Model reactions for coupling oxidation to phosphorylation.
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Adenosine Diphosphate↗
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Results for “Coupled model”
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Modelling of the coupling between brain electrical activity and metabolism.
In order to make an attempt at grouping the various aspects of brain functional imaging (fMRI, MRS, EEG-MEG, ...) within a coherent frame, we implemented a model consisting of a system of differential equations, that includes: (1) sodium membrane transport, (2) Na/K ATPase, (3) neuronal energy metabolism (i.e. glycolysis, buffering effect of phosphocreatine, and mitochondrial respiration), (4) blood-brain barrier exchanges and (5) brain hemodynamics, all the processes which are involved in the activation of brain areas. We assumed that the correlation between brain activation and metabolism could be due to either changes in the concentrations of ATP and ADP following activation of Na/K ATPase that result from the changes in ion concentrations, or the involvement, in different phases of metabolism, of a second messenger such as calcium. In this article, we show how this type of model enables interpretation of MRS and fMRI published data that were obtained during prolonged stimulations.
Adenosine Diphosphate↗
Simulation of cardiac memory in a computer model using capacitive coupling.
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Action Potentials↗
Calculations of NMR dipolar coupling strengths in model peptides.
Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N-H, C alpha-H alpha, C'-N, and C alpha-C' bonds, as well as for the two-bond C'-H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5-3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.
Acetamides↗
Alcohol use and intimate partner violence as predictors of separation among U.S. couples: a longitudinal model.
OBJECTIVE: The purpose of this study was to investigate the relationship between partner violence (male-to-female and female-to-male) and heavy drinking (consuming five or more drinks per occasion) and the effect of this relationship on marital separation. METHOD: Married and cohabiting couples were selected through multistage random probability sampling from U.S. households. In 1995, 1,635 couples were interviewed; 1,392 of these couples were re-interviewed in 2000. The final analysis included couples who were still married or living with the same partner (intact n = 1,136) from the baseline, and couples who had broken up (nonintact n = 191) sometime during the 5-year follow-up period. RESULTS: The findings indicate that couples who reported female-perpetrated violence, female alcohol-related problems and male heavy-drinking episodes (one to three times a month) were 2.5-3 times more at risk for separation. On the other hand, female heavy drinking (one to three times a month) is less likely to predict separation. Cohabiting couples are also more at risk for separation than married couples. Couples with longer relationships are less at risk for separation. CONCLUSIONS: Marital counseling, therapy or intervention programs must address issues pertaining to partner violence and alcohol use among couples while concurrently providing information about healthy relationships and helping couples develop skills to attain them. The importance of preventing partner violence is increasingly recognized in the field of public health.
Adolescent↗
The electromechanochemical model for energy coupling in mitochondria.
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Adenosine Triphosphate↗
Stereochemical identification of (R)- and (S)-ibuprofen using residual dipolar couplings, NMR, and modeling.
In this work, we describe an NMR-based method that utilizes an orientation media composed of the chiral polypeptide liquid crystal poly-gamma-benzyl-L-glutamate (PBLG) dissolved in CDCl(3), to measure the (1)H-(1)H, (1)H-(13)C and (13)C-(13)C residual dipolar couplings (RDCs) of (R) and (S)-ibuprofen. Calculated RDCs, obtained from the lowest energy conformers, are then compared with the experimentally measured RDCs to predict the stereochemistry of each enantiomer. Excellent agreement between calculated and experimental RDCs was found when the lowest energy structure of each enantiomer, obtained in a simulated PBLG/CDCl(3) environment, was used to back-calculate the RDCs. This method is generally useful for small molecular weight molecules that possess either one or two chiral centers, are soluble in low viscosity organic solvents, and will not crystallize (Clegg, Crystal Structure Analysis. Principles and Practice. New York: Oxford University Press; 2002) or cannot be derivatized with a Mosher's reagent (Dale and Mosher, J Am Chem Soc 1973;95:512-519).
Chemistry, Organic↗
A model for conformational coupling of membrane potential and proton translocation to ATP synthesis and to active transport.
Acceptance of a membrane potential and/or a proton gradient as a possible means of transmitting energy from oxidations to ATP synthesis rests in part on a satisfactory hypothesis for how the potential or proton gradient could drive ATP synthesis. Recognition that energy input may drive ATP synthesis by change in binding of reactants at the catalytic site has led to the suggestions presented in this paper. These are that in oxidative phosphorylation and photophosphorylation, the requisite conformational changes may be coupled to exposure of charged groups to different sides of the membrane. The cycle of charged group exposure or movement may be driven by the membrane potential or, through protonation and deprotonation, may be coupled to proton translocation across the membrane. Effects of proton gradient and membrane potential may be additive. Similar conformational coupling suggestions may explain proton translocation coupled to ATP cleavage and active transport of metabolites coupled to membrane potential, proton gradients of ATP cleavage.
