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A cellular automata model of ligand passage over a protein hydrodynamic landscape.

The subject of ligand passage to an active site on a protein is addressed. Current views on the mechanism and the possible role of surface water are discussed. A theory is presented in which the pattern of hydropathic states of protein surface amino acid side chains is invoked as the influence on the relative hydrophobic effects of nearby water. The theory describes a ligand passage through the hydrodynamic near-surface water which exhibits temporary organized cavities resembling the chreodes introduced by Waddington. The passage of the ligand to the active site is facilitated by this dynamic mechanism. Cellular automata models of preferential directional diffusion through these chreodes support the theory. The theory may be invoked to explain a number of ligand-active site observations and serves as an idea for further studies.

Animals↗

Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.

Understanding X-ray crystallographic diffuse scattering is likely to improve our comprehension of equilibrium collective protein dynamics. Here, using molecular dynamics (MD) simulation, a detailed analysis is performed of the origins of diffuse scattering in crystalline Staphylococcal nuclease, for which the complete diffuse scattering pattern has been determined experimentally. The hydrogen-atom contribution and the scattering range over which the scattering can be considered to be a sum of solvent and protein scattering are determined. Two models of correlated protein motion are investigated by calculating the model-derived diffuse scattering and comparing with the scattering calculated directly from MD trajectories. In one model, previously used in diffuse scattering interpretation, the atomic displacement correlations decay isotropically with increasing separation. Model correlation lengths are obtained by refining the model scattering against the simulation-derived scattering pattern, and are found to be significantly different from those correlation lengths derived directly from the MD trajectories. Furthermore, the convergence between the model-derived and MD-derived scattering is poor. The second model, in which the displacement correlations are calculated from the principal components of the MD trajectories, is capable of fully reproducing the MD-derived diffuse scattering if the approximately 50% lowest-frequency modes are included. However, a small number ( approximately 10) of lowest-frequency and largest-amplitude modes dominates the diffuse scattering and thus the correlated protein motions. A detailed analysis of the principal components is performed. In particular, the effective free energy profile associated with each principle mode is analyzed and the eigenfrequency and damping coefficient computed using a model of Brownian dynamics. Those collective modes with effective frequencies below approximately 0.5 THz, including those that determine the diffuse scattering, are overdamped.

Anisotropy↗

Weak dependence of mobility of membrane protein aggregates on aggregate size supports a viscous model of retardation of diffusion.

Proteins in plasma membranes diffuse more slowly than proteins inserted into artificial lipid bilayers. On a long-range scale (>250 nm), submembrane barriers, or skeleton fences that hinder long-range diffusion and create confinement zones, have been described. Even within such confinement zones, however, diffusion of proteins is much slower than predicted by the viscosity of the lipid. The cause of this slowing of diffusion on the micro scale has not been determined and is the focus of this paper. One way to approach this question is to determine the dependence of particle motion on particle size. Some current models predict that the diffusion coefficient of a membrane protein aggregate will depend strongly on its size, while others do not. We have measured the diffusion coefficients of membrane glycoprotein aggregates linked together by concanavalin A molecules bound to beads of various sizes, and also the diffusion coefficients of individual concanavalin A binding proteins. The measurements demonstrate at most a weak dependence of diffusion coefficient on aggregate size. This finding supports retardation by viscous effects, and is not consistent with models involving direct interaction of diffusing proteins with cytoskeletal elements.

Animals↗

Glancing-angle ion enhanced surface diffusion on gaAs(001) during molecular beam epitaxy.

We describe the effects of glancing incidence 3-4 keV Ar ion bombardment on homoepitaxial growth on vicinal GaAs(001). The average adatom lifetime on surface terraces, measured during growth using specular ion scattering, decreased monotonically with increasing ion current density. The results indicated that surface diffusivity was increased by the ions. The ion beam also suppressed growth oscillations and decreased the film surface roughness. This indicates a change from two-dimensional island nucleation to step-flow growth due to increased adatom surface diffusivity. A simple model, involving direct momentum transfer from ions to adatoms, is shown to be consistent with the measured enhanced diffusion.

Journal Article↗

Gene networks capable of pattern formation: from induction to reaction-diffusion.

