Kinetics of ligand binding to receptor immobilized in a polymer matrix, as detected with an evanescent wave biosensor. I. A computer simulation of the influence of mass transport.

The influence of mass transport on ligand binding to receptor immobilized in a polymer matrix, as detected with an evanescent wave biosensor, was investigated. A one-dimensional computer model for the mass transport of ligand between the bulk solution and the polymer gel and within the gel was employed, and the influence of the diffusion coefficient, the partition coefficient, the thickness of the matrix, and the distribution of immobilized receptor were studied for a variety of conditions. Under conditions that may apply to many published experimental studies, diffusion within the matrix was found to decrease the overall ligand transport significantly. For relatively slow reactions, small spatial gradients of free and bound ligand in the gel are found, whereas for relatively rapid reactions strong inhomogeneities of ligand within the gel occur before establishment of equilibrium. Several types of deviations from ideal pseudo-first-order binding progress curves are described that resemble those of published experimental data. Extremely transport limited reactions can in some cases be fitted with apparently ideal binding progress curves, although with apparent reaction rates that are much lower than the true reaction rates. Nevertheless, the ratio of the apparent rate constants can be semiquantitatively consistent with the true equilibrium constant. Apparently "cooperative" binding can result from high chemical on rates at high receptor saturation. Dissociation in the presence of transport limitation was found to be well described empirically by a single or a double exponential, with both apparent rate constants considerably lower than the intrinsic chemical rate constant. Transport limitations in the gel can introduce many generally unknown factors into the binding progress curve. The simulations suggest that unexpected deviations from ideal binding progress curves may be due to highly transport influenced binding kinetics. The use of a thinner polymer matrix could significantly increase the range of detectable rate constants.     

The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria

Local damage (mainly burning, heating, and mechanical wounding) induces propagation of electrical signals, namely, variation potentials, which are important signals during the life of plants that regulate different physiological processes, including photosynthesis. It is known that the variation potential decreases the rate of CO₂ assimilation by the Calvin–Benson cycle; however, its influence on light reactions has been poorly investigated. The aim of our work was to investigate the influence of the variation potential on the light energy flow that is absorbed, trapped and dissipated per active reaction centre in photosystem II and on the flow of electrons through the chloroplast electron transport chain. We analysed chlorophyll fluorescence in pea leaves using JIP-test and PAM-fluorometry; we also investigated delayed fluorescence. The electrical signals were registered using extracellular electrodes. We showed that the burning-induced variation potential stimulated a nonphotochemical loss of energy in photosystem II under dark conditions. It was also shown that the variation potential gradually increased the flow of light energy absorbed, trapped and dissipated by photosystem II. These changes were likely caused by an increase in the fraction of absorbed light distributed to photosystem II. In addition, the variation potential induced a transient increase in electron flow through the photosynthetic electron transport chain. Some probable mechanisms for the influence of the variation potential on the light reactions of photosynthesis (including the potential role of intracellular pH decrease) are discussed in the work.     

Numerical simulation of convective and diffusive transport effects on a high-pressure-induced inactivation process

High-pressure-induced conversions, such as the inactivation of enzymes or of microorganisms, are dependent on the applied pressure and the temperature of the process. The former can be considered to be a spatially homogeneous quantity, while the latter, being a transport quantity, varies over space and time. Here we question whether the uniformity of a high-pressure conversion can be disturbed by convective and conductive heat and mass transport conditions. Enzyme inactivation is taken as a model process for a high-pressure conversion. To cover a broad range of parameters and to consider scale-up effects, the investigation is based on mathematical modeling and numerical simulation for different sizes of the pressure chamber and different solvent viscosities. Apart from viscosity, the physical properties of the enzyme solutions are assumed to be identical in all cases. Therefore, matrix effects other than that of viscosity are excluded. Moreover, the authors postulate that viscosity solely acts on the continuum mechanical scale of momentum exchange but not on the molecular scale on the inactivation kinetics. It has been found that nonuniform thermal conditions can strongly influence the result of a high-pressure process. A variation of the activity retention between 28% and 48% can be observed after 20 minutes for a 0.8-L high-pressure chamber and a matrix fluid with a viscosity comparable to that of edible oils. The same process carried out in a 6.3-L device leads to an activity retention that varies between 16% and 40%. From the analysis of the time scales for the inactivation and for hydrodynamic and thermal compensation, it can be deduced that a nonuniform activity retention has to be expected if the inactivation time scale is larger than the hydrodynamic time scale and smaller than the thermal compensation time scale.     

