The proton-driven rotor of ATP synthase: ohmic conductance (10 fS), and absence of voltage gating

Directed proton transfer from Fo to F1 extends the multifaceted proton functions in ATP synthase

The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.

Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase

F1Fo ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded Fo motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F1 motor that catalyze ATP synthesis. In E. coli, the Fo motor is composed of a c10 ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To further investigate the role of these residues and the chemical requirements for activity at these positions, we generated 13 substitution mutants and assayed their in vitro ATP synthesis, H+ pumping, and passive H+ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge or removal of polarity caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with cardiolipin.

The Need for Consistency with Physical Laws and Logic in Choosing Between Competing Molecular Mechanisms in Biological Processes: A Case Study in Modeling ATP Synthesis

Traditionally, proposed molecular mechanisms of fundamental biological processes have been tested against experiment. However, owing to a plethora of reasons-difficulty in designing, carrying out, and interpreting key experiments, use of different experimental models and systems, conduct of studies under widely varying experimental conditions, fineness in distinctions between competing mechanisms, complexity of the scientific issues, and the resistance of some scientists to discoveries that are contrary to popularly held beliefs-this has not solved the problem despite decades of work in the field/s. The author would like to prescribe an alternative way: that of testing competing models/mechanisms for their adherence to scientific laws and principles, and checking for errors in logic. Such tests are fairly commonly carried out in the mathematics, physics, and engineering literature. Further, reported experimental measurements should not be smaller than minimum detectable values for the measurement technique employed and should truly reflect function of the actual system without inapplicable extrapolation. Progress in the biological fields would be greatly accelerated, and considerable scientific acrimony avoided by adopting this approach. Some examples from the fundamental field of ATP synthesis in oxidative phosphorylation (OXPHOS) have been reviewed that also serve to illustrate the approach. The approach has never let the author down in his 35-yr-long experience on biological mechanisms. This change in thinking should lead to a considerable saving of both time and resources, help channel research efforts toward solution of the right problems, and hopefully provide new vistas to a younger generation of open-minded biological scientists.

F1FO ATP synthase molecular motor mechanisms

The F-ATP synthase, consisting of F1 and FO motors connected by a central rotor and the stators, is the enzyme responsible for synthesizing the majority of ATP in all organisms. The F1 (αβ)3 ring stator contains three catalytic sites. Single-molecule F1 rotation studies revealed that ATP hydrolysis at each catalytic site (0°) precedes a power-stroke that rotates subunit-γ 120° with angular velocities that vary with rotational position. Catalytic site conformations vary relative to subunit-γ position (βE, empty; βD, ADP bound; βT, ATP-bound). During a power stroke, βE binds ATP (0°–60°) and βD releases ADP (60°–120°). Årrhenius analysis of the power stroke revealed that elastic energy powers rotation via unwinding the γ-subunit coiled-coil. Energy from ATP binding at 34° closes βE upon subunit-γ to drive rotation to 120° and forcing the subunit-γ to exchange its tether from βE to βD, which changes catalytic site conformations. In F1FO, the membrane-bound FO complex contains a ring of c-subunits that is attached to subunit-γ. This c-ring rotates relative to the subunit-a stator in response to transmembrane proton flow driven by a pH gradient, which drives subunit-γ rotation in the opposite direction to force ATP synthesis in F1. Single-molecule studies of F1FO embedded in lipid bilayer nanodisks showed that the c-ring transiently stopped F1-ATPase-driven rotation every 36° (at each c-subunit in the c10-ring of E. coli F1FO) and was able to rotate 11° in the direction of ATP synthesis. Protonation and deprotonation of the conserved carboxyl group on each c-subunit is facilitated by separate groups of subunit-a residues, which were determined to have different pKa’s. Mutations of any of any residue from either group changed both pKa values, which changed the occurrence of the 11° rotation proportionately. This supports a Grotthuss mechanism for proton translocation and indicates that proton translocation occurs during the 11° steps. This is consistent with a mechanism in which each 36° of rotation the c-ring during ATP synthesis involves a proton translocation-dependent 11° rotation of the c-ring, followed by a 25° rotation driven by electrostatic interaction of the negatively charged unprotonated carboxyl group to the positively charged essential arginine in subunit-a.

Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution

F_o subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor's directionality naturally arises from the interplay between intraprotein interactions and energetics of protonation of the c-ring. Notably, our calculations reveal that the strictly conserved arginine in the a-subunit (R176) serves as a jack-of-all-trades: it dictates the direction of rotation, controls the protonation state of the proton-release site, and separates the two proton-access half-channels. Therefore, arginine is necessary to avoid slippage between the proton flux and the mechanical output and guarantees highly efficient energy conversion. We also provide mechanistic explanations for the reported defective mutations of R176, reconciling the structural information on the F_o motor with previous functional and single-molecule data.

pH-dependent 11° F1FO ATP synthase sub-steps reveal insight into the FO torque generating mechanism

Most cellular ATP is made by rotary F₁F_O ATP synthases using proton translocation-generated clockwise torque on the F_O c-ring rotor, while F₁-ATP hydrolysis can force counterclockwise rotation and proton pumping. The F_O torque-generating mechanism remains elusive even though the F_O interface of stator subunit-a, which contains the transmembrane proton half-channels, and the c-ring is known from recent F₁F_O structures. Here, single-molecule F₁F_O rotation studies determined that the pKa values of the half-channels differ, show that mutations of residues in these channels change the pKa values of both half-channels, and reveal the ability of F_O to undergo single c-subunit rotational stepping. These experiments provide evidence to support the hypothesis that proton translocation through F_O operates via a Grotthuss mechanism involving a column of single water molecules in each half-channel linked by proton translocation-dependent c-ring rotation. We also observed pH-dependent 11° ATP synthase-direction sub-steps of the Escherichia coli c₁₀-ring of F₁F_O against the torque of F₁-ATPase-dependent rotation that result from H⁺ transfer events from F_O subunit-a groups with a low pKa to one c-subunit in the c-ring, and from an adjacent c-subunit to stator groups with a high pKa. These results support a mechanism in which alternating proton translocation-dependent 11° and 25° synthase-direction rotational sub-steps of the c₁₀-ring occur to sustain F₁F_O ATP synthesis.

ATP Synthase K+- and H+-Fluxes Drive ATP Synthesis and Enable Mitochondrial K+-"Uniporter" Function: I. Characterization of Ion Fluxes

ATP synthase (F₁F_o) synthesizes daily our body's weight in ATP, whose production-rate can be transiently increased several-fold to meet changes in energy utilization. Using purified mammalian F₁F_o-reconstituted proteoliposomes and isolated mitochondria, we show F₁F_o can utilize both ΔΨ_m-driven H⁺- and K⁺-transport to synthesize ATP under physiological pH = 7.2 and K⁺ = 140 mEq/L conditions. Purely K⁺-driven ATP synthesis from single F₁F_o molecules measured by bioluminescence photon detection could be directly demonstrated along with simultaneous measurements of unitary K⁺ currents by voltage clamp, both blocked by specific F_o inhibitors. In the presence of K⁺, compared to osmotically-matched conditions in which this cation is absent, isolated mitochondria display 3.5-fold higher rates of ATP synthesis, at the expense of 2.6-fold higher rates of oxygen consumption, these fluxes being driven by a 2.7:1 K⁺: H⁺ stoichiometry. The excellent agreement between the functional data obtained from purified F₁F_o single molecule experiments and ATP synthase studied in the intact mitochondrion under unaltered OxPhos coupling by K⁺ presence, is entirely consistent with K⁺ transport through the ATP synthase driving the observed increase in ATP synthesis. Thus, both K⁺ (harnessing ΔΨ_m) and H⁺ (harnessing its chemical potential energy, Δμ_H) drive ATP generation during normal physiology.

ATP synthase: Evolution, energetics, and membrane interactions

The synthesis of ATP, life’s “universal energy currency,” is the most prevalent chemical reaction in biological systems and is responsible for fueling nearly all cellular processes, from nerve impulse propagation to DNA synthesis. ATP synthases, the family of enzymes that carry out this endless task, are nearly as ubiquitous as the energy-laden molecule they are responsible for making. The F-type ATP synthase (F-ATPase) is found in every domain of life and has facilitated the survival of organisms in a wide range of habitats, ranging from the deep-sea thermal vents to the human intestine. Accordingly, there has been a large amount of work dedicated toward understanding the structural and functional details of ATP synthases in a wide range of species. Less attention, however, has been paid toward integrating these advances in ATP synthase molecular biology within the context of its evolutionary history. In this review, we present an overview of several structural and functional features of the F-type ATPases that vary across taxa and are purported to be adaptive or otherwise evolutionarily significant: ion channel selectivity, rotor ring size and stoichiometry, ATPase dimeric structure and localization in the mitochondrial inner membrane, and interactions with membrane lipids. We emphasize the importance of studying these features within the context of the enzyme’s particular lipid environment. Just as the interactions between an organism and its physical environment shape its evolutionary trajectory, ATPases are impacted by the membranes within which they reside. We argue that a comprehensive understanding of the structure, function, and evolution of membrane proteins—including ATP synthase—requires such an integrative approach.

Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance

V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V₁ domain, with proton flow through the V_o membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V₁ domain, the V_o domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the V_o domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated V_o at near-atomic resolution, respectively. These structures clarify how the isolated V_o domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited V_o form.

