Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Equilibrium optimization”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources

Airway smooth muscle, tidal stretches, and dynamically determined contractile states.

In the classic theory of airway lumen narrowing in asthma, active force in airway smooth muscle is presumed to be in static mechanical equilibrium with the external load against which the muscle has shortened. This theory is useful because it identifies the static equilibrium length toward which activated airway smooth muscle would tend if given enough time. The corresponding state toward which myosin-actin interactions would tend is called the latch state. But are the concepts of a static mechanical equilibrium and the latch state applicable in the setting of tidal loading, as occurs during breathing? To address this question, we have studied isolated, maximally contracted bovine tracheal smooth muscle subjected to tidal stretches imposed at 0.33 Hz. We measured the active force (F) and stiffness (E), which reflect numbers of actin-myosin interactions, and hysteresivity (eta) which reflects the rate of turnover of those interactions. When the amplitude of imposed tidal stretch (epsilon) was very small, 0.25% of muscle optimal length, the steady-state value of F approximated the isometric force, E was large, and eta was small. When epsilon was increased beyond 1%, however, F and E promptly decreased and eta promptly increased. The muscle could be maintained in these steady, dynamically determined contractile states for as long as the tidal stretches were sustained; when epsilon subsequently decreased back to 0.25%, F, E, and eta returned slowly toward their previous values. The provocative stretch amplitude required to cause active force or muscle stiffness to fall by half, or hysteresivity to double, was slightly greater than 2%. These observations are consistent with a direct effect of stretch upon bridge dynamics in which, with increasing tidal stretch amplitude, the number of actin-myosin interactions decreases and their rate of turnover increases. We conclude that the interactions of myosin with actin are at every instant tending toward those that would prevail in the isometric steady state, but tidal changes of muscle length cause an excess in the rate of detachment. These stretch-induced detachment events can come so fast compared with the rate of attachment that static equilibrium conditions are never attained. If so, then airway lumenal narrowing and the underlying contractile state would be governed by a dynamic mechanical process rather than by a mechanical equilibrium of static forces.

Animals↗

Biochemical mechanisms of New Molecular Entities (NMEs) approved by United States FDA during 2001-2004: mechanisms leading to optimal efficacy and safety.

The United States FDA approved 85 New Molecular Entities (NMEs) during the period from January 2001 to November 2004 of which 60 were pharmaceuticals with known molecular targets. The majority targeted enzymes (48%) or G-protein coupled receptors (GPCRs) (33%). Eighty percent of the NMEs interacted at the same site as endogenous effector; either as competitive inhibitor/antagonist (67%) or agonist (13%). Three biochemical operations defined the modes of action of the NMEs: 1) mass action competition (equilibrium), 2) a drug stabilized conformational change in the target that is important to the response (conformational) and/or 3) drug action is less-responsive to mass action competition with effectors due to non-equilibrium kinetics (non-equilibrium kinetic). Approximately 80% of the NMEs elicit a response utilizing conformational and/or non-equilibrium kinetic mechanisms. The remaining 20% of NMEs find mass action competition with the endogenous substrate or ligand sufficient for therapeutic utility. These observations indicate that for the majority of drug targets, mass action driven equilibrium binding alone may not be sufficient for maximal therapeutic utility. A key determinant of the biochemical mode of action for these NMEs was to minimize the potential for toxicity, either by providing a maximal response at a low dose to minimize off-target toxicities, or by providing a mechanism to minimize the incidence of mechanism-based toxicity while retaining a sufficiently efficacious response. This principle appears to be independent of target class and provides insight as to intrinsic biochemical features and approaches required for a maximal therapeutic index.

Animals↗

Effects of friction at the digit-object interface on the digit forces in multi-finger prehension.

