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Kinetic models of coupling between H+ and Na(+)-translocation and ATP synthesis/hydrolysis by F0F1-ATPases: can a cell utilize both delta mu H+ and delta mu Na+ for ATP synthesis under in vivo conditions using the same enzyme?

Kinetic models of the F0F1-ATPase able to transport H+ or/and Na+ ions are proposed. It is assumed that (i) H+ and Na+ compete for the same binding sites, (ii) ion translocation through F0 is coupled to the rate-limiting step of the F1-catalyzed reaction. The main characteristics of the dependences of ATP synthesis and hydrolysis rates on delta psi, delta pH, and delta pNa are predicted for various versions of the coupling model. The mechanism of the switchover from delta mu H(+)-dependent synthesis to the delta mu Na(+)-dependent one is demonstrated. It is shown that even with a drastic drop in delta mu H+, ATP hydrolysis by the proton mode of catalysis can be effectively inhibited by delta psi and delta pNa. The results obtained strongly support the possibility that the same F0F1-ATPase in bacterial cells can utilize both delta muH+ and delta muNa+ for ATP synthesis under in vivo conditions.

Adenosine Triphosphate↗

Oscillatory isozymes as the simplest model for coupled biochemical oscillators.

We analyze a simple model for two autocatalytic reactions catalyzed by two distinct isozymes transforming, with different kinetic properties, a given substrate into the same product. This two-variable system can be viewed as the simplest model of chemically coupled biochemical oscillators. Phase-plane analysis indicates how the kinetic differences between the two enzymes give rise to complex oscillatory phenomena such as the coexistence of a stable steady state and a stable limit cycle, or the co-existence of two simultaneously stable oscillatory regimes (birhythmicity). The model allows one to verify a previously proposed conjecture for the origin of birhythmicity. In other conditions, the system admits multiple oscillatory domains as a function of a control parameter whose variation gives rise to markedly different types of oscillations. The latter behavior provides an explanation for the occurrence of multiple modes of oscillations in thalamic neurons.

Algorithms↗

A cable model for coupled neurons with somatic gap junctions.

A cable model is presented for a pair of electrotonically coupled neurons to investigate the spatial effects of soma-somatic gap junctions. The model extends that of Poznanski et al.(1995) in which each neuron is represented by a tapered equivalent cable attached to an isopotential soma with the two somas being electrically coupled. The model is posed generally, so that both active and passive properties can be considered. In the active case a system of nonlinear integral equations is derived for the voltage, whilst in the passive case these have an exact solution that also holds for inputs modelled as synaptic reversal potentials. Analytical and numerical methods are used to examine the sensitivity of the soma potentials (in particular) to the coupling resistance.

Algorithms↗

Conductance fluctuations from the inactivation process of sodium channels in myelinated nerve fibres.

1. Na currents and fluctuations of Na currents were studied under voltage clamp in the same myelinated nerve fibres of Rana esculenta at 13 degrees C. The results were used to test several kinetic models for the gating process of Na channels.2. Long voltage pulses, depolarizing the membrane by 16-48 mV from a hyperpolarizing holding level of - 28 mV, were applied in 4 sec intervals. The d.c. and a.c. components of the membrane current were recorded during the last 328 msec of the 473 msec pulses. For each depolarization, ninety-six trials were made with the node in Ringer solution and, again, after adding 300 nm-tetrodotoxin (TTX) in that solution.3. The TTX-sensitive d.c. component declined during the 328 msec records by 14-51% of its time average. The a.c. component was corrected for this trend by subtracting the first from the second of each pair of subsequent records. The TTX-sensitive part of its variance declined, on the average, in parallel to the current, as if the open probability rather than the conductance of the individual Na channels was reduced by a slow process.4. Single-channel conductances, gamma, were calculated on the assumption that Na channels have only one non-zero conductance and were corrected for the limited band width (5 kHz) of the a.c. records. Values of gamma increased slightly (< 30% from 16 to 40 mV), and averaged 8.85 +/- 0.7 pS (s.e. of mean, seventeen measurements on ten fibres). This small degree of change in gamma suggests that deviations from the all-or-none gating are very small.5. Power spectral densities of the fluctuations between 3 Hz and 5 kHz were calculated from the trend-free a.c. records and corrected for the TTX-insensitive noise component. Control calculations showed that the only effect of the nonstationarity in the Na current was to enhance the low-frequency points of such spectra by less than 10%. The spectra revealed at least two Lorentzian components with cut-off frequencies in the range expected from the activation and inactivation kinetics. The low-frequency component became dominant as depolarization was increased.6. Na currents recorded during brief (< 40 msec) depolarizations were analysed in terms of various all-or-none gating models, in which inactivation either was independent of activation (Hodgkin-Huxley (HH) model) or could occur only from the partly or fully activated states (coupled models). The transient Na currents were reproduced by all models.7. With the parameters from such fits, the fluctuation spectra expected for each model were calculated. The predictions differed in the fraction, r(h), of the variance contributed by the slow (inactivation) fluctuations; r(h) was larger in the coupled models than in the HH model.8. The experimental spectra were divided into two spectral components to yield empirical values for r(h). We used as templates the spectral curves derived for the fast and for the slow fluctuations of the HH model. The empirical r(h) values were one (48 mV) to four (16 mV) times larger than those expected for the HH model. They were also larger than the theoretical r(h) of the coupled models at the small depolarizations, but became equal or smaller than those at the largest depolarization. Direct comparison of the measured and theoretical spectra revealed the same discrepancies.9. We conclude that all of the simple gating models considered in this paper are inconsistent with the fluctuation measurements, the coupled models giving slightly smaller deviations than the model with independent activation and inactivation.

