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At least 721 records · Page 40Linked to original sources
PubMed2006

Theoretical model of interactions between ligand-binding sites in a dimeric protein and its application for the analysis of thiamine diphosphate binding to yeast transketolase.

The binding of thiamin diphosphate (ThDP) to yeast dimeric apotransketolase (apoTK) is accompanied by the appearance of a band in the absorption spectrum with maximum at 320 nm. The saturation function has been analyzed using a scheme that involves binding of ThDP to each subunit followed by the conformational transition of this subunit. It is assumed that the binding of ThDP to one subunit may affect the conformational transition of the other subunit. Rigorous mathematical expressions describing the dependence of the optical absorption on the total concentration of ThDP are first developed. Equilibrium constants and corresponding rate constants for the binding of ThDP to apoTK have been estimated. The negative cooperativity in the ThDP binding has been characterized by the function reflecting the dependence of the conformational change on the saturation of apoTK by ThDP.

Binding Sites↗
PubMed2004

Synergistic effects of hyperoxic gas breathing and reduced oxygen consumption on tumor oxygenation: a theoretical model.

PURPOSE: To simulate effects of reduced oxygen consumption combined with hyperoxic gas breathing on tumor oxygenation, and to test for synergistic effects. METHODS AND MATERIALS: Diffusive oxygen transport was simulated for a small region of tumor containing a three-dimensional network of microvessels whose geometry was derived from in vivo observations. Changes in tissue partial pressure of oxygen (PO(2)) and hypoxic fraction (PO(2) < 5 mm Hg) resulting from a 30% reduction in oxygen consumption rate or breathing 100% oxygen were estimated. The synergistic effect was defined as the change in PO(2) with the two treatments combined, minus the sum of the changes with the separate treatments. RESULTS: Predicted hypoxic fractions were 37% in the control state, 11% with reduced consumption, 23% with oxygen breathing alone, and 0% with the combined treatment. The synergistic effect was about 4 mm Hg at tissue points with very low initial PO(2) levels and decreased as initial PO(2) increased. CONCLUSIONS: Reduction of oxygen consumption via the Crabtree effect, by administration of glucose, has been proposed as a means to improve tumor oxygenation during radiation treatment. The results support previous experimental studies showing that this approach is more effective when combined with breathing of hyperoxic gases.

Animals↗
PubMed2006

Theoretical modeling of the hydroxylation of methane as mediated by the particulate methane monooxygenase.

We present here the results of density functional theory (DFT) calculations directed toward elucidation of the CH bond activation mechanism that might be adopted by the particulate methane monooxygenase (pMMO) in the hydroxylation of methane and related small alkanes. In these calculations, we considered three of the most probable models for the transition metal active site mediating the "oxo-transfer": (i) the trinuclear copper cluster bis(mu(3)-oxo)trinuclear copper(II, II, III) complex 1, recently proposed by Chan et al. [S.I. Chan, K.H.-C. Chen, S.S.-F. Yu, C.-L. Chen, S.S.-J. Kuo, Biochemistry 43 (2004) 4421-4430.]; (ii) the most frequently used model complex, bis(mu-oxo)Cu(III)(2) complex 2; and (iii) the mixed-valence bis(mu-oxo)Cu(II)Cu(III) complex 3. The results obtained indicate that the methane hydroxylation chemistry mediated by the trinuclear copper cluster bis(mu(3)-oxo)trinuclear copper(II, II, III) complex 1 offers the most facile pathway for methane hydroxylation, and this model yields KIE values that are in good agreement with experiment. In this mechanism, the reaction proceeds along a "singlet" potential surface and a "singlet oxene" is directly inserted across a CH bond in a concerted manner. Kinetic isotope effects (k(H)/k(D) or KIE) associated with the concerted oxene insertion process mediated by complex 1 are calculated to be 5.2 at 300K when tunneling effects are included. Overall rate constants for the methane hydroxylation by the three models have been calculated as a function of temperature, and the rates are at least 5-6 orders of magnitude more facile when the chemistry is mediated by complex 1 compared to complex 2 or complex 3.

Binding Sites↗
PubMed2006

Chronic pain in a couples context: a review and integration of theoretical models and empirical evidence.

UNLABELLED: Researchers have become increasingly interested in the social context of chronic pain conditions. The purpose of this article is to provide an integrated review of the evidence linking marital functioning with chronic pain outcomes including pain severity, physical disability, pain behaviors, and psychological distress. We first present an overview of existing models that identify an association between marital functioning and pain variables. We then review the empirical evidence for a relationship between pain variables and several marital functioning variables including marital satisfaction, spousal support, spouse responses to pain, and marital interaction. On the basis of the evidence, we present a working model of marital and pain variables, identify gaps in the literature, and offer recommendations for research and clinical work. PERSPECTIVE: The authors provide a comprehensive review of the relationships between marital functioning and chronic pain variables to advance future research and help treatment providers understand marital processes in chronic pain.