One of the main aims of developmental biology is to understand how a single and apparently homogeneous egg cell achieves the intricate complexity of the adult. Here we present two models to explain the generation of developmental patterns through interactions at the gene level. One model considers direct-contact induction between cells while the other takes into account diffusion of hormones. We show that sets of cells involving identical gene networks and communicating through hormones spontaneously exhibit ordered patterns. We have characterized these patterns and the specific networks responsible for them. The models allow to (i) compare diffusion and direct-contact induction processes as mechanisms of pattern generation; (ii) identify the possible range of behaviour of real gene networks and (iii) suggest causal mechanisms to generate known patterns. The evolutionary implications are discussed.

Animals↗

A model for protein-DNA interaction dynamics.

We map a simplified version of the protein-DNA interaction problem into an Ising-model in a random magnetic field. The model includes a "head" which moves along the chain while interacting with the underlying spins. The head moves by using the statistical fluctuations of base openings. A Monte Carlo (MC) simulation of this model reveals the possibility of biased diffusion in one direction, followed by sequence identification and binding. The model provides some insight into the mechanisms used by some repressor proteins to diffuse and bind to specific DNA-binding sites.

Animals↗

Aqueous Solutions of Ethyl (Hydroxyethyl) Cellulose and Hydrophobic Modified Ethyl (Hydroxyethyl) Cellulose Polymer: Dynamic Surface Tension Measurements

The dynamic surface tension of aqueous solutions of ethyl (hydroxyethyl) cellulose (EHEC) and hydrophobic modified ethyl (hydroxyethyl) cellulose (HM-EHEC) were determined using the maximum bubble pressure method. Values were monitored over surface lifetimes ranging from 0.15 to 2.5 s (after dead time corrections). In the low concentration range (<100 ppm) HM-EHEC was shown to be more surface active, and the presence of salt (0.1 M) was shown to increase the surface activity of both polymer systems. The results were compared with surface tension measurements carried out over longer time scales, determined using the du Nouy ring technique. From these results, isotherms were constructed relating surface tension to surface aging time. Although the results could not be directly correlated to interfacial diffusion models, the isotherms were found to be comparable to previous data reported for lower-molecular-weight poly(oxyethylene ether) surfactants and a higher-molecular-weight EHEC polymer determined using the pendant drop technique. Essentially, the isotherms could be divided into distinct regions: induction period, fast fall region where surface coverage occurs fairly rapidly, and finally the meso-equilibrium region. From the Gibbs equation, the number of segments of polymer per unit surface area at saturated adsorption levels was calculated over regions of different aging times, and the results are discussed in terms of configuration changes of the polymer at the interface. Copyright 1997Academic Press

Journal Article↗

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm.

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Journal Article↗

Inhibition of glyoxalase I by the enediol mimic S-(N-hydroxy-N-methylcarbamoyl)glutathione. The possible basis of a tumor-selective anticancer strategy.

In principle, competitive inhibitors of glyoxalase I that also serve as substrates for the thioester hydrolase glyoxalase II might function as tumor-selective anti-cancer agents, given the role of these enzymes in removing cytotoxic methylglyoxal from cells and the observation that glyoxalase II activity is abnormally low in some types of cancer cells. In support of the feasibility of this anticancer strategy, an inhibitor of this type has been synthesized by a thioester-interchange reaction between glutathione and N-hydroxy-N-methylcarbamate 4-chlorophenyl ester to give S-(N-hydroxy-N-methylcarbamoyl)glutathione (1). This compound was designed to be a tight-binding inhibitor of glyoxalase I, on the basis of its stereoelectronic similarity to the enediol(ate) intermediate that forms along the reaction pathway of this enzyme. Indeed, 1 is a competitive inhibitor of yeast glyoxalase I, with an inhibition constant (Ki = 68 microM) that is approximately 30-fold lower than that reported for S-D-lactoylglutathione and approximately 7-fold lower than the Km for glutathione-methylglyoxal thiohemiacetal. In addition, 1 is a substrate for bovine liver glyoxalase II, with a Km (0.48 mM) approximately equal to that of the normal substrate S-D-lactoyglutathione and a kcat approximately 2 x 10(-5)-fold that of the normal substrate. Membrane transport studies show that 1 can be delivered into human erythrocytes (used here as a model cell) either by direct diffusion of 1 across the cell membrane or by more rapid diffusion of the glycylethyl ester of 1 across the cell membrane, followed by the catalyzed hydrolysis of the ester to give 1.

Animals↗

Cell proliferation drives neural crest cell invasion of the intestine.