Kinetic coupling of the respiratory chain with ATP synthase, but not proton gradients, drives ATP production in cristae membranes

Mitochondria have a characteristic ultrastructure with invaginations of the inner membrane called cristae that contain the protein complexes of the oxidative phosphorylation system. How this particular morphology of the respiratory membrane impacts energy conversion is currently unknown. One proposed role of cristae formation is to facilitate the establishment of local proton gradients to fuel ATP synthesis. Here, we determined the local pH values at defined sublocations within mitochondria of respiring yeast cells by fusing a pH-sensitive GFP to proteins residing in different mitochondrial subcompartments. Only a small proton gradient was detected over the inner membrane in wild type or cristae-lacking cells. Conversely, the obtained pH values did barely permit ATP synthesis in a reconstituted system containing purified yeast F₁F₀ ATP synthase, although, thermodynamically, a sufficiently high driving force was applied. At higher driving forces, where robust ATP synthesis was observed, a P-side pH value of 6 increased the ATP synthesis rate 3-fold compared to pH 7. In contrast, when ATP synthase was coreconstituted with an active proton-translocating cytochrome oxidase, ATP synthesis readily occurred at the measured, physiological pH values. Our study thus reveals that the morphology of the inner membrane does not influence the subcompartmental pH values and is not necessary for robust oxidative phosphorylation in mitochondria. Instead, it is likely that the dense packing of the oxidative phosphorylation complexes in the cristae membranes assists kinetic coupling between proton pumping and ATP synthesis.

Revisiting the protomotive vectorial motion of F0-ATPase

The elucidation of the detailed mechanism used by F₀ to convert proton gradient to torque and rotational motion presents a major puzzle despite significant biophysical and structural progress. Although the conceptual model has advanced our understanding of the working principles of such systems, it is crucial to explore the actual mechanism using structure-based models that actually reproduce a unidirectional proton-driven rotation. Our previous work used a coarse-grained (CG) model to simulate the action of F₀ However, the simulations were based on a very tentative structural model of the interaction between subunit a and subunit c. Here, we again use a CG model but with a recent cryo-EM structure of cF₁F₀ and also explore the proton path using our water flooding and protein dipole Langevin dipole semimacroscopic formalism with its linear response approximation version (PDLD/S-LRA) approaches. The simulations are done in the combined space defined by the rotational coordinate and the proton transport coordinate. The study reproduced the effect of the protomotive force on the rotation of the F₀ while establishing the electrostatic origin of this effect. Our landscape reproduces the correct unidirectionality of the synthetic direction of the F₀ rotation and shows that it reflects the combined electrostatic coupling between the proton transport path and the c-ring conformational change. This work provides guidance for further studies in other proton-driven mechanochemical systems and should lead (when combined with studies of F₁) to a complete energy transduction picture of the F₀F₁-ATPase system.

Proton-Conducting Poly-γ-glutamic Acid Nanofiber Embedded Sulfonated Poly(ether sulfone) for Proton Exchange Membranes

Development and fabrication of novel proton exchange membranes (PEMs) with excellent performance have a great significance to the commercial application of PEM fuel cell. Inspired from the proton-conducting mechanism, γ-poly(glutamic acid) (γ-PGA) nanofibers (NFs) are first fabricated by solution blowing with the help of polylactic acid (PLA) and designed to form amino acid arrays as efficient proton channels for PEMs. The NFs with 50% γ-PGA exhibit a high proton conductivity of 0.572 S cm^-1 at 80 °C/50% relative humidity (RH), and 1.28 S cm^-1 at 40 °C/90% RH. Density functional theory is carried out to explain the mechanisms of proton hopping in γ-PGA, and the activation energy barriers from NH to COO^- for trans and cis conformations under anhydrous conditions are only 0.64 and 0.62 eV, respectively. Then the γ-PGA/PLA NFs are incorporated into sulfonated poly(ether sulfone) to prepare PEMs, which show remarkable performance compared with the Nafion membrane. The composite membrane with 30 wt % NFs exhibits the highest proton conductivity (0.261 S cm^-1 at 80 °C/100% RH). The direct methanol fuel cells with this membrane show a maximum power density (202.3 mW cm^-2) among all of the PEMs, showing great application potential in the field of PEMs.

Optimization of ATP Synthase c-Rings for Oxygenic Photosynthesis

The conversion of sunlight into useable cellular energy occurs via the proton-coupled electron transfer reactions of photosynthesis. Light is absorbed by photosynthetic pigments and transferred to photochemical reaction centers to initiate electron and proton transfer reactions to store energy in a redox gradient and an electrochemical proton gradient (proton motive force, pmf), composed of a concentration gradient (ΔpH) and an electric field (Δψ), which drives the synthesis of ATP through the thylakoid F_oF₁-ATP synthase. Although ATP synthase structure and function are conserved across biological kingdoms, the number of membrane-embedded ion-binding c subunits varies between organisms, ranging from 8 to 17, theoretically altering the H⁺/ATP ratio for different ATP synthase complexes, with profound implications for the bioenergetic processes of cellular metabolism. Of the known c-ring stoichiometries, photosynthetic c-rings are among the largest identified stoichiometries, and it has been proposed that decreasing the c-stoichiometry could increase the energy conversion efficiency of photosynthesis. Indeed, there is strong evidence that the high H⁺/ATP of the chloroplast ATP synthase results in a low ATP/nicotinamide adenine dinucleotide phosphate (NADPH) ratio produced by photosynthetic linear electron flow, requiring secondary processes such as cyclic electron flow to support downstream metabolism. We hypothesize that the larger c subunit stoichiometry observed in photosynthetic ATP synthases was selected for because it allows the thylakoid to maintain pmf in a range where ATP synthesis is supported, but avoids excess Δψ and ΔpH, both of which can lead to production of reactive oxygen species and subsequent photodamage. Numerical kinetic simulations of the energetics of chloroplast photosynthetic reactions with altered c-ring size predicts the energy storage of pmf and its effects on the photochemical reaction centers strongly support this hypothesis, suggesting that, despite the low efficiency and suboptimal ATP/NADPH ratio, a high H⁺/ATP is favored to avoid photodamage. This has important implications for the evolution and regulation of photosynthesis as well as for synthetic biology efforts to alter photosynthetic efficiency by engineering the ATP synthase.

