A critique of the chemosmotic model of energy coupling

Coupling mechanisms in ATP synthesis: Rejoinder to "Response to molecular-level understanding of biological energy coupling and transduction"

Recently, an exchange of views on key fundamental aspects of biological energy coupling and ATP synthesis in the vital process of oxidative phosphorylation appeared in the pages of this journal. The very difficult scientific problems are analyzed and clarified. Errors in the mathematical/thermodynamic equations of a previous analysis have been identified that invalidate previous assertions, and the correct equations are derived. The major differences between the two competing models - localized versus delocalized - for biological energy coupling and transduction are discussed from physical, chemical, and mathematical perspectives. The opposing views are summarized, so that the reader can assess for himself or herself the merits of the two coupling mechanisms. A fresh attempt has been made to go to the root of bioenergetics by calculating the desolvation free energy barrier, ∆G_desolvation for ion transport across biomembranes. Several constructive suggestions are made that have the power to resolve the basic contradictions and the areas of fundamental conflict, and reach a consensus by catalyzing the progress of future research in this interdisciplinary field.

Molecular-level understanding of biological energy coupling and transduction: Response to "Chemiosmotic misunderstandings"

In a recent paper entitled "Chemiosmotic misunderstandings", it is claimed that "enough shortcomings in Mitchell's chemiosmotic theory have not been found and that a novel paradigm that offers at least as much explanatory power as chemiosmosis is not ready." This view is refuted by a wealth of molecular-level experimental data and strong new theoretical and computational evidence. It is shown that the chemiosmotic theory was beset with a large number of major shortcomings ever since the time when it was first proposed in the 1960s. These multiple shortcomings and flaws of chemiosmosis were repeatedly pointed out in incisive critiques by biochemical authorities of the late 20th century. All the shortcomings and flaws have been shown to be rectified by a quantitative, unified molecular-level theory that leads to a deeper and far more accurate understanding of biological energy coupling and ATP synthesis. The new theory is shown to be consistent with pioneering X-ray and cryo-EM structures and validated by state-of-the-art single-molecule techniques. Several new biochemical experimental tests are proposed and constructive ways for providing a revitalizing conceptual background and theory for integration of the available experimental information are suggested.

Molecular mechanistic insights into coupling of ion transport to ATP synthesis

A wealth of molecular mechanistic insights has been provided into the coupling of ion transport to ATP synthesis based on a two-ion theory of biological energy coupling. A kinetic scheme that considers the mode of functioning of a single F₁F_O-ATP synthase molecule with H⁺-A^- cotransport and unidirectional rotation of the c-rotor in the membrane-bound F_O-portion of the enzyme has been developed. Mathematical analysis leads to a detailed enzyme kinetic model applicable to a population of molecules which is compared with experimental data on the pH dependence of ATP synthesis. The model agrees well with the experimental data, and a single equation with a single set of standard enzymological kinetic parameters has been shown to explain the experimental data over the entire range of conditions for the chloroplast ATP synthase. The analysis gives novel insights into kinetic and mechanistic characteristics of ATP synthesis in F_O. These include an order imposed on ion binding and unbinding events in F_O, the essential role of the anion in direct activation of the ATP synthase (in addition to its role as a permeant ion), and the integration in a novel way of the functions of cooperativity and cotransport of dicarboxylic acid anions and protons during physiological ATP synthesis. Further, Wyman's pioneering classical work on the thermodynamics of linked functions has been shown to offer a new approach to distinguish between various models of energy coupling in ATP synthesis. All these results have been found to be inconsistent with Mitchell's chemiosmotic theory and are shown to be in agreement with Nath's torsional mechanism of energy transduction and ATP synthesis.