Adenosine Triphosphate↗
Minireview: Insights into G protein-coupled receptor function using molecular models.
G protein-coupled receptors (GPCRs) represent the largest family of signal-transducing molecules known. They convey signals for light and many extracellular regulatory molecules. GPCRs have been found to be dysfunctional/dysregulated in a growing number of human diseases and have been estimated to be the targets of more than 30% of the drugs used in clinical medicine today. Thus, understanding how GPCRs function at the molecular level is an important goal of biological research. In order to understand function at this level, it is necessary to delineate the 3D structure of these receptors. Recently, the 3D structure of rhodopsin has been resolved, but in the absence of experimentally determined 3D structures of other GPCRs, a powerful approach is to construct a theoretical model for the receptor and refine it based on experimental results. Computer-generated models for many GPCRs have been constructed. In this article, we will review these studies. We will place the greatest emphasis on an iterative, bi-directional approach in which models are used to generate hypotheses that are tested by experimentation and the experimental findings are, in turn, used to refine the model. The success of this approach is due to the synergistic interaction between theory and experiment.
Amino Acid Sequence↗
A neural network model as a globally coupled map and applications based on chaos.
First, a neural network model as the globally coupled map (GCM) is proposed. The model is obtained by modification of a Hopfield network model that has a negative self-feedback connection. Second, information processed by this model is interpreted in terms of the variety of the maps acting on the network elements, and a new, dynamic information processing model is described. The search for information using vague keywords, and solution of the traveling salesman problem (TSP) are introduced as applications.
Journal Article↗
A model for the coupling of alpha-helix and tertiary contact formation.
Peptides corresponding to excised alpha-helical segments of natural proteins can spontaneously form helices in solution. However, peptide helices are usually substantially less stable in solution than in the structural context of a folded protein, because of the additional interactions possible between helices in a protein. Such interactions can be thought of as coupling helix formation and tertiary contact formation. The relative energetic contributions of the two processes to the total energy of the folded state of a protein is a matter of current debate. To investigate this balance, an extended helix-coil model (XHC) that incorporates both effects has been constructed. The model treats helix formation with the Lifson-Roig formalism, which describes helix initiation and propagation through cooperative local interactions. The model postulates an additional parameter representing participation of a site in a tertiary contact. In the model, greater helix stability can be achieved through combinations of these short-range and long-range interactions. For instance, stronger tertiary contacts can compensate for helices with little intrinsic stability. By varying the strength of the nonlocal interactions, the model can exhibit behavior consistent with a variety of qualitative models describing the relative importance of secondary and tertiary structure. Moreover, the model is explicit in that it can be used to fit experimental data to individual peptide sequences, providing a means to quantify the two contributions on a common energetic basis.
Algorithms↗
A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca2+ channels.
Although there is consensus that localized Ca(2+) elevations known as Ca(2+) puffs and sparks arise from the cooperative activity of intracellular Ca(2+) channels, the precise relationship between single-channel kinetics and the collective phenomena of stochastic Ca(2+) excitability is not well understood. Here we present a formalism by which mathematical models for Ca(2+)-regulated Ca(2+) release sites are derived from stochastic models of single-channel gating that include Ca(2+) activation, Ca(2+) inactivation, or both. Such models are stochastic automata networks (SANs) that involve a large number of functional transitions, that is, the transition probabilities of the infinitesimal generator matrix of one of the automata (i.e., an individual channel) may depend on the local [Ca(2+)] and thus the state of the other channels. Simulation and analysis of the SAN descriptors representing homogeneous clusters of intracellular Ca(2+) channels show that (1) release site density can modify both the steady-state open probability and stochastic excitability of Ca(2+) release sites, (2) Ca(2+) inactivation is not a requirement for Ca(2+) puffs or sparks, and (3) a single-channel model with a bell-shaped open probability curve does not lead to release site activity that is a biphasic function of release site density. These findings are obtained using iterative, memory-efficient methods (novel in this biophysical context and distinct from Monte Carlo simulation) that leverage the highly structured SAN descriptor to unambiguously calculate the steady-state probability of each release site configuration and puff statistics such as puff duration and inter-puff interval. The validity of a mean field approximation that neglects the spatial organization of Ca(2+) release sites is also discussed.
Algorithms↗
Avoided crossings in three coupled oscillators as a model system of acoustic bubbles.
The resonance frequencies and oscillation phases of three acoustically coupled bubbles are examined to show that avoided crossings can appear in a multibubble system. Via a simple coupled oscillator model, we show that if at least three bubbles exist, it is possible for their resonance frequencies as functions of the separation distances between the bubbles to experience an avoided crossing. Furthermore, by focusing our attention on the oscillation phases and based on analysis of the transition frequencies [M. Ida, Phys. Lett. A 297, 210 (2002); J. Phys. Soc. Jpn. 71, 1214 (2002)] of the coupled bubbles, we show that a distinct state exchange takes place between the bubbles at a point in the avoided crossing region, where a resonance frequency of the triple-bubble system crosses with a transition frequency not corresponding to the resonance frequencies.
