(3) versus C(10-14)). We used the curvature of fluorescent actin filaments, attached to the rotating c-ring, as a spring balance (flexural rigidity of 8. 10(-26) Nm(2)) to gauge the angular profile of the output torque at F(O) during ATP hydrolysis by F(1) (see theoretical companion article (. Biophys. J. 81:1234-1244.)). The large average output torque (50 +/- 6 pN. nm) proved the absence of any slip. Variations of the torque were small, and the output free energy of the loaded enzyme decayed almost linearly over the angular reaction coordinate. Considering the threefold stepping and high activation barrier of the driving motor proper, the rather constant output torque implied a soft elastic power transmission between F(1) and F(O). It is considered as essential, not only for the robust operation of this ubiquitous enzyme under symmetry mismatch, but also for a high turnover rate of the two counteracting and stepping motor/generators.

Inter-subunit rotation and elastic power transmission in F0F1-ATPase

ATP synthase (F-ATPase) produces ATP at the expense of ion-motive force or vice versa. It is composed from two motor/generators, the ATPase (F1) and the ion translocator (F0), which both are rotary steppers. They are mechanically coupled by 360 degrees rotary motion of subunits against each other. The rotor, subunits gamma(epsilon)C10-14, moves against the stator, (alphabeta)3delta(ab2). The enzyme copes with symmetry mismatch (C3 versus C10-14) between its two motors, and it operates robustly in chimeric constructs or with drastically modified subunits. We scrutinized whether an elastic power transmission accounts for these properties. We used the curvature of fluorescent actin filaments, attached to the rotating c ring, as a spring balance (flexural rigidity of 8.10(-26) N x m2) to gauge the angular profile of the output torque at F0 during ATP hydrolysis by F1. The large average output torque (56 pN nm) proved the absence of any slip. Angular variations of the torque were small, so that the output free energy of the loaded enzyme decayed almost linearly over the angular reaction coordinate. Considering the three-fold stepping and high activation barrier (>40 kJ/mol) of the driving motor (F1) itself, the rather constant output torque seen by F0 implied a soft elastic power transmission between F1 and F0. It is considered as essential, not only for the robust operation of this ubiquitous enzyme under symmetry mismatch, but also for a high turnover rate under load of the two counteracting and stepping motors/generators.

Bacterial Na(+)-ATP synthase has an undecameric rotor

Synthesis of adenosine triphosphate (ATP) by the F(1)F(0) ATP synthase involves a membrane-embedded rotary engine, the F(0) domain, which drives the extra-membranous catalytic F(1) domain. The F(0) domain consists of subunits a(1)b(2) and a cylindrical rotor assembled from 9-14 alpha-helical hairpin-shaped c-subunits. According to structural analyses, rotors contain 10 c-subunits in yeast and 14 in chloroplast ATP synthases. We determined the rotor stoichiometry of Ilyobacter tartaricus ATP synthase by atomic force microscopy and cryo-electron microscopy, and show the cylindrical sodium-driven rotor to comprise 11 c-subunits.

Model of the carbon concentrating mechanism in chloroplasts of eukaryotic algae

A generic chloroplast-based model for the carbon concentrating mechanism (CCM) in eukaryotic algae is presented. The fine structure of chloroplasts is represented by separate compartments: marginal and bulk stroma, pyrenoid, girdle lamella, bulk thylakoids, and central lamella traversing the pyrenoid. The roles of the individual structural elements of the chloroplast with respect to the CCM and the effect of carbonic anhydrase activity in various compartments are analysed. Hypothetical HCO(-)(3)transport into the acidic thylakoid lumen is adjusted by imposing an optimization principle: a given [CO(2)] at the site of RuBisCO is achieved with minimum energy costs for the CCM. Our model is highly efficient in terms of saturation of RuBisCO carboxylase activity and the affinity of the chloroplast for CO(2), if either a girdle lamella or a pyrenoid is present. The highest efficiency is achieved with a pyrenoid. A eukaryotic CCM is not necessarily associated with accumulation of dissolved inorganic carbon (DIC) as in cyanobacteria. Chloroplasts are categorized into four types corresponding to morphological characteristics of all major algal classes with regard to the presence of pyrenoids, girdle lamellae, and the distribution of CA activity.

Electron pathways involved in H(2)-metabolism in the green alga Scenedesmus obliquus

The green alga Scenedesmus obliquus is capable of both uptake and production of H(2) after anaerobic adaptation (photoreduction of CO(2) or photohydrogen production). The essential enzyme for H(2)-metabolism is a NiFe-hydrogenase with a [2Fe-2S]-ferredoxin as its natural redox partner. Western blot analysis showed that the hydrogenase is constitutively expressed. The K(m) values were 79.5 microM and 12.5 microM, determined with ferredoxin and H(2), respectively, as electron donor for the hydrogenase. In vitro, NADP(+) was reduced by H(2) in the presence of the hydrogenase, the ferredoxin and a ferredoxin-NADP reductase. From these results and considerations on the stoichiometry we propose that this light-independent electron transfer is part of the photoreduction of CO(2) in vivo. For ATP synthesis, necessary for the photoreduction of CO(2), light-dependent cyclic electron transfer around Photosystem (PS) I accompanies this 'dark reaction'. PS II fluorescence data suggest that (a) in S. obliquus H(2)-reduction might function as the anaerobic counterpart of the O(2)-dependent Mehler reaction, and (b) the presence of either a ferredoxin quinone-reductase or NAD(P)-dehydrogenase (complex I) in S. obliquus chloroplasts.