A general mathematical model of cell invasion is developed and validated with an experimental system. The model incorporates two basic cell functions: non-directed (diffusive) motility and proliferation to a carrying capacity limit. The model is used here to investigate cell proliferation and motility differences along the axis of an invasion wave. Mathematical simulations yield surprising and counterintuitive predictions. In this general scenario, cells at the invasive front are proliferative and migrate into previously unoccupied tissues while those behind the front are essentially nonproliferative and do not directly migrate into unoccupied tissues. These differences are not innate to the cells, but are a function of proximity to uninvaded tissue. Therefore, proliferation at the invading front is the critical mechanism driving apparently directed invasion. An appropriate system to experimentally validate these predictions is the directional invasion and colonization of the gut by vagal neural crest cells that establish the enteric nervous system. An assay using gut organ culture with chick-quail grafting is used for this purpose. The experimental results are entirely concordant with the mathematical predictions. We conclude that proliferation at the wavefront is a key mechanism driving the invasive process. This has important implications not just for the neural crest, but for other invasion systems such as epidermal wound healing, carcinoma invasion and other developmental cell migrations.

Animals↗

Random-walk models of cell dispersal included in mechanobiological simulations of tissue differentiation.

Computational models have shown that biophysical stimuli can be correlated with observed patterns of tissue differentiation, and simulations have been performed that predict the time course of tissue differentiation in, for example, long bone fracture healing. Some simulations have used a diffusion model to simulate the migration and proliferation of cells with the differentiating tissue. However, despite the convenience of the diffusion model, diffusion is not the mechanism of cell dispersal: cells disperse by crawling or proliferation, or are transported in a moving fluid. In this paper, a random-walk model (i.e., a stochastic model), with and without a preferred direction, is studied as an approach to simulate cell proliferation/migration in differentiating tissues and it is compared with the diffusion model. A simulation of tissue differentiation of gap tissue in a two-dimensional model of a bone/implant interface was performed to demonstrate the differences between diffusion vs. random walk with a preferred direction. Results of diffusion and random-walk models are similar with respect to the change in the stiffness of the gap tissue but rather different results are obtained regarding tissue patterning in the differentiating tissues; the diffusion approach predicted continuous patterns of tissue differentiation whereas the random-walk model showed a more discontinuous pattern-histological results are not available that can unequivocally establish which is most similar to experimental observation. Comparing isotropic to anisotropic random walk (preferred direction of proliferation and cell migration), a more rapid reduction of the relative displacement between implant and bone is predicted. In conclusion, we have shown how random-walk models of cell dispersal and proliferation can be implemented, and shown where differences between them exist. Further study of the random-walk model is warranted, given the importance of cell seeding and cell dispersal/proliferation in many mechanobiological problems.

Animals↗

Fundamental properties of local anesthetics: half-maximal blocking concentrations for tonic block of Na+ and K+ channels in peripheral nerve.

UNLABELLED: Local anesthetics suppress excitability by interfering with ion channel function. Ensheathment of peripheral nerve fibers, however, impedes diffusion of drugs to the ion channels and may influence the evaluation of local anesthetic potencies. Investigating ion channels in excised membrane patches avoids these diffusion barriers. We investigated the effect of local anesthetics with voltage-dependent Na+ and K+ channels in enzymatically dissociated sciatic nerve fibers of Xenopus laevis using the patch clamp method. The outside-out configuration was chosen to apply drugs to the external face of the membrane. Local anesthetics reversibly blocked the transient Na+ inward current, as well as the steady-state K+ outward current. Half-maximal tonic inhibiting concentrations (IC50), as obtained from concentration-effect curves for Na+ current block were: tetracaine 0.7 microM, etidocaine 18 microM, bupivacaine 27 microM, procaine 60 microM, mepivacaine 149 microM, and lidocaine 204 microM. The values for voltage-dependent K+ current block were: bupivacaine 92 microM, etidocaine 176 microM, tetracaine 946 microM, lidocaine 1118 microM, mepivacaine 2305 microM, and procaine 6302 microM. Correlation of potencies with octanol:buffer partition coefficients (logP0) revealed that ester-bound local anesthetics were more potent in blocking Na+ channels than amide drugs. Within these groups, lipophilicity governed local anesthetic potency. We conclude that local anesthetic action on peripheral nerve ion channels is mediated via lipophilic drug-channel interactions. IMPLICATIONS: Half-maximal blocking concentrations of commonly used local anesthetics for Na+ and K+ channel block were determined on small membrane patches of peripheral nerve fibers. Because drugs can directly diffuse to the ion channel in this model, these data result from direct interactions of the drugs with ion channels.