Cerebrovascular response to decreased hematocrit: effect of cell-free hemoglobin,plasma viscosity,and CO2

The effect of transfusing a nonextravasating, zero-link polymer of cell-free hemoglobin on pial arteriolar diameter, cerebral blood flow (CBF), and O2 transport (CBF x arterial O2 content) was compared with that of transfusing an albumin solution at equivalent reductions in hematocrit (approximately 19%) in anesthetized cats. The influence of viscosity was assessed by coinfusion of a high-viscosity solution of polyvinylpyrrolidone (PVP), which increased plasma viscosity two- to threefold. Exchange transfusion of a 5% albumin solution resulted in pial arteriolar dilation, increased CBF, and unchanged O2 transport, whereas there were no significant changes over time in a control group. Exchange transfusion of a 12% polymeric hemoglobin solution resulted in pial arteriolar constriction and unchanged CBF and O2 transport. Coinfusion of PVP with albumin produced pial arteriolar dilation that was similar to that obtained with transfusion of albumin alone. In contrast, coinfusion of PVP with hemoglobin converted the constrictor response to a dilator response that prevented a decrease in CBF. Pial arteriolar dilation to hypercapnia was unimpaired in groups transfused with albumin or hemoglobin alone but was attenuated in the largest vessels in albumin and hemoglobin groups coinfused with PVP. Unexpectedly, hypocapnic vasoconstriction was blunted in all groups after transfusion of albumin or hemoglobin alone or with PVP. We conclude that 1) the increase in arteriolar diameter after albumin transfusion represents a compensatory response that prevents decreased O2 transport at reduced O2-carrying capacity, 2) the decrease in diameter associated with near-normal O2-carrying capacity after cell-free polymeric hemoglobin transfusion represents a compensatory mechanism that prevents increased O2 transport at reduced blood viscosity, 3) pial arterioles are capable of dilating to an increase in plasma viscosity when hemoglobin is present in the plasma, 4) decreasing hematocrit does not impair pial arteriolar dilation to hypercapnia unless plasma viscosity is increased, and 5) pial arteriolar constriction to hypocapnia is impaired at reduced hematocrit independently of O2-carrying capacity.     

Computational modeling of chemical reactions and interstitial growth and remodeling involving charged solutes and solid-bound molecules

Mechanobiological processes are rooted in mechanics and chemistry, and such processes may be modeled in a framework that couples their governing equations starting from fundamental principles. In many biological applications, the reactants and products of chemical reactions may be electrically charged, and these charge effects may produce driving forces and constraints that significantly influence outcomes. In this study, a novel formulation and computational implementation are presented for modeling chemical reactions in biological tissues that involve charged solutes and solid-bound molecules within a deformable porous hydrated solid matrix, coupling mechanics with chemistry while accounting for electric charges. The deposition or removal of solid-bound molecules contributes to the growth and remodeling of the solid matrix; in particular, volumetric growth may be driven by Donnan osmotic swelling, resulting from charged molecular species fixed to the solid matrix. This formulation incorporates the state of strain as a state variable in the production rate of chemical reactions, explicitly tying chemistry with mechanics for the purpose of modeling mechanobiology. To achieve these objectives, this treatment identifies the specific theoretical and computational challenges faced in modeling complex systems of interacting neutral and charged constituents while accommodating any number of simultaneous reactions where reactants and products may be modeled explicitly or implicitly. Several finite element verification problems are shown to agree with closed-form analytical solutions. An illustrative tissue engineering analysis demonstrates tissue growth and swelling resulting from the deposition of chondroitin sulfate, a charged solid-bound molecular species. This implementation is released in the open-source program FEBio (www.febio.org). The availability of this framework may be particularly beneficial to optimizing tissue engineering culture systems by examining the influence of nutrient availability on the evolution of inhomogeneous tissue composition and mechanical properties, the evolution of construct dimensions with growth, the influence of solute and solid matrix electric charge on the transport of cytokines, the influence of binding kinetics on transport, the influence of loading on binding kinetics, and the differential growth response to dynamically loaded versus free-swelling culture conditions.     

The flux-force relations across complex membranes with active transport

Equations are derived for the total material flux, and the total electric current flux, across a complex membrane system with active transport. The equations describe the fluxes as linear functions of forces across the system, and specifically of electrical potential, hydrostatic pressure, chemical potentials, and active transport rates. The equations can be simplified for experimental studies by making one or more of the forces equal to zero. The osmotic pressure difference across a membrane system is shown to be a function of the electrical potential and chemical potential differences and of the active transport rates. The transmembrane potential is shown to be the sum of a diffusion potential and an active transport potential. A simple equation is derived describing the current across a membrane as a linear function of the electrical potential and the active transport rate. Specific examples of the application of the equations to nerve membrane potentials are considered.     