Acoustics↗
Modeling and docking the endothelin G-protein-coupled receptor.
A model of the endothelin G-protein-coupled receptor (ET(A)) has been constructed using a segmented approach. The model was produced using a bovine rhodopsin model as a template for the seven transmembrane alpha-helices. The three cytoplasmic loop regions and the C-terminal region were modeled on NMR structures of corresponding segments from bovine rhodopsin. The three extracellular loops were modeled on homologous loop regions in other proteins of known structure. The N-terminal region was modeled as a three-helix domain based on its homology with a hydrolase protein. To test the model, the FTDOCK algorithm was used to predict the ligand-binding site for the crystal structure of human endothelin. The site of docking is consistent with mutational and biochemical data. The principal sites of interaction in the endothelin ligand all lie on one face of a helix that has been implicated by structure-activity relationship studies as being essential for binding. As further support for the model, attempts to dock bigET, an inactive precursor to endothelin that does not bind to the receptor, found no sites for tight binding. The model of the receptor-ligand complex produced forms a basis for rational drug design of agonists and antagonists for this G-protein-coupled receptor.
Algorithms↗
Paired moving charge model of energy coupling. III. Intrinsic ionophores in energy coupling systems.
The experimental basis for the postulated role of intrinsic ionophores in mitochondrial ion transport and energy coupling is summarized. Intrinsic ionophores appear to be linked to, or contained within, specific ionophoroproteins localized in the inner membrane, and the isolation of these ionophores requires their release from the ionophoroproteins. At least ten different species of ionophores have been isolated from the mitochondrion, five of which have been wholly or in part chemically identified. Intrinsic ionophores have been implicated in the activation of inorganic phosphate in ATP synthesis and hydrolysis, and in the contol of the coupling modes. The presence of ionophores in soluble proteins such as troponin and in ATP-energized kinases has been demonstrated.
Biological Transport, Active↗
A model of induced coupled movements in the human body: a case study.
We present a case study of involuntary motion in one part of the body induced by a voluntary motion in another part. The case investigated was that of a steady-state motion of the fingers at various frequencies, which induced a similar kind of motion in the legs. These phenomena were observed in a subject practicing sphincter gymnastics, a physical therapy method in which repetitive motion of different muscles is exercised, and is known to induce motions in other muscles of the body. We show that a linear model, for which we give an experimental transfer function and demonstrate its validity, can describe the generation of the induced periodic motions by the voluntary motions. We compare the results of the transfer function with those of Von Holst's statistical analysis.
Biomechanical Phenomena↗
Flow model for coupled-column gas chromatography systems.
One of the challenges in performing comprehensive two-dimensional gas chromatographic separations is being able to predict the average linear velocities of the carrier gas in the two columns, especially when they have different diameters. The problem is compounded for loop-type modulators, where two thermal trapping zones that switch from hot to cold and back simultaneously are separated by a delay loop. If the linear velocity in the loop is not tuned to the length of the loop and the modulation period, the dual-stage modulation may cease to work properly. A model has been developed that calculates the flow rates in the columns and predicts appropriate delay loop dimensions for a given set-up. Additionally, the model determines the pressure ramp that needs to be used in order to maintain constant average linear velocity within the modulator loop throughout the course of the separation.
Chromatography, Gas↗
Coupled atmosphere-ocean models of Titan's past.
We have developed a coupled atmosphere and ocean model of Titan's surface. The atmospheric model is a 1-D spectrally-resolved radiative-convective model. The ocean thermodynamics are based upon solution theory. The ocean, initially composed of CH4, becomes progressively enriched in ethane over time. The partial pressures of N2 and CH4 in the atmosphere are dependent on the ocean temperature and composition. We find that the resulting system is stable against a runaway greenhouse. Accounting for the decreased solar luminosity, we find that Titan's surface temperature was about 20 K colder 4 Gyr ago. Without an ocean, but only small CH4 lakes, the temperature change is 12 K. In both cases we find that the surface of Titan may have been ice covered about 3 Gyr ago. In the lakes case condensation of N2 provides the ice, whereas in the ocean case the ocean freezes. The dominant factor influencing the evolution of Titan's surface temperature is the change in the solar constant--amplified, if an ocean is present, by the temperature dependence of the solubility of N2. Accretional heating can dramatically alter the surface temperature; a surface thermal flux of 500 erg cm-2 sec-1, representative of small levels of accretional heating, results in a approximately 20 K change in surface temperatures.
Astronomical Phenomena↗