On the structural possibility of pore-forming mitochondrial FoF1 ATP synthase

The mitochondrial permeability transition is an inner mitochondrial membrane event involving the opening of the permeability transition pore concomitant with a sudden efflux of matrix solutes and breakdown of membrane potential. The mitochondrial F(o)F(1) ATP synthase has been proposed as the molecular identity of the permeability transition pore. The likeliness of potential pore-forming sites in the mitochondrial F(o)F(1) ATP synthase is discussed and a new model, the death finger model, is described. In this model, movement of a p-side density that connects the lipid-plug of the c-ring with the distal membrane bending Fo domain allows reversible opening of the c-ring and structural cross-talk with OSCP and the catalytic (αβ)(3) hexamer. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

The proton-driven ATP synthase (FOF1) is comprised of two rotary, stepping motors (FO and F1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other FO subunits (ab2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure. Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.

Bio-functionalized hybrid nanocomposite membranes for direct methanol fuel cells

Featured methanol-blocking characteristics of nanocomposite membrane.

Spatio-temporal resolution of primary processes of photosynthesis

Technical progress in laser-sources and detectors has allowed the temporal and spatial resolution of chemical reactions down to femtoseconds and Å-units. In photon-excitable systems the key to chemical kinetics, trajectories across the vibrational saddle landscape, are experimentally accessible. Simple and thus well-defined chemical compounds are preferred objects for calibrating new methodologies and carving out paradigms of chemical dynamics, as shown in several contributions to this Faraday Discussion. Aerobic life on earth is powered by solar energy, which is captured by microorganisms and plants. Oxygenic photosynthesis relies on a three billion year old molecular machinery which is as well defined as simpler chemical constructs. It has been analysed to a very high precision. The transfer of excitation between pigments in antennae proteins, of electrons between redox-cofactors in reaction centres, and the oxidation of water by a Mn4Ca-cluster are solid state reactions. ATP, the general energy currency of the cell, is synthesized by a most agile, rotary molecular machine. While the efficiency of photosynthesis competes well with photovoltaics at the time scale of nanoseconds, it is lower by an order of magnitude for crops and again lower for bio-fuels. The enormous energy demand of mankind calls for engineered (bio-mimetic or bio-inspired) solar-electric and solar-fuel devices.

ATP synthase

Oxygenic photosynthesis is the principal converter of sunlight into chemical energy. Cyanobacteria and plants provide aerobic life with oxygen, food, fuel, fibers, and platform chemicals. Four multisubunit membrane proteins are involved: photosystem I (PSI), photosystem II (PSII), cytochrome b6f (cyt b6f), and ATP synthase (FOF1). ATP synthase is likewise a key enzyme of cell respiration. Over three billion years, the basic machinery of oxygenic photosynthesis and respiration has been perfected to minimize wasteful reactions. The proton-driven ATP synthase is embedded in a proton tight-coupling membrane. It is composed of two rotary motors/generators, FO and F1, which do not slip against each other. The proton-driven FO and the ATP-synthesizing F1 are coupled via elastic torque transmission. Elastic transmission decouples the two motors in kinetic detail but keeps them perfectly coupled in thermodynamic equilibrium and (time-averaged) under steady turnover. Elastic transmission enables operation with different gear ratios in different organisms.

A mechano-chemiosmotic model for the coupling of electron and proton transfer to ATP synthesis in energy-transforming membranes: a personal perspective