Caregivers↗
PubMed2006

Bilateral processing in chemical synapses with electrical 'ephaptic' feedback: a theoretical model.

I have developed a detailed biophysical model of the chemical synapse which hosts voltage-dependent presynaptic ion channels and takes into account the capacitance of synaptic membranes. I find that at synapses with a relatively large cleft resistance (e.g., mossy fiber or giant calyx synapse) the rising postsynaptic current could activate, within the synaptic cleft, electrochemical phenomena that induce rapid widening of the presynaptic action potential (AP). This mechanism could boost fast Ca(2+) entry into the terminal thus increasing the probability of subsequent synaptic releases. The predicted difference in the AP waveforms generated inside and outside the synapse can explain the previously unexplained fast capacitance transient recorded in the postsynaptic cell at the giant calyx synapse. I propose therefore the mechanism of positive ephaptic feedback that acts between the postsynaptic and presynaptic cell contributing to the basal synaptic transmission at large central synapses. This mechanism could also explain the supralinear voltage dependence of EPSCs recorded at hyperpolarizing membrane potentials in low extracellular calcium concentration.

Action Potentials↗
PubMed2004

Theoretical model and experimental results for the nonlinear elastic behavior of human annulus fibrosus.

The physical properties of the annulus fibrosus are critical to the intervertebral disc's biomechanical function; alterations with degeneration and aging can contribute directly to joint dysfunction and pain. A constitutive model that links the mechanical structure of the annulus to its material properties is important for many bioengineering purposes. To this end, we developed a strain energy function with separate terms to represent the matrix, the fibers, and the interactions between the constituents. Additionally, we measured the tensile and compressive stress-strain response of the annulus in the circumferential direction. We simultaneously applied the strain energy function to these new data and to data from a wide range of experimental protocols reported in the literature. By choosing experimental protocols that use an unloaded reference configuration, we developed a comprehensive formulation for the multiaxial annular elastic behavior. As a partial validation, this formulation predicted experimental results that were not included in model parameter specification. We anticipate that this constitutive formulation will be useful for computational simulations of the disc's biomechanical response and for elucidating structure-function relationships of the annulus fibrosus.

Adolescent↗
PubMed2000

Developments in the theoretical modelling and experimental measurement of the surface potential of condensed monolayers.

In recent years considerable progress has been made in developing a theory for the surface potential of monolayers both at the air-water interface and deposited onto solid supports. This period has also seen the advent of scanning probe technology which has enabled surface potential to be measured to a hitherto undreamed of spatial resolution. This paper traces the key stages in these developments and explores the challenges that remain. Initially, the various models proposed for relating molecular and bond dipole moments to the surface potential are evaluated and the reliability of the moments obtained by applying the models to experimental results investigated. The limitations of the traditional Kelvin probe method of measuring surface potential are then highlighted and how these are overcome in the new generation of scanning force microscopes. Finally, it is suggested that such instruments could readily form the basis of a 'READ' head for a molecular memory based on a self-assembled, macromolecular lattice.

Journal Article↗
PubMed1979

A theoretical model for lipid mixtures, phase transitions, and phase diagrams.

We present a new model for the thermodynamic properties of lipid bilayers. The model consists of a system of hard cylinders of varying radii that correspond to the different molecular radii of lipids having different numbers of gauche rotations in their chains. Scaled particle theory is used to provide an accurate estimate of the entropy of packing of the cylinders. To apply the model to bilayers we introduce a semiempirical attractive potential energy. Once the form of this potential is chosen, we adjust one parameter, the interaction strength, so that the model fits the transition temperatures and entropies for various phospholipids. The model then agrees quite well with other published data for these systems. We also directly generalize our model to lipid mixtures, and we obtain phase diagrams that we compare to existing data for these systems. We use the model to describe lipid protein interactions in bilayers as well.

Lipid Bilayers↗
PubMed1991

Mechanosensitive ion channels as reporters of bilayer expansion. A theoretical model.

