On the efficiency and reversibility of active ligand transport induced by alternating rectangular electric pulses.

The stationary-state kinetic properties of a simplified two-state electro-conformational coupling model (ECC) in the presence of alternating rectangular electric potential pulses are derived analytically. Analytic expressions for the transport flux, the rate of electric energy dissipation, and the efficiency of the transducing system are obtained as a function of the amplitude and frequency of the oscillation. These formulas clarify some fundamental concept of the ECC model and are directly applicable to the interpretation and design of experiments. Based on these formulas, the reversibility and the degree of coupling of the system can be studied quantitatively. It is found that the oscillation-induced free energy transduction is reversible and tight-coupled only when the amplitude of the oscillating electric field is infinitely large. In general, the coupling is not tight when the amplitude of the electric field is finite. Furthermore, depending on the kinetic parameters of the model, there may exist a "critical" electric field amplitude, below which free energy transduction is not reversible. That is, energy may be transduced from the electric to the chemical, but not from the chemical to the electric.     

On the coupling of electron transport to phosphorylation

After a general thermodynamic discussion of the coupling of oxidation to phosphorylation, quantitative treatments of free energy transduction based upon the proton gradient model, the charged membrane model and the chemical model respectively are summarized and compared with experimental data. The relationship between energy transduction and respiratory control is reexamined.Supported by a research grant (GM 04483) from the National Institute of General Medical Sciences, National Institutes of Health, Department of Health, Education and Welfare.     

Rethinking the P-type ATPase problem

There are very good reasons to stop thinking about the molecular mechanism of the P-type ion-translocating ATPases in terms of the traditional E1E2 model and to start thinking about it in more progressive ways. This makes it possible to see the ion-transport cycle as a rational series of discrete steps with well defined driving forces, including the crucial energy transduction step, where the chemical energy of ATP hydrolysis is exchanged for the osmotic energy of an ion gradient. Importantly, although major enzyme conformational changes accompany each of these steps, none of them drive the energy coupling reaction. Thus, neither the E1E2 model nor conformational energy coupling, the cornerstones of traditional thinking about the P-type ATPases, are reliable paradigms for future efforts to understand how these transporters work. Alternatives must be seriously considered.     

Resonance electroconformational coupling: A proposed mechanism for energy and signal transductions by membrane proteins

Recent experiments show that membrane ATPases are capable of absorbing free energy from an applied oscillating electric field and converting it to chemical bond energy of ATP or chemical potential energy of concentration gradients. Presumably these enzymes would also respond to endogenous transmembrane electric fields of similar intensity and waveform. A mechanism is proposed in which energy coupling is achieved via Coulombic interaction of an electric field and the conformational equilibria of an ATPase. Analysis indicates that only an oscillating or fluctuating electric field can be used by an enzyme to drive a chemical reaction away from equilibrium.In vivo, the stationary transmembrane potential of a cell must be modulated to become locally oscillatory if it is to derive energy and signal transduction processes.     

Molecular recognition and processing of periodic signals in cells: study of activation of membrane ATPases by alternating electric fields.

A molecule which is immobilized, oriented or tumbling more slowly than the frequency of a periodic field, may interact with the field to produce chemical effects that are uncommon in a homogeneous solution. Among these effects are the alteration of the rate of a chemical reaction and the exchange of energy between the oscillating field and the conformation of the molecule. When certain conditions are satisfied, this exchange allows the molecule to absorb and couple the energy of the field to drive an endergonic reaction. The efficiency of energy coupling depends on field strength and frequency and on the ligand concentration. There are windows of these parameters to achieve efficient coupling. These windows can be expressed in terms of the rate constants and equilibrium constants of the catalytic reactions, and the amplitude and frequency of the periodic field. This mechanism allows cells to receive, process and transmit energy of high and medium level periodic potentials by means of membrane enzymes or receptors. A theory for the transduction of electric energy, electroconformational coupling (ECC) will be discussed. The electric field induced cation pumping activities of Na,K-ATPase and Ca-ATPase of human erythrocytes and the ATP synthetic activity of beef heart mitochondrial ATPase will then be used to test an ECC membrane transport model. For the processing of low level periodic signals, a theory of an oscillatory activation barrier (OAB), which considers resonance transduction between an oscillating field and the activation barrier of the rate limiting step in an enzymic reaction, will be discussed. The OAB mechanism successfully interprets the AC stimulated ATP hydrolysis activity of Ecto-ATPase from chicken oviduct and F0F1-ATPase from beef heart. We propose that mechanisms similar to an OAB model are adopted by cells to sense weak electric, acoustic, mechanical, concentration (i.e., chemical potential) and other types of signals, and to communicate with other cells by these signals. The experimental data and mechanistic information presented in this communication give us a glimpse of the molecular electronic designs in living cells. This information is also relevant with respect to environmental issues. Environmental electromagnetic fields and sonic pollutants may interfere with normal communications of cells and organisms. Their benefit, if any, and detrimental effects can be assessed and dealt with only if we fully understand mechanisms of cellular interactions with these fields and pollutants, at the molecular level.     