Anesthetics, Local↗

Extravascular fluid dynamics of the embryonic chick wing bud.

While a number of models of positional information in the chick wing bud have involved the diffusion of morphogens to establish chemical gradients of morphogenetic activity, only recently have there been attempts to characterize the milieu in which such diffusion must take place. We report an analysis of the fluid dynamics of the extravascular (interstitial) spaces of stage 22-25 chick wing buds, into which aqueous aniline blue dye was microinjected as a visible, unreactive tracer. Six sites along the antero-posterior (A-P) and proximo-distal (P-D) axes were chosen for study. Injections of dye into the posterior half of the wing bud exhibited marked directionality of extravascular transport (mean of all posterior sites = 68%), while anterior injections showed little or no directionality (mean of all anterior sites = 13%). All instances of directed dye movement were disto-proximal, the same direction as the blood flow through the marginal veins. In embryos gassed in situ with CO2, which reversibly stopped the heartbeat and vascular flow, directionality was abolished, yet diffusion rates were unaffected. Posterior disto-proximal extravascular dye movement was correlated with the greater diameter, flow velocity, and volume flow rate of the posterior marginal vein, compared to the anterior marginal vein. Radial diffusion rates were measured, and posterior disto-proximal rates were corrected for measured disto-proximal directionality by the use of a simple diffusion-translation model. Three-way analysis of variance showed that directionality-uncorrected disto-proximal rates in posterior sites were not significantly different from anterior radial rates, but that directionality-corrected posterior rates did differ significantly (P less than 0.0001). A significant stage effect (P less than 0.005) and a significant interaction between the A-P axis and stage (P less than 0.05) were also found. We hypothesize that the spatial arrangement and flow patterns of the vasculature physically determine the fluid dynamics of the interstitium. Based on these observations, we also suggest that disto-proximal extravascular fluid movement in the posterior wing bud presents a barrier to the free diffusion of aqueous molecules, including morphogens originating in the "zone of polarizing activity."

Analysis of Variance↗

Direct determination of the kinetics of oxygen diffusion to the photocytes of a bioluminescent elaterid larva, measurement of gas- and aqueous-phase diffusional barriers and modelling of oxygen supply.

We describe the development and use of a direct kinetic technique to determine the time taken for oxygen to diffuse from the external environment into the light-producing cells (photocytes) in the prothorax of bioluminescent larvae of Pyrearinus termitilluminans. This was achieved by measuring the time course of the pseudoflash induced through sequential anoxia followed by normoxia. We have also determined the separate times taken for this oxygen diffusion in gaseous and tissue (predominantly aqueous) phases by using helium and nitrogen as the carrier gas. Of the total time taken for diffusion, that in the gas phase required 613+/-136 ms (mean +/- s.e. m., N=5) whilst that in the aqueous phase required 1313+/-187 ms. These values imply pathlengths of diffusion in the gaseous and aqueous phases of 4.80x10(-)(3)+/-0.53x10(-)(3) and 8. 89x10(-)(5)+/-0.61x10(-)(5 )m, respectively. In addition, the pathlength of gas-phase diffusion was used to derive a parameter relating to the tortuosity of the tracheal system. These values, together with those obtained upon bioluminescent oxygen consumption, have been used to model oxygen supply to the photocyte. From these studies, it would also appear that the modulation of tracheolar fluid levels might be a significant mechanism of control of tissue oxygen levels in at least some insects.

Animals↗

An integrated computational/experimental model of tumor invasion.