Various amphipathic compounds have been found to activate mechanosensitive (MS) ion channels in the bacterium Escherichia coli. These results were interpreted qualitatively in terms of the bilayer couple hypothesis. Here we present a mathematical model that describes the results quantitatively. According to the model, the uneven partitioning of amphipaths between the monolayers of the cell membrane causes one monolayer to be compressed and the other expanded. Because the open probability (Po) of the E. coli channels increased independently of which monolayer the amphipaths partitioned into, the model suggests that Po of the MS channels is determined by the monolayer having higher tension. We derived a relation between Po and amphipath concentration. The kinetics of Po variation after exposure of the cell membrane to the amphipaths was calculated based on this relation. The results fit satisfactorily the experimental data obtained with the cationic amphipath chlorpromazine and with the anionic amphipath trinitrophenol. Experiments which should further test the predictions following from the model are discussed.

Biomechanical Phenomena↗
PubMed1995

[Ca2+]i oscillations in sympathetic neurons: an experimental test of a theoretical model.

[Ca2+]i oscillations have been described in a variety of cells. This study focuses on caffeine-induced [Ca2+]i oscillations in sympathetic neurons. Previous work has shown that these oscillations require Ca2+ entry from the extracellular medium and Ca(2+)-induced Ca2+ release from a caffeine- and ryanodine-sensitive store. The aim of the study was to understand the mechanism responsible for the oscillations. As a starting point, [Ca2+]i relaxations were examined after membrane depolarization and exposure to caffeine. For both stimuli, post-stimulus relaxations could be described by the sum of two decaying exponential functions, consistent with a one-pool system in which Ca2+ transport between compartments is regulated by linear Ca2+ pumps and leaks. After modifying the store to include a [Ca2+]i-sensitive leak, the model also exhibits oscillations such as those observed experimentally. The model was tested by comparing measured and predicted net Ca2+ fluxes during the oscillatory cycle. Three independent fluxes were measured, describing the rates of 1) Ca2+ entry across the plasma membrane, 2) Ca2+ release by the internal store, and 3) Ca2+ extrusion across the plasma membrane and uptake by the internal store. Starting with estimates of the model parameters deduced from post-stimulus relaxations and the rapid upstroke, a set of parameter values was found that provides a good description of [Ca2+]i throughout the oscillatory cycle. With the same parameter values, there was also good agreement between the measured and simulated net fluxes. Thus, a one-pool model with a single [Ca2+]i-sensitive Ca2+ permeability is adequate to account for many of the quantitative properties of steady-state [Ca2+]i oscillations in sympathetic neurons. Inactivation of the intracellular Ca2+ permeability, cooperative nonlinear Ca2+ uptake and extrusion mechanisms, and functional links between plasma membrane Ca2+ transport and the internal store are not required.

Algorithms↗
PubMedDate not supplied

Toward the rational development of peptidomimetic analogs of the C-terminal endothelin hexapeptide: development of a theoretical model.

In an early report on the structure-activity relationship of endothelin (ET) peptides, it was reported that the C-terminal hexapeptide ET(16-21), His-Leu-Asp-Ile-Ile-Trp, is the minimum ET fragment which maintains biological activity in some, but not all the tissues responding to ETs. Subsequently, other authors described a series of analogs of this peptide, in which the His 16 residue was replaced by non-natural amino acids, characterized by bulky aromatic side chains. Among them, two well-characterized non-selective ETA/ETB antagonists were PD 142893 and PD 145065; interest in these potent ET antagonists was, however, reduced by their peptidic structure which was likely to lead to undesirable properties such as poor bioavailability and short duration of action. On the basis of these premises, our previous studies led to the development of a peptidomimetic ligand of ET receptors (compound 3), based on the replacement of the His 16 residue of ET(16-21) with an (E)-N-(benzyloxy)iminoacyl moiety; compound 3 proved to possess a certain affinity for ET receptors, albeit lower than that shown by PD 142893 and PD 145065. We report here on ETA/ETB binding affinity of compounds 4-12, designed as a new series of ET(16-21) analogs. Compounds 4 and 5 were practically devoid of any affinity; derivatives 6-12 exhibited appreciable affinity indices for ETB receptors higher than that shown by 3, even if still lower than that obtained for PD 145065. This paper also describes the development of a pharmacophoric model able to explain the ET receptor binding properties of our hexapeptide analogs compared with those of PD 142893 and PD 145065 and IRL2500, recently reported as a potent ETB selective endothelin antagonist.

Amino Acid Sequence↗
PubMed2000

The open section effect in a long bone with a longitudinal defect - a theoretical modeling study.