ATP is synthesized using ATP synthase by utilizing energy either from the oxidation of organic compounds, or from light, via redox reactions (oxidative- or photo phosphorylation), in energy-transforming membranes of mitochondria, chloroplasts, and bacteria. ATP synthase undergoes several changes during its functioning. The generally accepted model for ATP synthesis is the well-known rotatory model (see e.g., Junge et al., Nature 459:364-370, 2009; Junge and Müller, Science 333:704-705, 2011). Here, we present an alternative modified model for the coupling of electron and proton transfer to ATP synthesis, which was initially developed by Albert Lester Lehninger (1917-1986). Details of the molecular mechanism of ATP synthesis are described here that involves cyclic low-amplitude shrinkage and swelling of mitochondria. A comparison of the well-known current model and the mechano-chemiosmotic model is also presented. Based on structural, and other data, we suggest that ATP synthase is a Ca(2+)/H(+)-K(+) Cl(-)-pump-pore-enzyme complex, in which γ-subunit rotates 360° in steps of 30°, and 90° due to the binding of phosphate ions to positively charged amino acid residues in the N-terminal γ-subunit, while in the electric field. The coiled coil b 2-subunits are suggested to act as ropes that are shortened by binding of phosphate ions to positively charged lysines or arginines; this process is suggested to pull the α 3 β 3-hexamer to the membrane during the energization process. ATP is then synthesized during the reverse rotation of the γ-subunit by destabilizing the phosphated N-terminal γ-subunit and b 2-subunits under the influence of Ca(2+) ions, which are pumped over from storage-intermembrane space into the matrix, during swelling of intermembrane space. In the process of ATP synthesis, energy is first, predominantly, used in the delivery of phosphate ions and protons to the α 3 β 3-hexamer against the energy barrier with the help of C-terminal alpha-helix of γ-subunit that acts as a lift; then, in the formation of phosphoryl group; and lastly, in the release of ATP molecules from the active center of the enzyme and the loading of ADP. We are aware that our model is not an accepted model for ATP synthesis, but it is presented here for further examination and test.

Philosophy of voltage-gated proton channels

In this review, voltage-gated proton channels are considered from a mainly teleological perspective. Why do proton channels exist? What good are they? Why did they go to such lengths to develop several unique hallmark properties such as extreme selectivity and ΔpH-dependent gating? Why is their current so minuscule? How do they manage to be so selective? What is the basis for our belief that they conduct H(+) and not OH(-)? Why do they exist in many species as dimers when the monomeric form seems to work quite well? It is hoped that pondering these questions will provide an introduction to these channels and a way to logically organize their peculiar properties as well as to understand how they are able to carry out some of their better-established biological functions.

Half a century of molecular bioenergetics

Molecular bioenergetics deals with the construction, function and regulation of the powerhouses of life. The present overview sketches scenes and actors, farsighted goals and daring hypotheses, meticulous tool-making, painstaking benchwork, lucky discovery, serious scepticism, emphatic believing and strong characters with weak and others with hard arguments, told from a personal, admittedly limited, perspective. Bioenergetics will blossom further with the search focused on both where there is bright light for ever-finer detail and the obvious dark spots for surprise and discovery.

Electric field driven torque in ATP synthase

F_O-ATP synthase (F_O) is a rotary motor that converts potential energy from ions, usually protons, moving from high- to low-potential sides of a membrane into torque and rotary motion. Here we propose a mechanism whereby electric fields emanating from the proton entry and exit channels act on asymmetric charge distributions in the c-ring, due to protonated and deprotonated sites, and drive it to rotate. The model predicts a scaling between time-averaged torque and proton motive force, which can be hindered by mutations that adversely affect the channels. The torque created by the c-ring of F_O drives the γ-subunit to rotate within the ATP-producing complex (F₁) overcoming, with the aid of thermal fluctuations, an opposing torque that rises and falls with angular position. Using the analogy with thermal Brownian motion of a particle in a tilted washboard potential, we compute ATP production rates vs. proton motive force. The latter shows a minimum, needed to drive ATP production, which scales inversely with the number of proton binding sites on the c-ring.

Structure and flexibility of the C-ring in the electromotor of rotary F(0)F(1)-ATPase of pea chloroplasts

A ring of 8-15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous F(O)F(1)-ATPase. Here we present the crystal structure at 3.4Å resolution of the c-ring from chloroplasts of a higher plant (Pisum sativum), determined using a native preparation. The crystal structure was found to resemble that of an (ancestral) cyanobacterium. Using elastic network modeling to investigate the ring's eigen-modes, we found five dominant modes of motion that fell into three classes. They revealed the following deformations of the ring: (I) ellipsoidal, (II) opposite twisting of the luminal circular surface of the ring against the stromal surface, and (III) kinking of the hairpin-shaped monomers in the middle, resulting in bending/stretching of the ring. Extension of the elastic network analysis to rings of different c(n)-symmetry revealed the same classes of dominant modes as in P. sativum (c(14)). We suggest the following functional roles for these classes: The first and third classes of modes affect the interaction of the c-ring with its counterparts in F(O), namely subunits a and bb'. These modes are likely to be involved in ion-translocation and torque generation. The second class of deformation, along with deformations of subunits γ and ε might serve to elastically buffer the torque transmission between F(O) and F(1).