The effects of surface friction at the digit-object interface on digit forces were studied when subjects (n=8) statically held an object in a five-digit grasp. The friction conditions were SS (all surfaces are sandpaper), RR (all are rayon), SR (S for the thumb and R for the four fingers), and RS (the reverse of SR). The interaction effects of surface friction and external torque were also examined using five torques (-0.5, -0.25, 0, +0.25, +0.5 Nm). Forces and moments exerted by the digits on a handle were recorded. At zero torque conditions, in the SS and RR (symmetric) tasks the normal forces of the thumb and virtual finger (VF, an imagined finger with the mechanical effect equal to that of the four fingers) were larger for the RR than the SS conditions. In the SR and RS (asymmetric) tasks, the normal forces were between the RR and SS conditions. Tangential forces were smaller at the more slippery side than at the less slippery side. According to the mathematical optimization analysis decreasing the tangential forces at the more slippery sides decreases the cost function values. The difference between the thumb and VF tangential forces, DeltaF (t), generated a moment of the tangential forces (friction-induced moment). At non-zero torque conditions the friction-induced moment and the moment counterbalancing the external torque (equilibrium-necessitated moment) could be in same or in opposite directions. When the two moments were in the same direction, the contribution of the moment of tangential forces to the total moment was large, and the normal forces were relatively low. In contrast, when the two moments were in opposite directions, the contribution of the moment of tangential forces to the total moment markedly decreased, which was compensated by an increase in the moment of normal forces. The apparently complicated results were explained as the result of summation of the friction-related (elemental) and torque-related (synergy) components of the central commands to the individual digits.

Adaptation, Physiological↗

Socially strategic ecological restoration: a game-theoretic analysis [corrected].

Major transitions in a multiple-use or mosaic landscape often lead to frictions among new and existing users. In this article, we consider the problem of ecological restoration within a mosaic landscape in which restoration activities elicit feedbacks from individuals and groups that are harmed by restoration outcomes. Using game theory, we identify three potential outcomes ranked by the extent of restoration of ecosystem services and processes: nonstrategic, noncooperative strategic equilibrium, and cooperative bargaining solution. We identify conditions under which additional restoration can decrease the overall flow of ecosystem services and processes. A "strategic restorationist" will cease new restoration activities when the net effect of defensive response moves by farmers offsets gains. Imperfect information regarding expected payoffs to farmers can lead to inefficient overshooting or undershooting the optimal scale, geographical positioning, and form of restoration. Gains to all parties from cooperation might exist. As a case study and to aid model design, we consider restoration activities on California's upper Sacramento River.

Agriculture↗

Frequency and concentration windows for the electric activation of a membrane active transport system.

Previous work has shown that a simple four-state membrane transport system can interact with an oscillating electric field to become an active transport system if there is charge translocation associated with conformational changes of the transporter and if affinities of the transporter for the ligand on the two sides of membrane are different. The relationship between the transport flux and both the frequency of the applied field and the concentration of ligand have been examined based on the following assumptions: the rate of the electroconformational change of the transporter is much greater than that of the ligand association/dissociation reaction, and the oscillating electric field has a large amplitude. It was found that the transport flux depends strongly on the frequency of the field and on the concentration of the ligand and it displays a window of broad bandwidth both on the frequency and the concentration axes. The maximum concentration gradient, or the static head, which can be supported by this mechanism is shown to be constant for field frequencies smaller than the rate of the electroconformational change. The static head value diminishes completely when the field frequency exceeds the rate of the conformational change. The presence of an optimal field frequency has been shown experimentally in several membrane enzyme systems. The theory was applied to the description of Rb and Na pumping in human erythrocytes stimulated by an AC field. The prediction of a window for a ligand concentration and the static head value may be tested experimentally. In addition, the rate constants and the equilibrium constants of the four state model can be determined by measuring positions of windows, fluxes, and static head values under different experimental conditions. These results are equally applicable to the oscillation of pressure, membrane tension, substrate concentration, or temperature if these external parameters can induce functionally relevant conformational changes of the transporter.

Biological Transport, Active↗

Thermodynamic Calculations for Reactions Involving Hydrogen Halide Polymers, Ions, and Lewis Acid Adducts. 3. Systems Constituted from Al(3+), H(+), and Cl(-).