A longitudinal defect dramatically alters the stress distribution within a long bone. The altered stress distribution can influence the structural properties of the bone and the stimulus for repair and remodeling of the defect and the surrounding bone. For applied torsion, the defect interrupts the normal shear flow around the bone. Reversal of the shear flow along the inner cortex of the bone is the primary characteristic of the "open-section" effect. Stress concentration effects also produce large stresses at the defect corners. A finite element model of a femur mid-diaphysis with a rectangular defect in the posterior cortex was developed to quantify the femur stress distribution and torsional stiffness for defect widths ranging from one-tenth of the femur outer diameter (0.1 OD) to 0.3 OD, and defect lengths ranging from 0.5 to 5 OD. Defects with a length of 1 OD or shorter had little influence on the femur torsional stiffness or the femur shear-stress distribution. The torsional stiffness decreased most dramatically as the defect length increased from 2 to 3 OD, but began to approach an asymptote near 5 OD. Shear flow reversal peaked at the center of the defect for defects longer than 1 OD, and the magnitude of the reversal began to approach an asymptote near 5 OD. For each defect, the largest stresses within the bone, developed at the defect corners. The results indicate that the open-section effect decreases the torsional stiffness and stress concentration effects decrease the torsional strength of a long bone with a longitudinal defect.

Biomechanical Phenomena↗
PubMed1990

Theoretical modeling of biodegradation and biotransformation of hydrocarbons in subsurface environments.

Hydrocarbons such as TCE, PCE, TCA, gasoline and kerosene which are widely used in the industry, enter soils and groundwater from chemical waste disposal sites and from accidents. These types of substances are the most commonly encountered groundwater contaminants nationwide. Biotransformation of dissolved chlorinated hydrocarbons can provide complete mineralization to harmless end products such as CO2. It is the objective of this work to investigate the biodegradation and biotransformation, and transport of hydrocarbons in groundwater. This will be achieved first by defining and identifying relevant physical and biological processes which contribute to the fate of hydrocarbon contaminants in unsaturated/saturated soils, and providing a conceptual framework for incorporating these processes into a mathematical formulation. The conservation principles expressed in terms of quantifications of the physical, chemical and microbial processes described above lead to a system governing the phenomenon which consists of nonlinear partial differential equations. Microbial transformation conducted by both anaerobic and aerobic bacteria are considered.

Bacteria↗
PubMed1991

Sexual isolation in Drosophila. I. Theoretical models for multiple-choice experiments.

Several simple models are developed to calculate expected mating frequencies in ethological isolation experiments. They take into account the effect that the peculiar sexual behavior of Drosophila species can have in multiple-choice experiments. These models depend on only three basic parameters: male competitive ability (C), female receptivity (R) and the coefficient of females acceptance (A). Two types of model can be distinguished: (1) models with discrete preferences, in which A is a measure of the percentage of females accepting a particular kind of male and (2) models with continuous preferences, in which A represents the probability of acceptance for each courtship. It is demonstrated that the information rendered by just one experiment, although effective for determining whether sexual isolation exists, it is insufficient to estimate its degree or to demonstrate that it is asymmetrical. Further developments of the models under more complex conditions as well as their implications for reinforcement and founder effect theories are discussed.

Animals↗
PubMed1985

A theoretical model for immobilized whole cell enzyme.

A method of estimating effectiveness factor for immobilized whole cells is developed by considering microbial cells as microspheres containing enzyme activity dispersed in the gel phase of the support matrix. The proper model equations describing the system are solved and the corresponding effectiveness factors calculated for various bead sizes, and numbers and activities of cells. The cell wall resistance (permeability) is found to be one of most important variables in the system. The model is applied in predicting the experimental data of other investigators.

Cell Membrane Permeability↗
PubMed1986

A theoretical model to study the effect of convection and leaky junctions on macromolecule transport in artery walls.

A mathematical model is presented herein to determine the effect of convection on macromolecular transport across an artery wall due to transmural or osmotic pressure differences. The model is based on an extension of the leaky junction-cell turnover model of Weinbaum et al. (1985) to take into account a combined transport mechanism of convection and diffusion and also to provide the leaky junctions in the model with a finite resistance, thus allowing the results to be extended to intercellular clefts with a retarding extracellular matrix or to macromolecules whose dimensions are nearly the same as the junctional width. The results from this improved model show that the effect of pressure on transarterial macromolecular transport is important especially for cell turnover rates greater than 1% and that significant changes in the equilibrium balance of the cholesterol carrying LDL molecules in the arterial wall can occur due to a very small fraction of leaky junctions. At very high turnover rates (large fraction of leaky junctions) the effect of convection on macromolecular transport becomes dramatic and explains the very large increases in uptake observed experimentally after artificially inducing extensive endothelial damage.

Animals↗