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase

The molecular origin of the action of the F(0) proton gradient-driven rotor presents a major puzzle despite significant structural advances. Although important conceptual models have provided guidelines of how such systems should work, it has been challenging to generate a structure-based molecular model using physical principles that will consistently lead to the unidirectional proton-driven rotational motion during ATP synthesis. This work uses a coarse-grained (CG) model to simulate the energetics of the F(0)-ATPase system in the combined space defined by the rotational coordinate and the proton transport (PTR) from the periplasmic side (P) to the cytoplasmic side (N). The model establishes the molecular origin of the rotation, showing that this effect is due to asymmetry in the energetics of the proton path rather than only the asymmetry of the interaction of the Asp on the c-ring helices and Arg on the subunit-a. The simulation provides a clear conceptual background for further exploration of the electrostatic basis of proton-driven mechanochemical systems.

Implications of quantum metabolism and natural selection for the origin of cancer cells and tumor progression

Empirical studies give increased support for the hypothesis that the sporadic form of cancer is an age-related metabolic disease characterized by: (a) metabolic dysregulation with random abnormalities in mitochondrial DNA, and (b) metabolic alteration - the compensatory upregulation of glycolysis to offset mitochondrial impairments. This paper appeals to the theory of Quantum Metabolism and the principles of natural selection to formulate a conceptual framework for a quantitative analysis of the origin and proliferation of the disease. Quantum Metabolism, an analytical theory of energy transduction in cells inspired by the methodology of the quantum theory of solids, elucidates the molecular basis for differences in metabolic rate between normal cells, utilizing predominantly oxidative phosphorylation, and cancer cells utilizing predominantly glycolysis. The principles of natural selection account for the outcome of competition between the two classes of cells. Quantum Metabolism and the principles of natural selection give an ontogenic and evolutionary rationale for cancer proliferation and furnish a framework for effective therapeutic strategies to impede the spread of the disease.

Mechanism of proton/substrate coupling in the heptahelical lysosomal transporter cystinosin

Secondary active transporters use electrochemical gradients provided by primary ion pumps to translocate metabolites or drugs "uphill" across membranes. Here we report the ion-coupling mechanism of cystinosin, an unusual eukaryotic, proton-driven transporter distantly related to the proton pump bacteriorhodopsin. In humans, cystinosin exports the proteolysis-derived dimeric amino acid cystine from lysosomes and is impaired in cystinosis. Using voltage-dependence analysis of steady-state and transient currents elicited by cystine and neutralization-scanning mutagenesis of conserved protonatable residues, we show that cystine binding is coupled to protonation of a clinically relevant aspartate buried in the membrane. Deuterium isotope substitution experiments are consistent with an access of this aspartate from the lysosomal lumen through a deep proton channel. This aspartate lies in one of the two PQ-loop motifs shared by cystinosin with a set of eukaryotic membrane proteins of unknown function and is conserved in about half of them, thus suggesting that other PQ-loop proteins may translocate protons.

Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation

ATP synthases are the primary source of ATP in all living cells. To catalyze ATP synthesis, these membrane-associated complexes use a rotary mechanism powered by the transmembrane diffusion of ions down a concentration gradient. ATP synthases are assumed to be driven either by H(+) or Na(+), reflecting distinct structural motifs in their membrane domains, and distinct metabolisms of the host organisms. Here, we study the methanogenic archaeon Methanosarcina acetivorans using assays of ATP hydrolysis and ion transport in inverted membrane vesicles, and experimentally demonstrate that the rotary mechanism of its ATP synthase is coupled to the concurrent translocation of both H(+) and Na(+) across the membrane under physiological conditions. Using free-energy molecular simulations, we explain this unprecedented observation in terms of the ion selectivity of the binding sites in the membrane rotor, which appears to have been tuned via amino acid substitutions so that ATP synthesis in M. acetivorans can be driven by the H(+) and Na(+) gradients resulting from methanogenesis. We propose that this promiscuity is a molecular mechanism of adaptation to life at the thermodynamic limit.

Stabilization of Fo/Vo/Ao by a radial electric field

The membrane domain of rotary ATPases (Fo/Vo/Ao) contains a membrane-embedded rotor ring which rotates against an adjacent cation channel-forming subunit during catalysis. The mechanism that allows stabilization of the highly mobile and yet tightly connected domains during operation while not impeding rotation is unknown. Remarkably, all known ATPase rotor rings are filled by lipids. In the crystal structure of the rotor ring of a V-ATPase from Enterococcus hirae the ring filling lipids form a proper membrane that is lower with respect to the embedding membrane surrounding both subunits. I propose first, that a vertical shift between lumenal lipids and embedding outside membrane is a general feature of rotor rings and second that it leads to a radial potential fall-off between rotor ring and cation channel, creating attractive forces that impact rotor-stator interaction in Fo/Vo/Ao during rotation.

A role for anions in ATP synthesis and its molecular mechanistic interpretation

ATP, the 'universal biological energy currency', is synthesized by utilizing energy either from oxidation of fuels or from light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F(1)F(0)-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from ADP and inorganic phosphate (P(i)). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers 4,4'-diisothiocyanostilbene-2, 2'-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies, attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis. The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293-300, 2010a; J Bioenerg Biomembr 42:301-309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature 172:975-978, 1953; Williams J Theor Biol 1:1-17, 1961; Mitchell Nature 191:144-148, 1961; Mitchell Biol Rev 41:445-502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8-21, 2006a; Process Biochem 41:2218-2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms must be revised.

