Biomedical subjects

Salvador Mafé

Publications and source records attributed to Salvador Mafé.

8 recordsLinked to original sources

PubMed2006

Blocking of an ion channel by a highly charged drug: modeling the effects of applied voltage, electrolyte concentration, and drug concentration.

We present a simple physical model to estimate the blocked pore probability of an ion channel that can be blocked by a highly charged drug in solution. The model is inspired by recent experimental work on the blocking of the PA(63) channel, involved in the anthrax toxin infection, by a highly charged drug [Karginov PNAS 102, 15075 (2005)]. The drug binding to the pore is highly specific but the strong dependence of blocking on the applied voltage and electrolyte concentration suggests that long range electrostatic interactions are important. Since basic electrostatic concepts rather than detailed molecular models are considered, the microscopic details of the channel blocking are ignored, although the model captures most of the qualitative characteristics of the problem.

Computer Simulation↗

PubMed2006

Ionic conduction, rectification, and selectivity in single conical nanopores.

Modern track-etching methods allow the preparation of membranes containing a single charged conical nanopore that shows high ionic permselectivity due to the electrical interactions of the surface pore charges with the mobile ions in the aqueous solution. The nanopore has potential applications in electrically assisted single-particle detection, analysis, and separation of biomolecules. We present a detailed theoretical and experimental account of the effects of pore radii and electrolyte concentration on the current-voltage and current-concentration curves. The physical model used is based on the Nernst-Planck and Poisson equations. Since the validity of continuum models for the description of ion transport under different voltages and concentrations is recognized as one of the main issues in the modeling of future applications, special attention is paid to the fundamental understanding of the electrical interactions between the nanopore fixed charges and the mobile charges confined in the reduced volume of the inside solution.

Biological Transport↗

PubMed2005

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel.

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.

Binding Sites↗

PubMed2005

Modeling electrochemical deposition inside nanotubes to obtain metal-semiconductor multiscale nanocables or conical nanopores.

Nanocables with a radial metal-semiconductor heterostructure have recently been prepared by electrochemical deposition inside metal nanotubes. First, a bare nanoporous polycarbonate track-etched membrane is coated uniformly with a metal film by electroless deposition. The film forms a working electrode for further deposition of a semiconductor layer that grows radially inside the nanopore when the deposition rate is slow. We propose a new physical model for the nanocable synthesis and study the effects of the deposited species concentration, potential-dependent reaction rate, and nanopore dimensions on the electrochemical deposition. The problem involves both axial diffusion through the nanopore and radial transport to the nanopore surface, with a surface reaction rate that depends on the axial position and the time. This is so because the radial potential drop across the deposited semiconductor layer changes with the layer thickness through the nanopore. Since axially uniform nanocables are needed for most applications, we consider the relative role of reaction and axial diffusion rates on the deposition process. However, in those cases where partial, empty-core deposition should be desirable (e.g., for producing conical nanopores to be used in single nanoparticle detection), we give conditions where asymmetric geometries can be experimentally realized.

Journal Article↗

PubMed2005

Kinetic modeling of ion conduction in KcsA potassium channel.

KcsA constitutes a potassium channel of known structure that shows both high conduction rates and selectivity among monovalent cations. A kinetic model for ion conduction through this channel that assumes rapid ion transport within the filter has recently been presented by Nelson. In a recent, brief communication, we used the model to provide preliminary explanations to the experimental current-voltage J-V and conductance-concentration g-S curves obtained for a series of monovalent ions (K(+),Tl(+), and Rb(+)). We did not assume rapid ion transport in the calculations, since ion transport within the selectivity filter could be rate limiting for ions other than native K(+). This previous work is now significantly extended to the following experimental problems. First, the outward rectification of the J-V curves in K(+) symmetrical solutions is analyzed using a generalized kinetic model. Second, the J-V and g-S curves for NH(4) (+) are obtained and compared with those of other ions (the NH(4) (+) J-V curve is qualitatively different from those of Rb(+) and Tl(+)). Third, the effects of Na(+) block on K(+) and Rb(+) currents through single KcsA channels are studied and the different blocking behavior is related to the values of the translocation rate constants characteristic of ion transport within the filter. Finally, the significantly decreased K(+) conductance caused by mutation of the wild-type channel is also explained in terms of this rate constant. In order to keep the number of model parameters to a minimum, we do not allow the electrical distance (an empirical parameter of kinetic models that controls the exponential voltage dependence of the dissociation rate) to vary with the ionic species. Without introducing the relatively high number of adjustable parameters of more comprehensive site-based models, we show that ion association to the filter is rate controlling at low concentrations, but ion dissociation from the filter and ion transport within the filter could limit conduction at high concentration. Although some experimental data from other authors were included to allow qualitative comparison with model calculations, the absolute values of the effective rate constants obtained are only tentative. However, the relative changes in these constants needed to explain qualitatively the experiments should be of significance.