Transport of phosphate in membrane vesicles from mouse fibroblasts transformed by simian virus 40.

Membrane vesicles were prepared from mouse fibroblasts transformed by SV40 virus (SV3T3). Following disruption of the cells by nitrogen cavitation, the membrane vesicles were obtained by differential centrifugation. As measured by enzyme markers, they consist mainly of membrane from the plasma membrane and smooth and rough endoplasmic reticulum. The vesicles transport Pi by two separate, mediated systems: one is independent of Na+, and the other is secondary active transport driven by a Na+ gradient. Electrical and chemical energy can be provided by a Na+ gradient to drive the concentrative uptake of Pi by the vesicles, one or both forces being used to energize transport. Evidence is provided that both the electrical and chemical potentials produced by the asymmetric distribution of Na+ across the membrane of SV3T3 membrane vesicles are utilized to concentrate phosphate in the vesicles. Phosphate transport by the vesicles cannot be accounted for by a small contamination of this fraction with mitochondria (1 to 4%). The Pi transport properties of the membrane vesicles differ from those of the fraction enriched in mitochondria in the following respects: their kinetic properties, and their responses to a Na+ gradient, N-ethylmaleimide, mersalyl, and succinate/acetate. However, the membrane vesicles share some properties of Pi transport with mitochondria. Cyanide, azide, oligomycin, 2,4-dinitrophenol, and carbonyl cyanide m-cholophenylhydrazone, inhibitors of Pi transport by mitochondria, also inhibit membrane vesicle, Pi transport. The vesicles retain all the features of Pi transport by SV3T3 cells that have been examined. They provide a simplified system for a determination of the details of the mechanism of Pi transport under conditions where transport is dissociated from intracellular reactions and in the presence of a defined electrochemical driving force.     

Understanding the effect of adsorption on activated processes using molecular theory and simulation

Most chemical reactions of practical interest are catalysed by porous materials, which can improve reaction rates and equilibrium yields through various interactions with the reacting mixture. Nucleation, another kind of activated process, can also be substantially affected by the presence of a surface or by the confinement within a porous material. There are several different effects that can influence such activated processes, such as the reduced dimensionality of the porous space or the adsorbed layer, physical or chemical interactions with the adsorbate and transport limitations. This paper presents a unifying perspective on the influence of each of these effects on chemical reactions and crystallisation processes through the discussion of selected examples from the literature. The common aspects and the differences between these two different kinds of activated processes are considered in the context of each effect. Finally, some of the important issues that could benefit from the development of new molecular simulations methods are discussed.     

Isotope effects on electron tunneling reactions in biological systems conformational mobility of proteins

Effects of D2O substitution on electron transport reactions in proteins were analysed on the basis of generally adopted ideas of electronic vibration interactions and conformational mobility of macromolecules. At the molecular level, a mechanism for cytochrome c oxidation was established. On the basis of general viscosity and elasticity properties of proteins, the effects of temperature and chemical composition of the medium on conformational relaxation were analysed. For chromatophores of photosynthetising bacteria, a mechanism is discussed by which abnormal effects of temperature and abnormal isotope effects may be exercised on charge recombination.     

Annulated Dialkoxybenzenes as Catholyte Materials for Non‐aqueous Redox Flow Batteries: Achieving High Chemical Stability through Bicyclic Substitution

1,4‐Dimethoxybenzene derivatives are materials of choice for use as catholytes in non‐aqueous redox flow batteries, as they exhibit high open‐circuit potentials and excellent electrochemical reversibility. However, chemical stability of these materials in their oxidized form needs to be improved. Disubstitution in the arene ring is used to suppress parasitic reactions of their radical cations, but this does not fully prevent ring‐addition reactions. By incorporating bicyclic substitutions and ether chains into the dialkoxybenzenes, a novel catholyte molecule, 9,10‐bis(2‐methoxyethoxy)‐1,2,3,4,5,6,7,8‐octahydro‐1,4:5,8‐dimethanenoanthracene (BODMA), is obtained and exhibits greater solubility and superior chemical stability in the charged state. A hybrid flow cell containing BODMA is operated for 150 charge–discharge cycles with a minimal loss of capacity.     