Structural bioenergetics and energy transduction mechanisms.

Life depends on transduction processes that couple cellular metabolism to environmental energy sources such as light or reduced compounds. These primary energy sources must be efficiently converted into forms that can be utilized by cells for biosynthesis, motility, transport, regulation, and other metabolic functions. In recent years, there has been an explosive increase in the determination of structures for proteins mediating energy transduction processes. These developments provide the opportunity to evaluate the structural basis for the efficient coupling of two energetic processes, which defines the area of structural bioenergetics. Here, we present some general features of energy transduction processes, including arguments that effective coupling of two processes by a transduction protein occurs by way of conformational states that are common to the catalysis of each process. This is illustrated by examples from the nucleotide switch family of proteins, with emphasis on the nitrogenase system where ATP hydrolysis is coupled to an electron transfer reaction.     

Hypothesis for Coupling Energy Transduction with ATP Synthesis or ATP Hydrolysis

A mechanistic hypothesis for coupling and energy transduction has been developed. It is suggested that membrane-bound ATPases play an intermediate high energy role.     

Finite time thermodynamic coupling in a biochemical network

The paper describes some thermodynamic constrains and relations in biochemical or metabolic network and provides a basis for entropy enthalpy compensation. Conventional definition of macroscopic forces and fluxes leads to a paradox namely, non-existence of positive efficiency of a chemically driven process. This paradox is resolved by deriving an appropriate definition of macroscopic force using the local balance equations. Entropy enthalpy compensation, whose thermodynamic basis is so far unclear, also follows. The method provides an account of how reactive pathways are coupled, the strength of coupling between a pathway pair depending on the product of their respective enthalpies. The obligatory role of the presence of a common chemical intermediate in defining coupling becomes unnecessary; such intermediate-free coupling being a key feature of metabolic energy transduction. The redefined flux and force can also be exploited to explain surface to volume ratio dependence of coupled networks. Lastly, the thermodynamic rationale for the Bergman’s eco-geographic rule, namely the reduced ability of larger animals to avoid stress follows from the generalized expression for coupling coefficients. Higher surface to volume ratio is shown to make the organism resistant to external perturbations.     

Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome

Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g. electron and proton transfer in proton-pumps. There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates. Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate. The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions. This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp. cytochromes from the same structural family.     

The application of mass and energy conservation laws in physiologically structured population models of heterotrophic organisms

Rules for energy uptake, and subsequent utilization, form the basis of population dynamics and, therefore, explain the dynamics of the ecosystem structure in terms of changes in standing crops and size distributions of individuals. Mass fluxes are concomitant with energy flows and delineate functional aspects of ecosystems by defining the roles of individuals and populations. The assumption of homeostasis of body components, and an assumption about the general structure of energy budgets, imply that mass fluxes can be written as weighted sums of three organizing energy fluxes with the weight coefficients determined by the conservation law of mass. These energy fluxes are assimilation, maintenance and growth, and provide a theoretical underpinning of the widely applied empirical method of indirect calorimetry, which relates dissipating heat linearly to three mass fluxes: carbon dioxide production, oxygen consumption and N-waste production. A generic approach to the stoichiometry of population energetics from the perspective of the individual organism is proposed and illustrated for heterotrophic organisms. This approach indicates that mass transformations can be identified by accounting for maintenance requirements and overhead costs for the various metabolic processes at the population level. The theoretical background for coupling the dynamics of the structure of communities to nutrient cycles, including the water balance, as well as explicit expressions for the dissipating heat at the population level are obtained based on the conservation law of energy. Specifications of the general theory employ the Dynamic Energy Budget model for individuals. Copyright 1999 Academic Press.     

Reversible mechanosensitive ion pumping as a part of mechanoelectrical transduction.