Animals↗

Sound propagation in concentrated emulsions: comparison of coupled phase model and core-shell model.

The predictions of two models of sound propagation in concentrated emulsions are compared with experimental measurements of ultrasonic velocity and attenuation in emulsions with volume fractions up to 0.7. The core-shell model includes irreversible heat transfer, viscoinertial forces, and multiple scattering [McClements et al., J. Acoust. Soc. Am. 105, 915-918 (1999)]. This model accounts for the effect of thermal interactions between neighboring particles by introducing an effective medium, and is valid for all volume fractions. The coupled phase model includes irreversible heat transfer and viscoinertial forces, and also is valid for all volume fractions, since it is derived from volume-averaged balance equations [J. M. Evans and K. Attenborough, J. Acoust. Soc. Am. 102, 278-282 (1997)]. This model has a significantly simpler formulation than the core-shell model and does not require the assumption of an effective medium. The coupled phase model is shown to be a good approximation to the core-shell model when the acoustic radius is small. Despite the fact that it does not include thermal interactions, the coupled phase model is shown to give at least as good agreement as the core-shell model with the experimental data, for all volume fractions, as long as the acoustic radius is less than 0.01.

Emulsions↗

The coupled dipole model: an integrated model for multiple MEG/EEG data sets.

Often MEG/EEG is measured in a few slightly different conditions to investigate the functionality of the human brain. This kind of data sets show similarities, though are different for each condition. When solving the inverse problem (IP), performing the source localization, one encounters the problem that this IP is ill-posed: constraints are necessary to solve and stabilize the solution to the IP. Moreover, a substantial amount of data is needed to avoid a signal to noise ratio (SNR) that is too poor for source localizations. In the case of similar conditions, this common information can be exploited by analyzing the data sets simultaneously. The here proposed coupled dipole model (CDM) provides an integrated method in which these similarities between conditions are used to solve and stabilize the inverse problem. The coupled dipole model is applicable when data sets contain common sources or common source time functions. The coupled dipole model uses a set of common sources and a set of common source time functions (STFs) to model all conditions in one single model. The data of each condition are mathematically described as a linear combination of these common spatial and common temporal components. This linear combination is specified in a coupling matrix for each data set. The coupled dipole model was applied in two simulation studies and in one experimental study. The simulations show that the errors in the estimated spatial and temporal parameters decrease compared to the standard separate analyses. A decrease in position error of a factor of 10 was shown for the localization of two nearby sources. In the experimental application, the coupled dipole model was shown to be necessary to obtain a plausible solution in at least 3 of 15 conditions investigated. Moreover, using the CDM, a direct comparison between parameters in different conditions is possible, whereas in separate models, the scaling of the amplitude parameters varies in general from data set to data set.

Algorithms↗

Coupled map models for chaos in extended systems.

