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At least 613 records · Page 34Linked to original sources
PubMed1995

Dynamics of peak dispersion in capillary zone electrophoresis including wall adsorption I. Theoretical model and results of simulation.

A mathematical model is described for the simulation of peak profiles in capillary zone electrophoresis taking wall adsorption into account. It is based on such physico-chemical relations as mass balance equations, sorption rate equations and appropriate boundary conditions. The numerical solution of the model is carried out, allowing the depiction of the concentration profile of the sample in the capillary as a result of the dynamics of the processes involved, which depend on a number of input parameters: rate constants, adsorption isotherms, column dimensions, field strength etc. Four cases are discussed in detail, namely those with either slow or fast adsorption kinetics and linear or nonlinear isotherms.

Adsorption↗
PubMed2002

A theoretical model of adolescent suicide and some evidence from US data.

Suicide rates for adolescents have doubled since 1970 and tripled since 1960, even as rates for other age groups have declined. Using a Becker-type model of household production and consumption, we demonstrate conditions under which utility maximizing parents allocate time away from time-intensive commodities like children's well-being, and towards market work and less time-intensive consumption commodities. This reallocation of time towards market work has mixed effects on children' mental health: higher money income tends to improve family and children's well-being, but the loss of parental time has an opposite effect on children's mental health and increases the risk of adolescent suicide. Empirical evidence using state panel regressions of adolescent suicide rates on economic, social and demographic variables is consistent with predictions based on our model; our results indicate that the favorable effect of higher incomes has more than offset the negative effect of lost parental time.

Adolescent↗
PubMed1995

Theoretical model for water diffusion in tissues.

Water diffusion in a tissue model is studied both analytically and numerically. Tissue is regarded as a periodic array of boxes surrounded by partially permeable membranes (cells), embedded in an extracellular medium. intracellular and extracellular diffusion coefficients may differ. Expressions for the apparent diffusion coefficients (ADC) in isotropic and nonisotropic tissues are derived and compared with Monte Carlo simulations. Calculated ADCs disagree with values obtained from the widely used "fast exchange" formula. Effects of differences between intracellular and extracellular T2 relaxation times on measured values of ADC and T2 are discussed. The general analysis is specifically applied to the changes occurring in ADC following ischemic insults to brain tissue. It is found that although membranes affect ADC significantly, the observed changes in diffusion cannot be due to reduced membrane permeabilities. They may result from the combined effect of changes in cellular volume fraction, extracellular and intracellular diffusion.

Acute Disease↗
PubMed2005

Amphoteric, buffering chromatographic beads for proteome prefractionation. I: theoretical model.

The possibility is reported here of fractionating proteins on amphoteric, buffering resins via ion-exchange chromatography. A given protein's adsorption to a particular amphoteric buffering resin is characterized by a bell-shaped curve in which the maximum protein binding capacity is observed at an optimum pH value lying approximately midway between the isoelectric point values (pI) of the resin and the protein. On either side of this maximum the protein binding capacity declines steadily, reaching zero at the pI of either the protein or exchanger. For instance, on beads of pI equal to 8, four proteins, two acidic (bovine albumin and ovalbumin) and two basic (cytochrome c and lysozyme), exhibit binding curves reaching zero values for the whole set when the exchanger is conditioned at pH 8.0. Away from the pI, and on both sides of the pH scale, the bell-shaped adsorption curves reach a maximum, for each protein, at a pH located at the midpoint between the pI values of each protein and that of the exchanger, and decline steadily to reach zero at the pI value of each protein species. Separation of model proteins using different amphoteric buffering resins of various pI was possible at different pH values according to both the pI of the proteins and of the exchangers. It was also demonstrated, using surface enhanced laser desorption/ionization mass spectrometry and two dimensional electrophoretic mapping, that separation of an Escherichia coli cell lysate on columns packed with amphoteric buffering resins of different pI and titrated to a particular pH value, delivered two distinctly different fractions, i.e. characteristically composed of, on the one hand, proteins having a pI below the buffer pH (the 'adsorbed' fraction), and on the other, of alkaline proteins possessing a pI above the pH of the buffer (the 'unadsorbed' fraction). This approach represents an attractive addition and/or alternative to the armory of protein pre-fractionation techniques currently employed in proteomics.

Albumins↗
PubMed2006

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Type II restriction enzymes are commercially important deoxyribonucleases and very attractive targets for protein engineering of new specificities. At the same time they are a very challenging test bed for protein structure prediction methods. Typically, enzymes that recognize different sequences show little or no amino acid sequence similarity to each other and to other proteins. Based on crystallographic analyses that revealed the same PD-(D/E)XK fold for more than a dozen case studies, they were nevertheless considered to be related until the combination of bioinformatics and mutational analyses has demonstrated that some of these proteins belong to other, unrelated folds PLD, HNH, and GIY-YIG. As a part of a large-scale project aiming at identification of a three-dimensional fold for all type II REases with known sequences (currently approximately 1000 proteins), we carried out preliminary structure prediction and selected candidates for experimental validation. Here, we present the analysis of HpaI REase, an ORFan with no detectable homologs, for which we detected a structural template by protein fold recognition, constructed a model using the FRankenstein monster approach and identified a number of residues important for the DNA binding and catalysis. These predictions were confirmed by site-directed mutagenesis and in vitro analysis of the mutant proteins. The experimentally validated model of HpaI will serve as a low-resolution structural platform for evolutionary considerations in the subgroup of blunt-cutting REases with different specificities. The research protocol developed in the course of this work represents a streamlined version of the previously used techniques and can be used in a high-throughput fashion to build and validate models for other enzymes, especially ORFans that exhibit no sequence similarity to any other protein in the database.