Two-ion theory of energy coupling in ATP synthesis rectifies a fundamental flaw in the governing equations of the chemiosmotic theory

The vital coupled processes of oxidative phosphorylation and photosynthetic phosphorylation synthesize molecules of adenosine-5'-triphosphate (ATP), the universal biological energy currency, and sustain all life on our planet. The chemiosmotic theory of energy coupling in oxidative and photophosphorylation was proposed by Mitchell >50years ago. It has had a contentious history, with part of the accumulated body of experimental evidence supporting it, and part of it in conflict with the theory. Although the theory was strongly criticized by many prominent scientists, the controversy has never been resolved. Here, the mathematical steps of Mitchell's original derivation leading to the principal equation of the chemiosmotic theory are scrutinized, and a fundamental flaw in them has been identified. Surprisingly, this flaw had not been detected earlier. Discovery of such a defect negates, or at least considerably weakens, the theoretical foundations on which the chemiosmotic theory is based. Ad hoc or simplistic ways to remedy this defect are shown to be scientifically unproductive and sterile. A novel two-ion theory of biological energy coupling salvages the situation by rectifying the fundamental flaw in the chemiosmotic theory, and the governing equations of the new theory have been shown to accurately quantify and predict extensive recent experimental data on ATP synthesis by F₁F_O-ATP synthase without using adjustable parameters. Some major biological implications arising from the new thinking are discussed. The principles of energy transduction and coupling proposed in the new paradigm are shown to be of a very general and universal nature. It is concluded that the timely availability after a 25-year research struggle of Nath's torsional mechanism of energy transduction and ATP synthesis is a rational alternative that has the power to solve the problems arising from the past, and also meet present and future challenges in this important interdisciplinary field of research.

Analysis of molecular mechanisms of ATP synthesis from the standpoint of the principle of electrical neutrality

Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis. Mitchell's chemiosmotic theory is found to violate the electroneutrality of bulk aqueous phases and is shown to be untenable on these grounds. Purely electroneutral mechanisms or mechanisms where the anion/countercation gradient is dissipated or simply flows through the lipid bilayer are also shown to be inadequate. A dynamically electrogenic but overall electroneutral mode of ion transport postulated by Nath's torsional mechanism of energy transduction and ATP synthesis is shown to be consistent both with the experimental findings and the principle of electrical neutrality. It is concluded that the ATP synthase functions as a proton-dicarboxylic acid anion cotransporter in OX PHOS or PHOTO PHOS. A logical chemical explanation for the selection of dicarboxylic acids as intermediates in OX PHOS and PHOTO PHOS is suggested based on the pioneering classical thermodynamic work of Christensen, Izatt, and Hansen. The nonequilibrium thermodynamic consequences for theories in which the protons originate from water vis-a-vis weak organic acids are compared and contrasted, and several new mechanistic and thermodynamic insights into biological energy transduction by ATP synthase are offered. These considerations make the new theory of energy coupling more complete, and lead to a deeper understanding of the molecular mechanism of ATP synthesis.

Oxidative phosphorylation revisited

The fundamentals of oxidative phosphorylation and photophosphorylation are revisited. New experimental data on the involvement of succinate and malate anions respectively in oxidative phosphorylation and photophosphorylation are presented. These new data offer a novel molecular mechanistic explanation for the energy coupling and ATP synthesis carried out in mitochondria and chloroplast thylakoids. The mechanism does not suffer from the flaws in Mitchell's chemiosmotic theory that have been pointed out in many studies since its first appearance 50 years ago, when it was hailed as a ground-breaking mechanistic explanation of what is perhaps the most important process in cellular energetics. The new findings fit very well with the predictions of Nath's torsional mechanism of energy transduction and ATP synthesis. It is argued that this mechanism, based on at least 15 years of experimental and theoretical work by Sunil Nath, constitutes a fundamentally different theory of the energy conversion process that eliminates all the inconsistencies in Mitchell's chemiosmotic theory pointed out by other authors. It is concluded that the energy-transducing complexes in oxidative phosphorylation and photosynthesis are proton-dicarboxylic acid anion cotransporters and not simply electrogenic proton translocators. These results necessitate revision of previous theories of biological energy transduction, coupling, and ATP synthesis. The novel molecular mechanism is extended to cover ATP synthesis in prokaryotes, in particular to alkaliphilic and haloalkaliphilic bacteria, essentially making it a complete theory addressing mechanistic, kinetic, and thermodynamic details. Finally, based on the new interpretation of oxidative phosphorylation, quantitative values for the P/O ratio, the amount of ATP generated per redox package of the reduced substrates, are calculated and compared with experimental values for fermentation on different substrates. It is our hope that the presentation of oxidative phosphorylation and photophosphorylation from a wholly new perspective will rekindle scientific discussion of a key process in bioenergetics and catalyze new avenues of research in a truly interdisciplinary field.

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.