Coupled maps with conserved quantities are introduced as models for chaos in extended systems. The long-wavelength limit of a simple one-dimensional example is investigated in detail. A Langevin equation for this system is derived, and the applicability of the fluctuation-dissipation theorem is discussed. Several numerical experiments to investigate possible thermodynamic properties are described.

Journal Article↗

A coupled-oscillator model of ovarian-cycle synchrony among female rats.

The ovarian cycles of female rats become synchronized when they live together, as do the cycles of many other mammals. Ovarian cycles also become synchronized when rats live apart if they share a common air supply, indicating that ovarian-cycle synchrony is mediated by pheromones. We developed a coupled-oscillator model of ovarian-cycle synchrony to test several hypotheses about its pheromonal and neuroendocrine mechanisms and to guide our experimental research. The model spans three levels of organization: the group, the rat, and the neuroendocrine components of the ovarian system. The ovarian system (not the ovaries themselves) are modeled as an oscillating system. Coupling among ovarian systems is mediated by the exchange of two pheromones, one that delays the phase of the ovarian system and one that advances it. Computer simulation experiments showed that this coupled-oscillator model can explain the levels of ovarian-cycle synchrony observed in groups of female rats while, at the same time, matching an empirical distribution of ovarian-cycle lengths. By successfully matching computer simulation data with empirical data, we were able to infer theoretical predictions in a number of areas: (1) effect of initial conditions on the probability that a group will change to different synchrony level and phase relationships, i.e. the transition probability between all synchrony levels and phase relationships; (2) effects of individual differences in pheromone sensitivity on ovarian-cycle synchrony; (3) the timing of pheromone sensitivity during the ovarian cycle; and (4) the existence of partial luteinizing hormone surges, which may cause the "spontaneous" prolonged ovarian cycles associated with ovarian-cycle synchrony. The paper concludes by discussing the integrative role of this model for experimental research. In particular, we focus on the role of this model in interpreting theoretical aspects of ovarian-cycle synchrony as well as for guiding future experimental research into its mechanisms and functions.

Animals↗

Synchronized action of synaptically coupled chaotic model neurons.

Experimental observations of the intracellular recorded electrical activity in individual neurons show that the temporal behavior is often chaotic. We discuss both our own observations on a cell from the stomatogastric central pattern generator of lobster and earlier observations in other cells. In this paper we work with models with chaotic neurons, building on models by Hindmarsh and Rose for bursting, spiking activity in neurons. The key feature of these simplified models of neurons is the presence of coupled slow and fast subsystems. We analyze the model neurons using the same tools employed in the analysis of our experimental data. We couple two model neurons both electrotonically and electrochemically in inhibitory and excitatory fashions. In each of these cases, we demonstrate that the model neurons can synchronize in phase and out of phase depending on the strength of the coupling. For normal synaptic coupling, we have a time delay between the action of one neuron and the response of the other. We also analyze how the synchronization depends on this delay. A rich spectrum of synchronized behaviors is possible for electrically coupled neurons and for inhibitory coupling between neurons. In synchronous neurons one typically sees chaotic motion of the coupled neurons. Excitatory coupling produces essentially periodic voltage trajectories, which are also synchronized. We display and discuss these synchronized behaviors using two "distance" measures of the synchronization.

Action Potentials↗

Models of coupled salt and water transport across leaky epithelia.

A general formulation is presented for the verification of isotonic transport and for the assignment of a degree of osmotic coupling in any epithelial model. In particular, it is shown that the concentration of the transported fluid in the presence of exactly equal bathing media is, in general, not a sufficient calculation by which to decide the issue of isotonicity of transport. Within this framework, two epithelial models are considered: (1) A nonelectrolyte compartment model of the lateral intercellular space is presented along with its linearization about the condition of zero flux. This latter approximate model is shown to be useful in the estimation of deviation from isotonicity, intraepithelial solute polarization effects, and the capacity to transport water against a gradient. In the case of uphill water transport, some limitations of a model of fixed geometry are indicated and the advantage of modeling a compliant interspace is suggested. (2) A comprehensive model of cell and channel is described which includes the major electrolytes and the possible presence of intraepithelial gradients. The general approach to verification of isotonicity is illustrated for this numerical model. In addition, the insights about parameter dependence gained from the linear compartment model are shown to be applicable to understanding this large simulation.

Animals↗

Symmetry breaking, bifurcations, quasiperiodicity, and chaos due to electric fields in a coupled cell model.