Amino Acid Sequence↗
PubMed2007

Theoretical model of human apolipoprotein B100 tertiary structure.

Low density lipoprotein (LDL) particles are the main cholesterol carriers in human plasma. The organization of the particle, composed of apolar lipids and phospholipid monolayer stabilized by apolipoprotein B100 (apoB), is highly complex and still unknown. ApoB is an extremely large protein (4563 amino acids) and very little is known about its structure. A 3D model of the N-terminal region has been recently proposed and has provided interesting insights about the physico-chemical properties of the protein and putative interaction zones with lipids. In the present article, we propose the first tentative 3D modelling for most remaining residues. All predicted features emerging from the models are confronted with agreement to experimental data available. Using different up-to-date prediction methods, we decomposed the protein into eight domains and predicted 3D structure for each of them. The analysis of hydrophobic patches, polar regions, coupled with functional predictions based on the 3D models, gives new clues to understanding of the functional role of apoB. We suggest precise regions putatively involved in the lipid interactions, and discuss the position of apoB on the LDL particle. Finally, we propose relative organization of the domains, providing a shape quite compatible with the low resolution electron microscopy map.

Amino Acid Sequence↗
PubMed1996

Direct Spectroscopic Measurement and Theoretical Modeling of the Diffusion of a Single Species in a Two-Phase Unstirred System

The diffusion of 8-hydroxyquinoline from an aqueous phase into an organic phase and vice versa has been measured using a static transfer cell. The total change in concentration in either phase can be accurately predicted by considering one-dimensional diffusion in the plane normal to the oil/water interface. It was found that any turbulent mixing that occurs during the initiation of the experiment dies out in the first few minutes. The relevance of this technique to the study of metal ion extraction from an aqueous phase into an organic phase is discussed.

Journal Article↗
PubMed2000

A Theoretical Model of Pulmonary Surfactant Multilayer Collapse under Oscillating Area Conditions.

Monolayers of adsorbed pulmonary surfactant collapse under compression and respread to the interface when the area expands. These mechanisms contribute to the large area hysteresis seen experimentally in a pulsating bubble surfactometer. This paper presents an analytical model which adds monolayer collapse and respreading to the more standard transport processes (diffusion, adsorption, and desorption). The model is robust and can mimic a large range of responses, from that of an insoluble monolayer to the large area hysteresis indicative of collapse and respreading. Our model suggests that multilayer dynamics are necessary to mimic the ultralow surface tensions of pulmonary surfactant. Copyright 2000 Academic Press.

Journal Article↗
PubMed2001

Folding energetics of ligand binding proteins. I. Theoretical model.

Heat capacity curves as obtained from differential scanning calorimetry are an outstanding source for molecular information on protein folding and ligand-binding energetics. However, deconvolution of C(p) data of proteins in the presence of ligands can be compromised by indeterminacies concerning the correct choice of the statistical thermodynamic ensemble. By convent, the assumption of constant free ligand concentration has been used to derive formulae for the enthalpy. Unless the ligand occurs at large excess, this assumption is incorrect. Still the relevant ensemble is the grand canonical ensemble. We derive formulae for both constraints, constancy of total or free ligand concentration and illustrate the equations by application to the typical equilibrium Nx <=> N + x <=> D + x. It is demonstrated that as long as the thermodynamic properties of the ligand can be completely corrected for by performing a reference measurement, the grand canonical approach provides the proper and mathematically significantly simpler choice. We demonstrate on the two cases of sequential or independent ligand-binding the fact, that similar binding mechanisms result in different and distinguishable heat capacity equations. Finally, we propose adequate strategies for DSC experiments as well as for obtaining first estimates of the characteristic thermodynamic parameters, which can be used as starting values in a global fit of DSC data.

Binding Sites↗
PubMed1993

Pressure changes in the eye due to an injection of inert gases: a theoretical model.

In the repair of retinal tears and detachments, the vitreous humor is often completely replaced with a temporary mixture of gases, one of which is not normally found in the bloodstream. The resulting bubble can then support the healing retina. There is diffusion of gases, however, from the bubble into the bloodstream and vice versa. This alters the intraocular pressure, with possible adverse consequences, as the intraocular pressure must be maintained within a certain range for the procedure to be successful. A simple model has been developed to predict the evolution of intraocular pressure over time, given a certain initial mixture of injected gases. This model could be useful in determining what mixture to use to support effectively and safely a healing retina.

Capillaries↗
PubMed1999

Bacterial lysis by phage--a theoretical model.

The similarity to materials corrosion is invoked to develop a model for phage-infected bacterial lysis based on the statistics of extremes. The importance of cell size, envelope thickness and lysozyme eclipse time on the final probability distribution of lysis is considered. Experiments are suggested to test the model.

Animals↗