Beyond the chemiosmotic theory: analysis of key fundamental aspects of energy coupling in oxidative phosphorylation in the light of a torsional mechanism of energy transduction and ATP synthesis--invited review part 1

In Part 1 of this invited article, we consider the fundamental aspects of energy coupling in oxidative phosphorylation. The central concepts of the chemiosmotic theory are re-examined and the major problems with its experimental verification are analyzed and reassessed from first principles. Several of its assumptions and interpretations (with regard, for instance, to consideration of the membrane as an inert barrier, the occurrence of energy transduction at thermodynamic equilibrium, the completely delocalized nature of the protonmotive force, and the notion of indirect coupling) are shown to be questionable. Important biological implications of this analysis for molecular mechanisms of biological energy transduction are enumerated. A fresh molecular mechanism of the uncoupling of oxidative phosphorylation by classical weak acid anion uncouplers and an adequate explanation for the existence of uncoupler-resistant mutants (which until now has remained a mystery) has been proposed based on novel insights arising from a new torsional mechanism of energy transduction and ATP synthesis.

Beyond the chemiosmotic theory: analysis of key fundamental aspects of energy coupling in oxidative phosphorylation in the light of a torsional mechanism of energy transduction and ATP synthesis--invited review part 2

The core of this second article shows how logical errors and inconsistencies in previous theories of energy coupling in oxidative phosphorylation are overcome by use of a torsional mechanism and the unified theory of ATP synthesis/hydrolysis. The torsional mechanism is shown to satisfy the pioneering and verified features of previous mechanisms. A considerable amount of data is identified that is incompatible with older theories but is now explained in a logically consistent and unified way. Key deficiencies in older theories are pinpointed and their resolution elucidated. Finally, major differences between old and new approaches are tabulated. The new theory now provides the elusive details of energy coupling and transduction, and allows several novel and experimentally verifiable predictions to be made and a considerable number of applications in nanotechnology, energy conversion, systems biology, and in health and disease are foreseen.

Energy transfer from adenosine triphosphate: quantitative analysis and mechanistic insights

The ATP-ADP thermodynamic cycle is the fundamental mode of energy exchange in oxidative phosphorylation, photophosphorylation, muscle contraction, and intracellular transport by various molecular motors and is therefore of vital importance in biological energy transduction and storage. Following a recent suggestion in the pages of this journal (Ross, J. J. Phys. Chem. B 2006, 110, 6987-6990), we have carried out a simple quantitative analysis of a direct molecular mechanism of energy transfer from adenosine triphosphate (ATP). The simulation provides new insights into the mechanistic events following terminal phosphorus-oxygen bond cleavage during ATP hydrolysis. This approach also allows for the division of the energy-transfer process into elementary steps and for the prediction of the distribution of the standard-state Gibbs free energy of the overall ATP hydrolysis process among the various steps of substrate binding, bond cleavage, and product release in the enzymatic cycle, which had proved very difficult to specify previously. These predictions are consistent with available experimental data on ATP hydrolysis by protein biomolecular machines. The fundamental biological implications arising from our results are also discussed in detail. The aspects considered in this work enable us to look at the entire process of ATP synthesis/hydrolysis and energy transduction and storage in various biological molecular machines in a logically consistent and unified way.

The new unified theory of ATP synthesis/hydrolysis and muscle contraction, its manifold fundamental consequences and mechanistic implications and its applications in health and disease

Complete details of the thermodynamics and molecular mechanisms of ATP synthesis/hydrolysis and muscle contraction are offered from the standpoint of the torsional mechanism of energy transduction and ATP synthesis and the rotation-uncoiling-tilt (RUT) energy storage mechanism of muscle contraction. The manifold fundamental consequences and mechanistic implications of the unified theory for oxidative phosphorylation and muscle contraction are explained. The consistency of current mechanisms of ATP synthesis and muscle contraction with experiment is assessed, and the novel insights of the unified theory are shown to take us beyond the binding change mechanism, the chemiosmotic theory and the lever arm model. It is shown from first principles how previous theories of ATP synthesis and muscle contraction violate both the first and second laws of thermodynamics, necessitating their revision. It is concluded that the new paradigm, ten years after making its first appearance, is now perfectly poised to replace the older theories. Finally, applications of the unified theory in cell life and cell death are outlined and prospects for future research are explored. While it is impossible to cover each and every specific aspect of the above, an attempt has been made here to address all the pertinent details and what is presented should be sufficient to convince the reader of the novelty, originality, breakthrough nature and power of the unified theory, its manifold fundamental consequences and mechanistic implications, and its applications in health and disease.