A model for the asymmetric coupling of two oscillatory cells is considered. The coupling between the cells is both through diffusional exchange (symmetric) and through the electromigration of ionic reactant species from one cell to the other (asymmetric) in applied electric fields. The kinetics in each cell are the same and based on the Gray-Scott scheme. Without the electric field, only simple, stable dynamics are seen. The effect of the asymmetry (applying electric fields) is to create a wide variety of stable dynamics, multistability, multiperiodic oscillations, quasiperiodicity and chaos being observed, this complexity in response being more prevalent at weaker coupling rates and at weaker field strengths. The results are obtained using a standard dynamical systems continuation program, though asymptotic results are obtained for strong coupling rates and strong electric fields. These are seen to agree well with the numerically determined values in the appropriate parameter regimes. (c) 2002 American Institute of Physics.

Journal Article↗

A continuous-wave ultrasound system for displacement amplitude and phase measurement.

A noninvasive, continuous-wave ultrasonic technique was developed to measure the displacement amplitude and phase of mechanical structures. The measurement system was based on a method developed by Rogers and Hastings ["Noninvasive vibration measurement system and method for measuring amplitude of vibration of tissue in an object being investigated," U.S. Patent No. 4,819,643 (1989)] and expanded to include phase measurement. A low-frequency sound source was used to generate harmonic vibrations in a target of interest. The target was simultaneously insonified by a low-power, continuous-wave ultrasonic source. Reflected ultrasound was phase modulated by the target motion and detected with a separate ultrasonic transducer. The target displacement amplitude was obtained directly from the received ultrasound frequency spectrum by comparing the carrier and sideband amplitudes. Phase information was obtained by demodulating the received signal using a double-balanced mixer and low-pass filter. A theoretical model for the ultrasonic receiver field is also presented. This model coupled existing models for focused piston radiators and for pulse-echo ultrasonic fields. Experimental measurements of the resulting receiver fields compared favorably with theoretical predictions.

Air Sacs↗

BTEVAL: a server for evaluation of beta-turn prediction methods.

This paper describes a web server BTEVAL, developed for assessing the performance of newly developed beta-turn prediction method and it's ranking with respect to other existing beta-turn prediction methods. Evaluation of a method can be carried out on a single protein or a number of proteins. It consists of clean data set of 426 non-homologous proteins with seven subsets of these proteins. Users can evaluate their method on any subset or a complete set of data. The method is assessed at amino acid level and performance is evaluated in terms of Qtotal, Qpredicted, Qobserved and MCC measures. The server also compares the performance of the method with other existing beta-turn prediction methods such as Chou-Fasman algorithm, Thornton's algorithm, GORBTURN, 1-4 and 2-3 Correlation model, Sequence coupled model and BTPRED. The server is accessible from http://imtech.res.in/raghava/bteval/

Algorithms↗

Models for coupling of salt and water transport; Proximal tubular reabsorption in Necturus kidney.

Models for coupling of salt and water transport are developed with two important assumptions appropriate for leaky epithelia. (a) The tight junction is permeable to both sale and water. (b) Active Na transport into the lateral speces is assumed to occur uniformly along the length of the channel. The proposed models deal specifically with the intraepithelial mechanism of proximal tubular resbsorption in the Necturus kidney although they have implications for epithelial transport in the gallbladder and small intestine as well. The first model (continuous version) is similar to the standing gradient model devised by Diamond and Bossert but used different boundary conditions. In contrast to Diamond and Bossert's model, the predicted concentration profiles are relatively flat with no sizable gradients along the interspace. The second model (compartment version) expands Curran's model of epithelial salt and water transport by including additional compartments and considering both electrical and chemical driving forces for individual Na and Cl ions as well as hydraulic and osmotic driving forces for water. In both models, ion and water fluxes are investigated as a function of the transport parameters. The behavior of the models is consistent with previously suggested mechanisms for the control of net transport, particularly during saline diuresis. Under all conditions the predicted ratio of net solute to solvent flux, or emergent concentration, deviates from exact isotonicity (except when the basement membrane has an appreciable salt reflection coefficient). However, the degree of hypertonicity may be small enough to be experimentally indistinguishable from isotonic transport.

Animals↗

Role of the Pauli principle in collective-model coupled-channel calculations.