Semiempirical (MNDO, AM1 and PM3), ab initio (HF/3-21+G(d,p), MP2/3-21+G(d,p), HF/6-311+G(d,p), and MP2/6-311+G(d,p)), and density functional (BVWN/3-21+G(d,p) and BVWN/6-311+G(d,p)) energy minimization and frequency calculations have been carried out on AlCl(3), AlCl(4)(-), AlCl(2)(+), HAlCl(4), HAlCl(3)(+), and ClHAlCl(4)(-). The same computational set, except for MP2/6-311+G(d,p) frequency calculations, was performed on Al(2)Cl(6) and Al(2)Cl(7)(-). For ClHAl(2)Cl(7)(-), only semiempirical calculations, as well as Hartree-Fock and BVWN optimizations using the 3-21+G(d,p) and 6-311+G(d,p) basis sets, were carried out along with Hartree-Fock frequency determinations. DeltaG degrees, DeltaH degrees, and DeltaS degrees values have been calculated for a number of reactions involving these species along with a variety of ions derived from HCl. Thermodynamic data and equilibrium constants at 298 K are presented for 22 reactions using calculations at the best level, along with a comparison of DeltaG degrees values obtained from all molecular orbital methods used.

Journal Article↗

Bacillus subtilis DesR functions as a phosphorylation-activated switch to control membrane lipid fluidity.

The Des pathway of Bacillus subtilis regulates the synthesis of the cold-shock induced membrane-bound enzyme Delta5-fatty acid desaturase (Delta5-Des). A central component of the Des pathway is the response regulator, DesR, which is activated by a membrane-associated kinase, DesK, in response to a decrease in membrane lipid fluidity. Despite genetic and biochemical studies, specific details of the interaction between DesR and the DNA remain unknown. In this study we show that only the phosphorylated form of protein DesR is able to bind to a regulatory region immediately upstream of the promoter of the Delta5-Des gene (Pdes). Phosphorylation of the regulatory domain of dimeric DesR promotes, in a cooperative fashion, the hierarchical occupation of two adjacent, non-identical, DesR-P DNA binding sites, so that there is a shift in the equilibrium toward the tetrameric active form of the response regulator. Subsequently, this phosphorylation signal propagation leads to the activation of the des gene through recruitment of RNA polymerase to Pdes. This is the first dissected example of a transcription factor functioning as a phosphorylation-activated switch for a cold-shock gene, allowing the cell to optimize the fluidity of membrane phospholipids.

Bacillus subtilis↗

Liquid chromatographic studies of the effect of phosphate on the binding properties of silica-immobilized bovine serum albumin.

High-performance liquid chromatography has been used to examine how phosphate ions affect the binding properties of bovine serum albumin (BSA) immobilized to porous silica. In doing this, the time dependence of the protein to reach conformational equilibrium is measured as a function of the concentration of phosphate in the eluent using the D- and L-isomers of tryptophan and kynurenine as solutes. The overall binding and chiral selectivity (alphaD,L) of the protein toward these solutes appear to be related to two types of effects: one being those that are site-selective and only influence the retention of the L-isomers and the other being those that are nonselective and influence the retention of both enantiomers. An interesting feature of the concentration-dependent data is a maximum in alphaD,L at intermediate phosphate concentrations (i.e., 10 to 50mM phosphate) indicative of both cooperative and antagonistic binding effects. Phosphate eluents within this concentration range provide selectivity advantages, and those at higher concentrations decrease the time required for the protein or column to reach equilibrium. A final set of studies has also been carried out using four alternate buffer systems (i.e., borate, carbonate, acetate, and arsenate eluents). Although the borate eluents affect the BSA's binding properties and alphaD,L similar to the phosphate eluents, the other buffers result in poor separations. Observations from this study are useful in helping to optimize separations carried out on immobilized BSA as well as addressing biological and mechanistic questions related to how anions influence the native binding properties of serum albumins.

Chromatography, High Pressure Liquid↗

Cooperation and self-regulation in a model of agents playing different games.

A simple model for cooperation between "selfish" agents, which play an extended version of the prisoner's dilemma game, in which they use arbitrary payoffs, is presented and studied. A continuous variable, representing the probability of cooperation, p(k)(t) in [0,1], is assigned to each agent k at time t. At each time step t a pair of agents, chosen at random, interact by playing the game. The players update their p(k)(t) using a criterion based on the comparison of their utilities with the simplest estimate for expected income. The agents have no memory and do not use strategies based on direct reciprocity or "tags." Depending on the payoff matrix, the system self-organizes-after a transient-into stationary states characterized by their average probability of cooperation p(eq) and average equilibrium per-capita income p(eq),U(infinity). It turns out that the model exhibits some results that contradict the intuition. In particular, some games that a priori seem to favor defection most, may produce a relatively high degree of cooperation. Conversely, other games, which one would bet lead to maximum cooperation, indeed are not the optimal for producing cooperation.