Molecular mechanisms of energy transduction in cells: engineering applications and biological implications

The synthesis of ATP from ADP and inorganic phosphate by F1F0-ATP synthase, the universal enzyme in biological energy conversion, using the energy of a transmembrane gradient of ions, and the use of ATP by the myosin-actin system to cause muscular contraction are among the most fundamental processes in biology. Both the ATP synthase and the myosin-actin may be looked upon as molecular machines. A detailed analysis of the molecular mechanisms of energy transduction by these molecular machines has been carried out in order to understand the means by which living cells produce and consume energy. These mechanisms have been compared with each other and their biological implications have been discussed. The thermodynamics of energy coupling in the oxidative phosphorylation process has been developed and the consistency of the mechanisms with the thermodynamics has been explored. Novel engineering applications that can result have been discussed in detail and several directions for future work have been pointed out.

Mechanism of active transport: free energy dissipation and free energy transduction

The thermodynamic pathway for "chemiosmotic" free energy transduction in active transport is discussed with an ATP-driven Ca2+ pump as an illustrative example. Two innovations are made in the analysis. (i) Free energy dissipated as heat is rigorously excluded from overall free energy bookkeeping by focusing on the dynamic equilibrium state of the chemiosmotic process. (ii) Separate chemical potential terms for free energy donor and transported ions are used to keep track of the thermodynamic state of each substrate through the reaction cycle. These procedures clarify the mechanism of free energy transduction, even without step-by-step analysis. The results show that free energy exchange must occur in its entirety among protein-bound species. Imposition of conditions for an adequate rate of physiological function further indicates (i) that the standard free energy of hydrolysis of protein-bound ATP (to yield protein-bound products) needs to differ substantially from the standard free energy of hydrolysis in solution and (ii) that binding sites for the transported ions must have different affinities when facing opposite sides of the membrane. The results also demonstrate that step-by-step "basic" free energy changes (often used in the form of free energy level diagrams) are inherently unsuited for analysis of the mechanism of free energy transduction.

On the enzymic mechanism of oxidative phosphorylation

Oxidative phosphorylation, like substrate-level phosphorylation, involves oxidative conversion of inorganic phosphate to a reactive species followed by interaction of this species with enzyme-bound ADP to form enzyme-bound ATP. The reactive species in a phosphoryl ester in substrate-level phosphorylation and phosphonium ion of orthophosphate in oxidative phosphorylation. The coupled synthesis is mediated by a combination of two classical enzymes in substrate-level phosphorylation and by a set of energy-coupled enzymes in oxidative phosphorylation. The full range of experimental evidence supporting this proposed enzymic mechanism of oxidative phosphorylation is presented as well as the rationalization of phenomena that hitherto have eluded explanation.

Universal energy principle of biological systems and the unity of bioenergetics

Electronic energy (chemical bond energy) is the exclusive source of utilizable energy in biological systems. The release of this energy is mediated enzymically. The energy required to rupture a single covalent or ionic bond is prohibitively high under physiological conditions [in the range of 80-200 kcal/mol (1 kcal = 4.18 kJ)]. By the technique of the pairing of bond rupture (two juxtaposed bonds ruptured simultaneously) and the pairing of bond formation, enzymes can bypass the huge thermodynamic barrier to chemical change inherent in rupture of a single bond and operate within thermal limits. Enzymes accordingly can be conceived of as the energy machines that translate this principle. The principle of this transduction is that the energy required for forming a new covalent bond can fall within thermal limits when the original charged atom partner to the bond is displaced by a substitute charged atom under conditions in which the charge field of the bond remains constant during the substitution. In the transition from classical enzymology to energy coupling, muscular contraction, template-dependent replication, etc., new dimensions and possibilities are added to the basic enzymatic machinery. Specialized molecular devices (membranes, filaments, channels, templates, etc.) have to be introduced to make possible these extensions and permutations of enzymology. But it is demonstrable that the basis pairing principle is fully preserved during any of these modifications or extensions. Long range movement--of an ion, a filament, or a template--is the most important property introduced into classical enzymology in the transition to energy coupling systems.