Structural bases of physiological functions and roles of the vacuolar H(+)-ATPase

Vacuolar-type H(+)-ATPases (V-ATPases) is a large multi-protein complex containing at least 14 different subunits, in which subunits A, B, C, D, E, F, G, and H compose the peripheral 500-kDa V(1) responsible for ATP hydrolysis, and subunits a, c, c', c″, and d assembly the 250-kDa membrane-integral V(0) harboring the rotary mechanism to transport protons across the membrane. The assembly of V-ATPases requires the presence of all V(1) and V(0) subunits, in which the V(1) must be completely assembled prior to association with the V(0), accordingly the V(0) failing to assemble cannot provide a membrane anchor for the V(1), thereby prohibiting membrane association of the V-ATPase subunits. The V-ATPase mediates acidification of intracellular compartments and regulates diverse critical physiological processes of cell for functions of its numerous functional subunits. The core catalytic mechanism of the V-ATPase is a rotational catalytic mechanism. The V-ATPase holoenzyme activity is regulated by the reversible assembly/disassembly of the V(1) and V(0), the targeting and recycling of V-ATPase-containing vesicles to and from the plasma membrane, the coupling ratio between ATP hydrolysis and proton pumping, ATP, Ca(2+), and its inhibitors and activators.

Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments

Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now straightforwardly be applied to other currently less well characterized but biologically more relevant systems.

Channel character of uncoupling protein-mediated transport

Mitochondrial uncoupling proteins (UCPs) are pure anion uniporters, which mediate fatty acid (FA) uniport leading to FA cycling. Protonated FAs then flip-flop back across the lipid bilayer. An existence of pure proton channel in UCPs is excluded by the equivalent flux-voltage dependencies for uniport of FAs and halide anions, which are best described by the Eyring barrier variant with a single energy well in the middle of two peaks. Experiments with FAs unable to flip and alkylsulfonates also support this view. Phylogenetically, UCPs took advantage of the common FA-uncoupling function of SLC25 family carriers and dropped their solute transport function.

Cancer proliferation and therapy: the Warburg effect and quantum metabolism

Background

Most cancer cells, in contrast to normal differentiated cells, rely on aerobic glycolysis instead of oxidative phosphorylation to generate metabolic energy, a phenomenon called the Warburg effect.

Model

Quantum metabolism is an analytic theory of metabolic regulation which exploits the methodology of quantum mechanics to derive allometric rules relating cellular metabolic rate and cell size. This theory explains differences in the metabolic rates of cells utilizing OxPhos and cells utilizing glycolysis. This article appeals to an analytic relation between metabolic rate and evolutionary entropy - a demographic measure of Darwinian fitness - to: (a) provide an evolutionary rationale for the Warburg effect, and (b) propose methods based on entropic principles of natural selection for regulating the incidence of OxPhos and glycolysis in cancer cells.

Conclusion

The regulatory interventions proposed on the basis of quantum metabolism have applications in therapeutic strategies to combat cancer. These procedures, based on metabolic regulation, are non-invasive, and complement the standard therapeutic methods involving radiation and chemotherapy

Essentials for ATP synthesis by F1F0 ATP synthases

The majority of cellular energy in the form of adenosine triphosphate (ATP) is synthesized by the ubiquitous F(1)F(0) ATP synthase. Power for ATP synthesis derives from an electrochemical proton (or Na(+)) gradient, which drives rotation of membranous F(0) motor components. Efficient rotation not only requires a significant driving force (DeltamuH(+)), consisting of membrane potential (Deltapsi) and proton concentration gradient (DeltapH), but also a high proton concentration at the source P side. In vivo this is maintained by dynamic proton movements across and along the surface of the membrane. The torque-generating unit consists of the interface of the rotating c ring and the stator a subunit. Ion translocation through this unit involves a sophisticated interplay between the c-ring binding sites, the stator arginine, and the coupling ions on both sides of the membrane. c-ring rotation is transmitted to the eccentric shaft gamma-subunit to elicit conformational changes in the catalytic sites of F(1), leading to ATP synthesis.

Torque generation and elastic power transmission in the rotary F(O)F(1)-ATPase

Adenosine triphosphate (ATP), the universal fuel of the cell, is synthesized from adenosine diphosphate (ADP) and inorganic phosphate (P(i)) by 'ATP synthase' (F(O)F(1)-ATPase). During respiration or photosynthesis, an electrochemical potential difference of protons is set up across the respective membranes. This powers the enzyme's electrical rotary nanomotor (F(O)), which drives the chemical nanomotor (F(1)) by elastic mechanical-power transmission, producing ATP with high kinetic efficiency. Attempts to understand in detail the mechanisms of torque generation in this simple and robust system have been both aided and complicated by a wealth of sometimes conflicting data.