Kinetics of carbonic anhydrase catalysis in solvents of increased viscosity: a partially diffusion-controlled reaction

Steady-state kinetic studies of the bovine carbonic anhydrase B-catalyzed hydration of CO2, dehydration of HCO3-, and hydrolysis of p-nitrophenylacetate were made in glycerol/water solvents of increased viscosity in order that the effect of diffusion-control on the substrate association reactions could be determined. The minimum association rate constants (kmin = V/(Km[E0])) were obtained at low substrate concentrations. The esterase activity did not depend upon the solvent viscosity. However, both the CO2 hydration and HCO3- dehydration reactions depended upon the solvent viscosity consistent with partial diffusion control. Thus both chemical activation and diffusion control processes contribute to the observed kmin. In low-viscosity aqueous solutions both hydration and dehydration are largely controlled by chemical activation. However, at higher viscosities, equal to that found in the interior of the erythrocyte, both reactions are largely diffusion controlled. This result can be interpreted to mean that carbonic anhydrase is a highly evolved enzyme that has approached its maximum efficiency. The extent of diffusion control observed rules out H2CO3 as a significant reactant with the enzyme. Several models that yield minimum steric requirements for access of substrate to the active site are examined. Minimum steric constraints are less for the smaller CO2. The slower esterase reaction is not influenced by diffusion.     

Kinetics of the lactate dehydrogenase reaction in high-viscosity media

The effect of the medium viscosity on kinetics parameters of lactate dehydrogenase reaction was studied. The viscosity increase results in a sharp decline in the catalytic rate for both the pyruvate reduction and lactate oxidation reactions. It is shown that the catalytic step and its associated conformational motions is the only step which is considerably retarded when the viscosity increases. The reaction is not sensitive to changes in the dielectric properties of the medium. An inverse power function observed between the rate constant and viscosity cannot be explained by the theory of absolute reaction rates. However, it can easily be interpreted on the basis of the Kramers theory dealing with the transition over the activation barrier as a diffusional motion in the field of random forces. The influence of the medium's viscosity on the kinetic parameters indicates the existence of strong coupling between the dynamics of the solvent and the conformational motions of the protein molecule, which are correlated with the catalytic step.     

Active transport: Definitions and criteria

The thermodynamic definition of active transport is restated in terms of the rate of entropy production. A substance is said to be transported actively when the product of its flux by the force acting upon it across the membrane is negative. A general expression for the rate of entropy production in a complex membrane is which chemical reactions may occur is given, and this expression is developed for a somewhat simplified case. The resulting relation is used as a basis for defining and establishing experimental criteria for types of active transport. Two basic types are distinguished and are designatedcoupled transport andforced transport, respectively. Only the latter type is dependent upon energyielding chemical reactions.     

The effect of PAF in the cochlea of guinea pigs

The influence of 10(-10) and 10(-9) M PAF/animal given into the jugular vein over 30 sec on inner ear potentials, i.e. endolymphatic potential (EP), summating potential (SP) and cochlear microphonics (CM) was investigated. The EP showed the most pronounced changes. When infusing a specific PAF receptor antagonist, ginkgolide B, or the TXA2 receptor antagonist, sulotraban, before the the infusion of PAF, the changes in cochlear potentials could be completely prevented. A second TXA2 receptor antagonist, daltroban, did not effectively prevent PAF actions. It is hypothesized that these PAF effects are due to an interference with ion transport in the non-sensory structures of the inner ear.     

Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase

In order to better understand how the complex, densely packed, heterogeneous milieu of a cell influences enzyme kinetics, we exposed opposing reactions catalyzed by yeast alcohol dehydrogenase (YADH) to both synthetic and protein crowders ranging from 10 to 550 kDa. The results reveal that the effects from macromolecular crowding depend on the direction of the reaction. The presence of the synthetic polymers, Ficoll and dextran, decrease V_max and K_m for ethanol oxidation. In contrast, these crowders have little effect or even increase these kinetic parameters for acetaldehyde reduction. This increase in V_max is likely due to excluded volume effects, which are partially counteracted by viscosity hindering release of the NAD⁺ product. Macromolecular crowding is further complicated by the presence of a depletion layer in solutions of dextran larger than YADH, which diminishes the hindrance from viscosity. The disparate effects from 25 g/L dextran or glucose compared to 25 g/L Ficoll or sucrose reveals that soft interactions must also be considered. Data from binary mixtures of glucose, dextran, and Ficoll support this “tuning” of opposing factors. While macromolecular crowding was originally proposed to influence proteins mainly through excluded volume effects, this work compliments the growing body of evidence revealing that other factors, such as preferential hydration, chemical interactions, and the presence of a depletion layer also contribute to the overall effect of crowding.     