To explain the ability of some mechanosensitive cells to reverse the process of mechanotransduction and to generate mechanical oscillations and emit sound, a piezo-conformational coupling model (PCC model) is proposed. The model includes a transport protein which changes either its volume (PV-coupling) or its area in the membrane (gamma A-coupling) when undergoing conformational transitions. Such a protein can interact with an oscillating pressure to pump ions and create a transmembrane gradient if the affinities of the protein for ions are different at the two sides of membrane. The frequency and concentration windows for mechanical energy transduction were determined. Under optimal conditions, the efficiency of energy transduction can approach the theoretical maximum of 100%. If the concentration gradient exceeds the static head value (quasi-equilibrium which can be built up and maintained by this transport system), the energy transduction reverses and the transporter becomes a generator of mechanical oscillations at the expense of a concentration gradient. Estimation of thermodynamic parameters of the pump shows that the PV-coupling model would require large pressure oscillations to work while the gamma A-coupling model could work in physiological conditions. The gamma A-coupling mechanism may be used by cells for two purposes. In the reverse mode, it can be a force generator for various applications. In the direct mode, it may serve bioenergetic purposes by harvesting the energy of mechanical oscillations and storing it in the form of a concentration gradient.(ABSTRACT TRUNCATED AT 250 WORDS)     

Energy Transduction Inside of Amphiphilic Vesicles: Encapsulation of Photochemically Active Semiconducting Particles

Amphiphilic bilayer membrane structures (vesicles) have been postulated to have been abiotically formed and spontaneously assemble on the prebiotic Earth, providing compartmentalization for the origin of life. These vesicles are similar to modern cellular membranes and can serve to contain water-soluble species, concentrate species, and have the potential to catalyze reactions. The origin of the use of photochemical energy in metabolism (i.e. energy transduction) is one of the central issues in the origin of life. This includes such questions as how energy transduction may have occurred before complex enzymatic systems, such as required by contemporary photosynthesis, had developed and how simple a photochemical system is possible. It has been postulated that vesicle structures developed the ability to capture and transduce light, providing energy for reactions. It has also been shown that pH gradients across the membrane surface can be photochemically created, but coupling these to drive chemical reactions has been difficult. Colloidal semiconducting mineral particles are known to photochemically drive redox chemistry. We propose that encapsulation of these particles has the potential to provide a source of energy transduction inside vesicles, and thereby drive protocellular chemistry, and represents a model system for early photosynthesis. In our experiments we show that TiO₂ particles, in the ~20 nm size range, can be incorporated into vesicles and retain their photoactivity through the dehydration/rehydration cycles that have been shown to concentrate species inside a vesicle.     

Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis

PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of their partners. PDZ domains are thought also to play a signal transduction role by propagating the information that binding has occurred to remote sites. In this study, a molecular dynamics (MD) simulation-based approach, referred to as an interaction correlation analysis, is applied to the PDZ2 domain to identify the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlations between all residue pairs obtained from the MD simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N-terminal side of helix alpha1 and the adjacent C-terminus of loop beta1-beta2. The other pathway is perpendicular to the central beta-sheet and extends toward the side of PDZ2 domain opposite to the ligand binding pocket. The results complement previous studies based on multiple sequence analysis, NMR, and MD simulations. Importantly, they reveal the energetic origin of the long-range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction.     

Baroreceptor mechanisms at the cellular level

Nothing is known of transduction mechanisms of baroreceptors in vivo. Not even the site of transduction is known. However, there are mechanotransducer ion channels that provide a useful model system of transduction. In these channels, transduction is accomplished by a strain-dependent increase in the probability of being open. Membrane tension is coupled to the channel by cytoskeletal strands that concentrate the strain energy from a large (approximately equal to 4000 A diameter) area of membrane and thereby provide high sensitivity. The channel is fast and does not inactivate, but viscoelastic coupling to the channel can dramatically alter the transfer function.     