Journal Article↗

PubMed2005

Ion conduction in the KcsA potassium channel analyzed with a minimal kinetic model.

We use a model by Nelson to study the current-voltage and conductance-concentration curves of bacterial potassium channel KcsA without assuming rapid ion translocation. Ion association to the channel filter is rate controlling at low concentrations, but dissociation and transport in the filter can limit conduction at high concentration for ions other than K+. The absolute values of the effective rate constants are tentative but the relative changes in these constants needed to qualitatively explain the experiments should be of significance.

Bacterial Proteins↗

PubMed2002

Donnan equilibrium of ionic drugs in pH-dependent fixed charge membranes: theoretical modeling.

We have studied theoretically the partition equilibrium of a cationic drug between an electrolyte solution and a membrane with pH-dependent fixed charges using an extended Donnan formalism. The aqueous solution within the fixed charge membrane is assumed to be in equilibrium with an external aqueous solution containing six ionic species: the cationic drug (DH(+)), the salt cations (Na(+) and Ca(2+)), the salt anion (Cl(-)), and the hydrogen and hydroxide ions. In addition to these mobile species, the membrane solution may also contain four fixed species attached to the membrane chains: strongly acid sulfonic groups (SO(3)(-)), weakly acid carboxylic groups in dissociated (COO(-)) and neutral (COOH) forms, and positively charged groups (COO...Ca(+)) resulting from Ca(2+) binding to dissociated weakly acid groups. The ionization state of the weak electrolyte groups attached to the membrane chains is analyzed as a function of the local pH, salt concentration, and drug concentration in the membrane solution, and particular attention is paid to the effects of the Ca(2+) binding to the negatively charged membrane fixed groups. The lipophilicity of the drug is simulated by the chemical partition coefficient between the membrane and external solutions giving the tendency of the drug to enter the membrane solution due to hydrophobic interactions. Comparison of the theoretical results with available experimental data allows us to explain qualitatively the effects that the pH, salt concentration, drug concentration, membrane fixed charge concentration, and Ca(2+) binding exert on the ionic drug equilibrium. The role of the interfacial (Donnan) electric potential difference between the membrane and the external solutions on this ionic drug equilibrium is emphasized throughout the paper.

Calcium↗

PubMed2000

Passive Transport of Ionic Drugs through Membranes with pH-Dependent Fixed Charges.

We have studied both theoretically and experimentally the passive transport of ionic drugs through membranes with pH-dependent fixed charge. The system considered constitutes a simplified model for pH-controlled drug delivery through membranes of biochemical and pharmaceutical interest. The theoretical approach employed is based on the Nernst-Planck flux equations and all of the species present in the system (the neutral or ionic drug and the hydrogen and hydroxide ions) have been taken into account together with a Langmuir-type isotherm for the adsorption of the ionic drug onto the membrane surface. The membrane permeabilities of cationic, anionic, and neutral drugs through porous membranes with graft-polymerized weak polyelectrolytes have been measured as a function of the external pH. According to the nature of the grafted polyelectrolyte, the ionized membrane fixed groups can be negative or positive. For the amphoteric membrane, both fixed charge groups are present in the grafted chains. In all cases, the ionization state of the weak polyelectrolyte fixed groups changes with the local pH within the membrane. A comparison of the theoretical results with the experimental data allows one to explain qualitatively the changes of the membrane flux with the external pH and gives new physical insights into the transport problem. Copyright 2000 Academic Press.

Journal Article↗