A multichannel algebraic scattering theory, to find solutions of coupled-channel scattering problems with interactions determined by collective models, has been structured to ensure that the Pauli principle is not violated. By tracking the results in the zero coupling limit, a correct interpretation of the subthreshold and resonant spectra of the compound system can be made. As an example, the neutron-12C system is studied defining properties of 13C to 10 MeV excitation. Accounting for the Pauli principle in collective coupled-channels models is crucial to the outcome.

Journal Article↗

A model for coupling of H(+) and substrate fluxes based on "time-sharing" of a common binding site.

Both prokaryotic and eukaryotic cells contain an array of membrane transport systems maintaining the cellular homeostasis. Some of them (primary pumps) derive energy from redox reactions, ATP hydrolysis, or light absorption, whereas others (ion-coupled transporters) utilize ion electrochemical gradients for active transport. Remarkable progress has been made in understanding the molecular mechanism of coupling in some of these systems. In many cases carboxylic residues are essential for either binding or coupling. Here we suggest a model for the molecular mechanism of coupling in EmrE, an Escherichia coli 12-kDa multidrug transporter. EmrE confers resistance to a variety of toxic cations by removing them from the cell interior in exchange for two protons. EmrE has only one membrane-embedded charged residue, Glu-14, which is conserved in more than 50 homologous proteins. We have used mutagenesis and chemical modification to show that Glu-14 is part of the substrate-binding site. Its role in proton binding and translocation was shown by a study of the effect of pH on ligand binding, uptake, efflux, and exchange reactions. The studies suggest that Glu-14 is an essential part of a binding site, which is common to substrates and protons. The occupancy of this site by H(+) and substrate is mutually exclusive and provides the basis of the simplest coupling for two fluxes.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Mechanistic model of G-protein signal transduction. Determinants of efficacy and effect of precoupled receptors.

Tissue-specific characteristics (e.g. receptor number) and agonist-specific characteristics (e.g. agonist binding kinetics) play roles in determining cellular response. The roles that these characteristics play are quantified by models of signal transduction. We examined signal transduction through G-protein-linked receptors, using a model based on the collision coupling model but including interconverting receptor states and the precoupling of receptors with G-proteins prior to the addition of agonist. Reaction and diffusion of molecules within the plasma membrane were simulated using Monte Carlo techniques. The G-protein activation produced by our model was compared with that produced by the collision coupling model. We quantitatively examined how the parameters characteristic of the tissue and agonist determine the midpoint and maximal response of the dose-response curve. Activation through agonist binding to precoupled receptors can produce significantly higher activation rates than does collision coupling. Tissue and agonist characteristics have qualitatively similar effects but quantitatively distinct effects on activation for the two models. Using standard experimental techniques, it may be possible to exploit these differences to determine the mechanism of G-protein activation in a specific cell system. A quantitative comparison of model predictions with published data on the beta-adrenergic receptor system (Stickle D and Barber R, Mole Pharmacol 40: 276-288, 1991) also is presented.

Animals↗

Interfacial Properties of Two-Carbon Fiber Reinforced Polycarbonate Composites Using Two-Synthesized Graft Copolymers as Coupling Agents.

Two model coupling agents, water-dispersible (WDGP) and tetrahydrofuran (THF)-soluble graft copolymers (TSGP), were synthesized for carbon fiber/polycarbonate (PC) composites. WDGP contains a long polyacrylamide (PAAm) chain grafted on a PC backbone, whereas TSGP contains a short grafted PAAm chain. Measurements of the interfacial shear strength (IFSS) and other interfacial properties were evaluated using a fragmentation test for two-fiber composites (TFC) to provide the same loading state. Optimal conditions for the treatment was established as a function of treatment time, temperature, initial concentration, and melting procedure. The amount adsorbed on the carbon fiber was higher for TSGP then for WDGP; the maximum improvements in IFSS for WDGP and TSGP were 54% and 74%, respectively. Mechanisms of energy adsorption for WDGP and intermolecular interaction for TSGP can be considered to contribute differently to IFSS improvement. The improvement in IFSS for both coupling agents may be due to chemical and hydrogen bonding in the interface between functional groups in the carbon fiber and PAAm in the coupling agents and to interdiffusion in the interface between PC in coupling agents and matrix PC. Copyright 2000 Academic Press.

Journal Article↗