Journal Article↗

Purification and properties of a low-molecular-weight, high-alkaline pectate lyase from an alkaliphilic strain of Bacillus.

A low-molecular-weight, high-alkaline pectate lyase (pectate transeliminase, EC 4.2.2.2) was found in an alkaline culture of Bacillus sp. strain KSM-P15, purified to homogeneity, and crystallized. The enzyme had a relative molecular weight of approximately 20,300 as measured by sedimentation equilibrium, with a sedimentation coefficient (s20,w0) of 1.73 S. It was a basic protein with an isoelectric point of pH 10.3, and the alpha-helical content was only 6.6%. In the presence of Ca2+ ions, the enzyme degraded polygalacturonic acid in a random manner to yield 4,5-unsaturated oligo-galacturonides and had its optimal activity around pH 10.5 and 50-55 degrees C. It also had a protopectinase-like activity on cotton fibers. The N-terminal amino acid sequences of the intact protein (28 amino acids) and its two lysyl endopeptidase-cleaved peptide fragments (8 and 12 amino acids) had very low sequence similarity with pectate lyases reported to date. These results strongly suggest that the pectate lyase of Bacillus sp. strain KSM-P15 may be a novel enzyme and belongs in a new family.

Amino Acid Sequence↗

Localization and characterization of melatonin receptors in rodent brain by in vitro autoradiography.

Little is known of the neural sites of action for the pineal hormone, melatonin. Thus, we developed an in vitro autoradiographic method using 125I-labeled melatonin (I-MEL) to study putative melatonin receptors in rodent brain. We first determined optimal in vitro labeling conditions for autoradiographic detection of I-MEL binding sites in rat median eminence, the most intensely labeled area in the rat brain. We then assessed the pharmacologic and kinetic properties of I-MEL binding sites in rat median eminence by quantitative autoradiography. These sites have high affinity for I-MEL (equilibrium dissociation constant = 43 pM). I-MEL binding was inhibited by nanomolar concentrations of melatonin or 6-chloromelatonin, but was not inhibited by serotonin, dopamine, or norepinephrine (100 microM). These results suggest that I-MEL binding sites identified by in vitro autoradiography represent specific, high-affinity melatonin receptors. Studies of the distribution of I-MEL binding in rat, Syrian hamster, and Djungarian hamster brain confirm that the median eminence and suprachiasmatic nucleus are major sites of I-MEL binding in rodent brain; other brain areas labeled in one or more of these species were the thalamus (paraventricular, anteroventral, and reuniens nuclei, nucleus of the stria medullaris, and medial part of the lateral habenular nucleus), hypothalamus (dorsomedial nucleus), subiculum, and area postrema. The presence of putative melatonin receptors in the suprachiasmatic nuclei and median eminence of these rodent species suggests that these brain regions are important loci for melatonin effects on circadian rhythms and reproduction.

Animals↗

[Effect of peripheral counterpulsation on the body of an animal with intact heart].

The effect of lasting peripheral counterpulsation upon the haemodynamics and the main biochemical factors of the blood was studied in 14 dogs with intact hearts. In cases of significant tachycardia counterpulsation in a 1:2 regimen results in only a partial reduction of the resistance to the cardiac output. This does not always permit to prevent the formation of the phenomenon of an elevated myocardial contractility. The haemodynamic conditions are most optimal in a 1:1 regimen of counterpulsation. Slowing down of the cardiac rhythm was achieved by means of hypothermia.

Acid-Base Equilibrium↗

Mechanisms underlying responsiveness to tetrahydrobiopterin in mild phenylketonuria mutations.