Concentration gradient effects of sodium and lithium ions and deuterium isotope effects on the activities of H+-ATP synthase from chloroplasts

We explored the concentration gradient effects of the sodium and lithium ions and the deuterium isotope's effects on the activities of H(+)-ATP synthase from chloroplasts (CF(0)F(1)). We found that the sodium concentration gradient can drive the ATP synthesis reaction of CF(0)F(1). In contrast, the lithium ion can be an efficient enzyme-inhibitor by blocking the entrance channel of the ion translocation pathway in CF(0). In the presence of sodium or lithium ions and with the application of a membrane potential, unexpected enzyme behaviors of CF(0)F(1) were evident. To account for these observations, we propose that both of the sodium and lithium ions could undergo localized hydrolysis reactions in the chemical environment of the ion channel of CF(0). The protons generated locally could proceed to complete the ion translocation process in the ATP synthesis reaction of CF(0)F(1). Experimental and theoretical deuterium isotope effects of the localized hydrolysis on the activities of CF(0)F(1), and the energetics of these related reactions, support this proposed mechanism. Our experimental observations could be understood in the framework of the well-established ion translocation models for the H(+)-ATP synthase from Escherichia coli, and the Na(+)-ATP synthase from Propionigenium modestum and Ilyobacter tartaricus.

Co-evolution of primordial membranes and membrane proteins

Studies of the past several decades have provided major insights into the structural organization of biological membranes and mechanisms of many membrane molecular machines. However, the origin(s) of the membrane(s) and membrane proteins remains enigmatic. We discuss different concepts of the origin and early evolution of membranes with a focus on the evolution of the (im)permeability to charged molecules such as proteins, nucleic acids and small ions. Reconstruction of the evolution of F-type and A/V-type membrane ATPases (ATP synthases), which are either proton- or sodium-dependent, might help us to understand not only the origin of membrane bioenergetics but also of membranes themselves. We argue that evolution of biological membranes occurred as a process of co-evolution of lipid bilayers, membrane proteins and membrane bioenergetics.

Functional asymmetry of the F(0) motor in bacterial ATP synthases

F(1)F(0) ATP synthases use the electrochemical potential of H(+) or Na(+) across biological membranes to synthesize ATP by a rotary mechanism. In bacteria, the enzymes can act in reverse as ATP-driven ion pumps creating the indispensable membrane potential. Here, we demonstrate that the F(0) parts of a Na(+)- and H(+)-dependent enzyme display major asymmetries with respect to their mode of operation, reflected by the requirement of approximately 100 times higher Na(+) or H(+) concentrations for the synthesis compared with the hydrolysis of ATP. A similar asymmetry is observed during ion transport through isolated F(0) parts, indicating different affinities for the binding sites in the a/c interface. Together with further data, we propose a model that provides a rationale for a differential usage of membrane potential and ion gradient during ATP synthesis as observed experimentally. The functional asymmetry might also reflect an important property of the ATP synthesis mechanism in vivo. In Escherichia coli, we observed respiratory chain-driven ATP production at pH 7-8, while P-site pH values < 6.5 were required for ATP synthesis in vitro. This discrepancy is discussed with respect to the hypothesis that during respiration lateral proton diffusion could lead to significant acidification at the membrane surface.

Dynamics and efficiency of Brownian rotors

Brownian rotors play an important role in biological systems and in future nanotechnological applications. However the mechanisms determining their dynamics, efficiency, and performance remain to be characterized. Here the F0 portion of the F-ATP synthase is considered as a paradigm of the Brownian rotor. In a generic analytical model we analyze the stochastic rotation of F0-like motors as a function of the driving free energy difference and of the free energy profile the rotor is subjected to. The latter is composed of the rotor interaction with its surroundings, of the free energy of chemical transitions, and of the workload. The dynamics and mechanical efficiency of the rotor depend on the magnitude of its stochastic motion driven by the free energy difference and its rectification on the reaction-diffusion path. We analyze which free energy profiles provide maximum flow and how their arrangement on the underlying reaction-diffusion path affects rectification and--by this--the efficiency.

Unique rotary ATP synthase and its biological diversity

F1F0 ATP synthases convert energy stored in an electrochemical gradient of H+ or Na+ across the membrane into mechanical rotation, which is subsequently converted into the chemical bond energy of ATP. The majority of cellular ATP is produced by the ATP synthase in organisms throughout the biological kingdom and therefore under diverse environmental conditions. The ATP synthase of each particular cell is confronted with specific challenges, imposed by the specific environment, and thus by necessity must adapt to these conditions for optimal operation. Examples of these adaptations include diverse mechanisms for regulating the ATP hydrolysis activity of the enzyme, the utilization of different coupling ions with distinct ion binding characteristics, different ion-to-ATP ratios reflected by variations in the size of the rotor c ring, the mode of ion delivery to the binding sites, and the different contributions of the electrical and chemical gradients to the driving force.