VenusA206 Dimers Behave Coherently at Room Temperature

Fluorescent proteins (FPs) have revolutionized cell biology by allowing genetic tagging of specific proteins inside living cells. In conjunction with Förster’s resonance energy transfer (FRET) measurements, FP-tagged proteins can be used to study protein-protein interactions and estimate distances between tagged proteins. FRET is mediated by weak Coulombic dipole-dipole coupling of donor and acceptor fluorophores that behave independently, with energy hopping discretely and incoherently between fluorophores. Stronger dipole-dipole coupling can mediate excitonic coupling in which excitation energy is distributed near instantaneously between coherently interacting excited states that behave as a single quantum entity. The interpretation of FP energy transfer measurements to estimate separation often assumes that donors and acceptors are very weakly coupled and therefore use a FRET mechanism. This assumption is considered reasonable as close fluorophore proximity, typically associated with strong excitonic coupling, is limited by the FP β-barrel structure. Furthermore, physiological temperatures promote rapid vibrational dephasing associated with a rapid decoherence of fluorophore-excited states. Recently, FP dephasing times that are 50 times slower than traditional organic fluorophores have been measured, raising the possibility that evolution has shaped FPs to allow stronger than expected coupling under physiological conditions. In this study, we test if excitonic coupling between FPs is possible at physiological temperatures. FRET and excitonic coupling can be distinguished by monitoring spectral changes associated with fluorophore dimerization. The weak coupling mediating FRET should not cause a change in fluorophore absorption, whereas strong excitonic coupling causes Davydov splitting. Circular dichroism spectroscopy revealed Davydov splitting when the yellow FP Venus_A206 dimerizes, and a novel approach combining photon antibunching and fluorescence correlation spectroscopy was used to confirm that the two fluorophores in a Venus_A206 homodimer behave as a single-photon emitter. We conclude that excitonic coupling between Venus_A206 fluorophores is possible at physiological temperatures.     

Inhibition of anion transport across the red cell membrane by dinitrophenylation of a specific lysine residue at the H2DIDS binding site of the band 3 protein

The mechanism of free energy coupling in active transport is discussed with special reference to the sarcoplasmic reticulum Ca²⁺-ATPase. In the current working schemes for cation transport ATPases, free energy transduction is nearly always based on enzyme conformational changes. The principal objective of the present article is to examine whether recent experimental results on Ca²⁺-ATPase may in fact be better explained by assuming the existence of a direct chemiosmotic process. In the scheme proposed, free energy transduction between ATP and calcium is based on a transfer of solvation water between the acylphosphate bond and the bound calcium ions.     

Kinetic Mechanisms of Biological Regulation in Photosynthetic Organisms

Principles of regulation on different levels of photosynthetic apparatus are discussed. Mathematical models of isolated photosynthetic reaction centers and general system of energy transduction in chloroplast are developed. A general approach to model these complex metabolic systems is suggested. Regulatory mechanisms in plant cell are correlated with the different patterns of fluorescence induction curve at different internal physiological states of the cells and external (environmental) conditions. Light regulation inside photosynthetic reaction centers, diffusion processes in thylakoid membrane, generation of transmembrane electrochemical potential, coupling with processes of CO₂ fixation in Calvin Cycle are considered as stages of control of energy transformation in chloroplasts in their connection with kinetic patterns of fluorescence induction curves and other spectrophotometric data.     

Single molecule processes on the stepwise movement of ATP-driven molecular motors

Movement is a fundamental characteristic of all living things. This biogenic function that is attributed to the molecular motors such as kinesin, dynein and myosin. Molecular motors generate forces by using chemical energy derived from the hydrolysis reaction of ATP molecules. Despite a large number of studies on this topic, the chemomechanical energy transduction mechanism is still unsolved. In this study, we have investigated the chemomechanical coupling of the ATPase cycle to the mechanical events of the molecular motor kinesin using single molecule detection (SMD) techniques. The SMD techniques allowed to detection of the movement of single kinesin molecules along a microtubule and showed that kinesin steps mainly in the forward direction, but occasionally in the backward. The stepping direction is determined by a certain load-dependent process, on which the stochastic behavior is well characterized by Feynman's thermal ratchet model. The driving force of the stepwise movement is essentially Brownian motion, but it is biased in the forward direction by using the free energy released from the hydrolysis of ATP.     

The major androgen-dependent protease in dog prostate belongs to the kallikrein family: confirmation by partial amino acid sequencing

Free energy transduction in active transport resembles other protein-catalyzed processes, occurring by an ordered sequence of discrete bond-breaking and bond-making steps. The bonds that affect the transported ion directly are chelation bonds, which alter the chemical potential of the bound ion, but not its chemical identity. Available data for the sarcoplasmic reticulum Ca pump (admittedly incomplete) suggest that more than 50% of the free energy transfer may be localized to a single step of the reaction cycle.