The intracellular and extracellular dynamics that govern tumor growth and invasiveness in vivo remain poorly understood. Cell genotype and phenotype, and nutrient, oxygen, and growth factor concentrations are key variables. In previous work, using a reaction-diffusion mathematical model based on variables that directly describe tumor cell cycle and biology, we formulated the hypothesis that tumor morphology is determined by the competition between heterogeneous cell proliferation caused by spatial diffusion gradients, e.g., of cell nutrients, driving shape instability and invasive tumor morphologies, and stabilizing mechanical forces, e.g., cell-to-cell and cell-to-matrix adhesion. To test this hypothesis, we here obtain variable-based statistics for input to the mathematical model from in vitro human and rat glioblastoma cultures. A linear stability analysis of the model predicts that glioma spheroid morphology is marginally stable. In agreement with this prediction, for a range of variable values, unbounded growth of the tumor mass and invasion of the environment are observed in vitro. The mechanism of invasion is recursive subspheroid component development at the tumor viable rim and separation from the parent spheroid. Results of computer simulations of the mathematical model closely resemble the morphologies and spatial arrangement of tumor cells from the in vitro model. We propose that tumor morphogenesis in vivo may be a function of marginally stable environmental conditions caused by spatial variations in cell nutrients, oxygen, and growth factors, and that controlling these conditions by decreasing spatial gradients could benefit treatment outcomes, whereas current treatment, and especially antiangiogenic therapy, may trigger spatial heterogeneity (e.g., local hypoxia), thus causing invasive instability.

Animals↗

An integrated sorption-diffusion model for the calculation of consistent distribution and diffusion coefficients in compacted bentonite.

A thermodynamic sorption model and a diffusion model based on electric double layer (EDL) theory are integrated to yield a surface chemical model that treats porewater chemistry, surface reactions, and the influence of charged pore walls on diffusing ions in a consistent fashion. The relative contribution of Stern and diffuse layer to the compensation of the permanent surface charge represents a key parameter; it is optimized for the diffusion of Cs in Kunipia-F bentonite, at a dry density of 400 kg/m3. The model is then directly used to predict apparent diffusivities (Da) of Cs, Sr, Cl-, I- and TcO4- and corresponding distribution coefficients (Kd) of Cs and Sr in different bentonites as a function of dry density, without any further adjustment of surface chemical and EDL parameters. Effective diffusivities (De) for Cs, HTO, and TcO4- are also calculated. All calculated values (Da, De, Kd) are fully consistent with each other. A comparison with published, measured data shows that the present model allows a good prediction and consistent explanation of (i) apparent and effective diffusivities for cations, anions, and neutral species in compacted bentonite, and of (ii) Kd values in batch and compacted systems.

Adsorption↗

Anisotropy in granular media: classical elasticity and directed-force chain network.

A general approach is presented for understanding the stress response function in anisotropic granular layers in two dimensions. The formalism accommodates both classical anisotropic elasticity theory and linear theories of anisotropic directed-force chain networks. Perhaps surprisingly, two-peak response functions can occur even for classical, anisotropic elastic materials, such as triangular networks of springs with different stiffnesses. In such cases, the peak widths grow linearly with the height of the layer, contrary to the diffusive spreading found in "stress-only" hyperbolic models. In principle, directed-force chain networks can exhibit the two-peak, diffusively spreading response function of hyperbolic models, but all models in a particular class studied here are found to be in the elliptic regime.

Journal Article↗

Real-time assessment of spatial and temporal coupled catalysis within polyelectrolyte microcapsules containing coimmobilized glucose oxidase and peroxidase.

The encapsulation of biological enzymes within polyelectrolyte microcapsules is an important step toward microscale devices for processing and analytical applications, one which could be applied to the realization of minimally invasive sensing technology. In this work, the encapsulation and functional characterization of a bienzymatic coupled catalytic system within polyelectrolyte microcapsules is described. The two components, glucose oxidase (GOx) and horseradish peroxidase (HRP), were coprecipitated with calcium carbonate microspheres, followed by layer-by-layer assembly to form ultrathin polymer film coatings that act as capsule walls after removal of the sacrificial carbonate cores. Encapsulated concentrations of GOx and HRP were determined to be 19.7 +/- 1.0 and 29.4 +/- 3.6 mg/mL, respectively. An 85% decrease in the rate of glucose consumption relative to GOx and HRP in free solution was observed, which is attributed to substrate diffusion limitations. To further understand the temporal and spatial dynamics of the two-step reaction, a technique for monitoring microscale glucose consumption was developed using confocal imaging techniques. Time-based acquisition of capsule/Amplex Red suspensions was performed, from which it was observed that the high concentration of enzyme immobilized within the capsule walls resulted in a greater rate and quantity of glucose consumption at the capsule periphery when compared to glucose consumption within the capsule interior. These findings demonstrate the function of a bienzymatic catalytic system within the controlled environment of polyelectrolyte microspheres and a novel approach to analysis of the internal reactions using confocal imaging that will allow direct comparison with reaction-diffusion modeling and further explorations to optimize the distribution and activity of the encapsulated species.

Aspergillus niger↗