Bioavailability of trace metals to aquatic microorganisms: importance of chemical, biological and physical processes on biouptake

An important challenge in environmental biogeochemistry is the determination of the bioavailability of toxic and essential trace compounds in natural media. For trace metals, it is now clear that chemical speciation must be taken into account when predicting bioavailability. Over the past 20 years, equilibrium models (free ion activity model (FIAM), biotic ligand model (BLM)) have been increasingly developed to describe metal bioavailability in environmental systems, despite the fact that environmental systems are always dynamic and rarely at equilibrium. In these simple (relatively successful) models, any reduction in the available, reactive species of the metal due to competition, complexation or other reactions will reduce metal bioaccumulation and thus biological effects. Recently, it has become clear that biological, physical and chemical reactions occurring in the immediate proximity of the biological surface also play an important role in controlling trace metal bioavailability through shifts in the limiting biouptake fluxes. Indeed, for microorganisms, examples of biological (transport across membrane), chemical (dissociation kinetics of metal complexes) and physical (diffusion) limitation can be demonstrated. Furthermore, the organism can employ a number of biological internalization strategies to get around limitations that are imposed on it by the physicochemistry of the medium. The use of a single transport site by several metals or the use of several transport sites by a single metal further complicates the prediction of uptake or effects using the simple chemical models. Finally, once inside the microorganism the cell is able to employ a large number of strategies including complexation, compartmentalization, efflux or the production of extracellular ligands to minimize or optimize the reactivity of the metal. The prediction of trace metal bioavailability will thus require multidisciplinary advances in our understanding of the reactions occurring at and near the biological interface. By taking into account medium constraints and biological adaptability, future bioavailability modeling will certainly become more robust.     

Trafficking coordinate description of intracellular transport control of signaling networks

Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized chemical reactions. There are many important situations, however, in which the properties of the compartments change continuously in a way that cannot naturally be described by chemical reactions. Here, we develop an approach based on transport along a trafficking coordinate to precisely describe these processes and we apply it explicitly to the TGF-β signal transduction network, which plays a fundamental role in many diseases and cellular processes. The results of this newly introduced approach accurately capture the distinct TGF-β signaling dynamics of cells with and without cancerous backgrounds and provide an avenue to predict the effects of chemical perturbations in a way that closely recapitulates the observed cellular behavior.     

The electrochemical proton gradient and phenylalanine transport in Escherichia coli irradiated with near-ultraviolet light.

Irradiation of Escherichia coli with near-ultraviolet (near-UV) light diminished the electrochemical proton gradient and the accumulation of L-phenylalanine. Inhibitors known to collapse the proton gradient and the comparison of two techniques measuring the electrical potential substantiated the estimates made. At several fluences (doses), a linear relationship was observed between the phenylalanine gradient and the combined electrical and chemical potentials (the electrochemical proton gradient), suggesting a close coupling between them. However, additional effects of near-UV light on the phenylalanine permease were not discounted. The combined potentials provided sufficient energy for the observed accumulation of phenylalanine, assuming a proton to amino acid cotransport ratio of 1. An increase in membrane permeability did not contribute to the loss of phenylalanine transport, as shown by an increase in the rate and extent of alpha-methylglucoside uptake.     

Photostability and Interaction of Ascorbic Acid in Cream Formulations

The kinetics of photolysis of ascorbic acid in cream formulations on UV irradiation has been studied using a specific spectrophotometric method with a reproducibility of ±5%. The apparent first-order rate constants (k _obs) for the photolysis of ascorbic acid in creams have been determined. The photoproducts formed in the cream formulations include dehydroascorbic acid and 2,3-diketogulonic acid. The photolysis of ascorbic acid appears to be affected by the concentration of active ingredient, pH, and viscosity of the medium and formulation characteristics. The study indicates that the ionized state and redox potentials of ascorbic acid are important factors in the photostability of the vitamin in cream formulations. The viscosity of the humectant present in the creams appears to influence the photostability of ascorbic acid. The results show that the physical stability of the creams is an important factor in the stabilization of the vitamin. In the cream formulations stored in the dark, ascorbic acid undergoes aerobic oxidation and the degradation is affected by similar factors as indicated in the photolysis reactions. The rate of oxidative degradation in the dark is about seventy times slower than that observed in the presence of light.