A subtype of phenylalanine hydroxylase (PAH) deficiency that responds to cofactor (tetrahydrobiopterin, BH4) supplementation has been associated with phenylketonuria (PKU) mutations. The underlying molecular mechanism of this responsiveness is as yet unknown and requires a detailed in vitro expression analysis of the associated mutations. With this aim, we optimized the analysis of the kinetic and cofactor binding properties in recombinant human PAH and in seven mild PKU mutations, i.e., c.194T>C (p.I65T), c.204A>T (p.R68S), c.731C>T (p.P244L), c.782G>A (p.R261Q), c.926C>T (p.A309V), c.1162G>A (p.V388M), and c.1162G>A (p.Y414C) expressed in E. coli. For p.I65T, p.R68S, and p.R261Q, we could in addition study the equilibrium binding of BH4 to the tetrameric forms by isothermal titration calorimetry (ITC). All the mutations resulted in catalytic defects, and p.I65T, p.R68S, p.P244L, and most probably p.A309V, showed reduced binding affinity for BH4. The possible stabilizing effect of the cofactor was explored using a cell-free in vitro synthesis assay combined with pulse-chase methodology. BH4 prevents the degradation of the proteins of folding variants p.A309V, p.V388M, and p.Y414C, acting as a chemical chaperone. In addition, for wild-type PAH and all mild PKU mutants analyzed in this study, BH4 increases the PAH activity of the synthesized protein and protects from the rapid inactivation observed in vitro. Catalase and superoxide dismutase partially mimic this protection. All together, our results indicate that the response to BH4 substitution therapy by PKU mutations may have a multifactorial basis. Both effects of BH4 on PAH, i.e., the chemical chaperone effect preventing protein misfolding and the protection from inactivation, may be relevant mechanisms of the responsive phenotype.

Biopterins↗

Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes.

The adsorption free energy of charged proteins on mixed membranes, containing varying amounts of (oppositely) charged lipids, is calculated based on a mean-field free energy expression that accounts explicitly for the ability of the lipids to demix locally, and for lateral interactions between the adsorbed proteins. Minimization of this free energy functional yields the familiar nonlinear Poisson-Boltzmann equation and the boundary condition at the membrane surface that allows for lipid charge rearrangement. These two self-consistent equations are solved simultaneously. The proteins are modeled as uniformly charged spheres and the (bare) membrane as an ideal two-dimensional binary mixture of charged and neutral lipids. Substantial variations in the lipid charge density profiles are found when highly charged proteins adsorb on weakly charged membranes; the lipids, at a certain demixing entropy penalty, adjust their concentration in the vicinity of the adsorbed protein to achieve optimal charge matching. Lateral repulsive interactions between the adsorbed proteins affect the lipid modulation profile and, at high densities, result in substantial lowering of the binding energy. Adsorption isotherms demonstrating the importance of lipid mobility and protein-protein interactions are calculated using an adsorption equation with a coverage-dependent binding constant. Typically, at bulk-surface equilibrium (i.e., when the membrane surface is "saturated" by adsorbed proteins), the membrane charges are "overcompensated" by the protein charges, because only about half of the protein charges (those on the hemispheres facing the membrane) are involved in charge neutralization. Finally, it is argued that the formation of lipid-protein domains may be enhanced by electrostatic adsorption of proteins, but its origin (e.g., elastic deformations associated with lipid demixing) is not purely electrostatic.

Adsorption↗

Force, velocity and energy dynamics of nine load-moving muscles.

Nine architecturally different muscles of the cat's hindlimb were investigated with respect to the kinetic energy, the potential energy, and the force variations associated with shortening contractions against gravitational loads. Insight about the energy dynamics of contractile muscle can provide a unifying concept for models of muscle performance capability. In this study, it was found that as contractions shortened from passive equilibrium against a constant mass load, acceleration and deceleration phases appeared. These phase were associated with muscular force variations of up to 25% of the mass weight in fast twitch muscles at low loads. In contrast, slow twitch muscles were associated with less than 10% force variations when shortening against a gravitational load. It also was found that optimal loads exist which maximize each muscle's ability to impart kinetic and potential energy, these optimal loads tend to be in the mid-force range for highly pennate muscle and in the low-force range for justform muscles. It was concluded that the kinetic energy provided by each muscle is a small percentage of that calculated from its length-force relationship, especially at low loads. This study confirms that the efficiency of kinetic energy conversion is very low at low loads (gradually improving as the loads increase) and thereby substantiates early experiments with heat and metabolic energy.