Detergent effect on anion exchange perfusion chromatography and gel filtration of intact chloroplast H(+)-ATP synthase

To gain a pure enzyme preparation for functional and crystallization studies, an additional purification step in the isolation of the chloroplast ATP synthase (CF(0)F(1)) has been introduced. By applying gel filtration or anion exchange perfusion chromatography in presence of the detergents CHAPS and n-dodecyl-beta-d-maltoside, respectively, Rubisco and other contaminants were separated from CF(0)F(1). The purity and activity depended on the chromatographic method and the detergent employed. The highest purity and activity were achieved by anion exchange chromatography for the detergent dodecyl-maltoside and by gel filtration for the detergent CHAPS. The detergent Triton X-100, which is frequently used to solubilize CF(0)F(1), was found to be inadequate to stabilize the ATP synthase during chromatography.

Kinetic modeling of rotary CF0F1-ATP synthase: storage of elastic energy during energy transduction

F0F1-ATP synthase uses proton-motive force to produce ATP from ADP and Pi. With regard to its rotary mechanics, this energy transducing molecular machine assumes a unique position among all enzymes. In the work presented here we put forward a detailed functional model which is based on experimental results obtained with ATP synthase from spinach chloroplasts. We focus on the role of the elastic element, realized by the stalk-like subunit gamma, whose function is energy transduction between F0 and F1 taking into account the H+/ATP coupling ratio of four. Fitting parameters are the rate constants and the torsional rigidity of gamma, which have been adjusted according to the experimental results where the influence of transmembrane DeltapH on the rates of ATP synthesis/hydrolysis is put to the test. We show that the input and output of torsional energy are regulated by purely statistical principles, giving rise to the amount of transiently stored energy to be sliding, depending on DeltapH. During conditions of maximal turnover gamma turns out to be wound up towards 102 degrees which corresponds to a torque of 5.3. 10-20 N.m.

Transient accumulation of elastic energy in proton translocating ATP synthase

ATP synthase is conceived as a rotatory engine with two reversible drives, the proton-transporting membrane portion, F0, and the catalytic peripheral portion, F1. They are mounted on a central shaft (subunit gamma) and held together by an eccentric bearing. It is established that the hydrolysis of three molecules of ATP in F1 drives the shaft over a full circle in three steps of 120 degrees each. Proton flow through F0 probably generates a 12-stepped rotation of the shaft so that four proton-translocating steps of 30 degrees each drive the synthesis of one molecule of ATP. We addressed the elasticity of the transmission between F0 and F1 in a model where the four smaller steps in F0 load a torsional spring which is only released under liberation of ATP from F1. The kinetic model of an elastic ATP synthase described a wealth of published data on the synthesis/hydrolysis of ATP by F0F1 and on proton conduction by F0 as function of the pH and the protonmotive force. The pK values of the proton-carrying group interacting with the acidic and basic sides of the membrane were estimated as 5.3-6.4 and 8.0-8.3, respectively.

Proton to electron stoichiometry in electron transport of spinach thylakoids

According to the concept of the Q-cycle, the H+/e- ratio of the electron transport chain of thylakoids can be raised from 2 to 3 by means of the rereduction of plastoquinone across the cytochrome b6f complex. In order to investigate the H+/e- ratio we compared stationary rates of electron transport and proton translocation in spinach thylakoids both in the presence of the artificial electron acceptor ferricyanide and in the presence of the natural acceptor system ferredoxin+NADP. The results may be summarised as follows: (1) a variability of the H+/e- ratio occurs with either acceptor. H+/e- ratios of 3 (or even higher in the case of the natural acceptor system, see below) are decreased towards 2 if strong light intensity and low membrane permeability are employed. Mechanistically this could be explained by proton channels connecting the plastoquinol binding site alternatively to the lumenal or stromal side of the cytochrome b6f complex, giving rise to a proton slip reaction at high transmembrane DeltapH. In this slip reaction protons are deposited on the stromal instead of the lumenal side. In addition to the pH effect there seems to be a contribution of the redox state of the plastoquinone pool to the control of proton translocation; switching over to stromal proton deposition is favoured when the reduced state of plastoquinone becomes dominant. (2) In the presence of NADP a competition of both NADP and oxygen for the electrons supplied by photosystem I takes place, inducing a general increase of the H+/e- ratios above the values obtained with ferricyanide. The implications with respect to the adjustment of a proper ATP/NADPH ratio for CO2 reduction are discussed.

ATP-synthase of Rhodobacter capsulatus: coupling of proton flow through F0 to reactions in F1 under the ATP synthesis and slip conditions

A stepwise increasing membrane potential was generated in chromatophores of the phototrophic bacterium Rhodobacter capsulatus by illumination with short flashes of light. Proton transfer through ATP-synthase (measured by electrochromic carotenoid bandshift and by pH-indicators) and ATP release (measured by luminescence of luciferin-luciferase) were monitored. The ratio between the amount of protons translocated by F0F1 and the ATP yield decreased with the flash number from an apparent value of 13 after the first flash to about 5 when averaged over three flashes. In the absence of ADP, protons slipped through F0F1. The proton transfer through F0F1 after the first flash contained two kinetic components, of about 6 ms and 20 ms both under the ATP synthesis conditions and under slip. The slower component of proton transfer was substantially suppressed in the absence of ADP. We attribute our observations to the mechanism of energy storage in the ATP-synthase needed to couple the transfer of four protons with the synthesis of one molecule of ATP. Most probably, the transfer of initial protons of each tetrad creates a strain in the enzyme that slows the translocation of the following protons.