Animals↗

Dynamics of capillary isoelectric focusing in the absence of fluid flow: high-resolution computer simulation and experimental validation with whole column optical imaging.

A 150-component, dynamic electrophoresis simulator was developed and applied to the description of capillary isoelectric focusing (CIEF) of amphoteric substances in quiescent solution. The simulator is shown to be capable of producing high-resolution pH 3-10 focusing data with 140 individual carrier ampholytes (20/pH unit) and at current densities that are used in CIEF, i.e., under conditions that were hitherto unaccessible by dynamic computer simulation. Having a focusing capillary of 5-cm length, the predicted focusing dynamics for amphoteric dyes obtained at a constant voltage of 1500 V (300 V/cm) are shown to qualitatively agree with data obtained by whole-column optical imaging. The simulation data provide detailed insight into the dynamics of the focusing process for the cases with the focusing column being sandwiched between 40 mM NaOH (catholyte) and 100 mM phosphoric acid (anolyte) or having the column ends only permeable for OH- and H+ at cathode and anode, respectively. Simulation data reveal that the number of sample boundaries migrating from the two ends of the column to the focusing positions is always equal to the number of sample components. The number of detectable migrating sample boundaries, however, can be lower. Whole-column optical imaging is demonstrated to be the method of choice for following the approach to equilibrium. With that detection format, transient sample peaks can be recognized and properly identified. This would also be possible with a scanning detector moving rapidly and repeatedly along the column but cannot be accomplished by a stationary detector placed at a specified location. The data presented demonstrate that the model together with imaging monitoring can be used to optimize the CIEF separation conditions.

Coloring Agents↗

Water-compatible molecularly imprinted polymers obtained via high-throughput synthesis and experimental design.

A technique allowing high-throughput synthesis and evaluation of molecularly imprinted polymer sorbents at a reduced scale (mini-MIPs) was developed and used for the optimization of MIPs for use in pure aqueous environments. The technique incorporated a 4-port liquid-handling robot for the rapid dispensing of monomers, templates, solvents and initiator into the reaction vessels of a 96-well plate. A library of 80 polymers, each ca. 50 mg, could thus be prepared in 24 h. The MIP rebinding capacity and selectivity could be rapidly assessed in the batch mode by quantifying nonbound fractions in parallel using a UV monochromator plate reader. This allowed a complete evaluation of the binding characteristics of an 80 polymer library in approximately 1 week. With the objective of optimizing a polymer imprinted with the local anaesthetic Bupivacaine for use in pure aqueous systems, a polymer library was prepared by varying the original poly(MAA-co-EDMA) MIP composition. The variable factors were the added amount of the hydrophilic comonomer, 2-hydroxyethyl methacrylate (HEMA), the cross-linking ratio, and the porogen. This optimization resulted in polymers showing high imprinting factors (IF = K(MIP)/K(NIP)) in water as a result, mainly, of reduced binding to the nonimprinted polymer. Normal scale batches of these materials showed strong retention of the template and low nonspecific binding when assessed as chromatographic stationary phases using pure phosphate buffer, pH 7.4, as mobile phase, by equilibrium batch rebinding experiments and as sorbents for extractions of the analyte from blood plasma samples.

Journal Article↗

Thermodynamic calculations in the system CH4-H2O and methane hydrate phase equilibria.

Using the Gibbs function of reaction, equilibrium pressure, temperature conditions for the formation of methane clathrate hydrate have been calculated from the thermodynamic properties of phases in the system CH4-H2O. The thermodynamic model accurately reproduces the published phase-equilibria data to within +/-2 K of the observed equilibrium boundaries in the range 0.08-117 MPa and 190-307 K. The model also provides an estimate of the third-law entropy of methane hydrate at 273.15 K, 0.1 MPa of 56.2 J mol(-1) K(-1) for 1/nCH4.H2O, where n is the hydrate number. Agreement between the calculated and published phase-equilibria data is optimized when the hydrate composition is fixed and independent of the pressure and temperature for the conditions modeled.

Journal Article↗