Blocker effect on diffusion resistance of a membrane channel. Dependence on the blocker geometry

Being motivated by recent progress in nanopore sensing, we develop a theory of the effect of large analytes, or blockers, trapped within the nanopore confines, on diffusion flow of small solutes. The focus is on the nanopore diffusion resistance which is the ratio of the solute concentration difference in the reservoirs connected by the nanopore to the solute flux driven by this difference. Analytical expressions for the diffusion resistance are derived for a cylindrically symmetric blocker whose axis coincides with the axis of a cylindrical nanopore in two limiting cases where the blocker radius changes either smoothly or abruptly. Comparison of our theoretical predictions with the results obtained from Brownian dynamics simulations shows good agreement between the two

Time and length scales of autocrine signals in three dimensions

A model of autocrine signaling in cultures of suspended cells is developed on the basis of the effective medium approximation. The fraction of autocrine ligands, the mean and distribution of distances traveled by paracrine ligands before binding, as well as the mean and distribution of the ligand lifetime are derived. Interferon signaling by dendritic immune cells is considered as an illustration.Comment: 15 page

Survival and residence times in disordered chains with bias

We present a unified framework for first-passage time and residence time of random walks in finite one-dimensional disordered biased systems. The derivation is based on exact expansion of the backward master equation in cumulants. The dependence on initial condition, system size, and bias strength is explicitly studied for models with weak and strong disorder. Application to thermally activated processes is also developed.Comment: 13 pages with 2 figures, RevTeX4; v2:minor grammatical changes, typos correcte

How β-Lactam Antibiotics Enter Bacteria: A Dialogue with the Porins

BACKGROUND:Multi-drug resistant (MDR) infections have become a major concern in hospitals worldwide. This study investigates membrane translocation, which is the first step required for drug action on internal bacterial targets. beta-lactams, a major antibiotic class, use porins to pass through the outer membrane barrier of Gram-negative bacteria. Clinical reports have linked the MDR phenotype to altered membrane permeability including porin modification and efflux pump expression. METHODOLOGY/PRINCIPAL FINDINGS: Here influx of beta-lactams through the major Enterobacter aerogenes porin Omp36 is characterized. Conductance measurements through a single Omp36 trimer reconstituted into a planar lipid bilayer allowed us to count the passage of single beta-lactam molecules. Statistical analysis of each transport event yielded the kinetic parameters of antibiotic travel through Omp36 and distinguishable translocation properties of beta-lactams were quantified for ertapenem and cefepime. Expression of Omp36 in an otherwise porin-null bacterial strain is shown to confer increases in the killing rate of these antibiotics and in the corresponding bacterial susceptibility. CONCLUSIONS/SIGNIFICANCE: We propose the idea of a molecular "passport" that allows rapid transport of substrates through porins. Deciphering antibiotic translocation provides new insights for the design of novel drugs that may be highly effective at passing through the porin constriction zone. Such data may hold the key for the next generation of antibiotics capable of rapid intracellular accumulation to circumvent the further development MDR infections

Note : Network random walk model of two-state protein folding : Test of the theory

We study two-state protein folding in the framework of a toy model of protein dynamics. This model has an important advantage: it allows for an analytical solution for the sum of folding and unfolding rate constants [A. M. Berezhkovskii, F. Tofoleanu, and N.-V. Buchete, J. Chem. Theory Comput. 7, 2370 (2011)10.1021/ct200281d] and hence for the reactive flux at equilibrium. We use the model to test the Kramers-type formula for the reactive flux, which was derived assuming that the protein dynamics is described by a Markov random walk on a network of complex connectivity [A. Berezhkovskii, G. Hummer, and A. Szabo, J. Chem. Phys. 130, 205102 (2009)10.1063/1.3139063]. It is shown that the Kramers-type formula leads to the same result for the reactive flux as the sum of the rate constants.AM

Drift and diffusion in periodic potentials: Upstream and downstream step times are distributed identically

This note deals with particles diffusing in one dimension in the presence of a periodic potential and a uniform driving force. We show that (i) the probabilities for the particle to make a step of the length L, where L is the period, in the upstream and downstream directions are independent of the periodic potential, and (ii) the distributions of the step time are independent of the step direction. These two characteristics are used to derive expressions for the effective drift velocity and diffusion coefficient

Optimizing Transport of Metabolites through Large Channels: Molecular Sieves with and without Binding

Using a diffusion model of molecules moving through a pore, we rationalize why biological channels have an affinity for the molecules they have evolved to translocate

Biased diffusion in tubes formed by spherical compartments

We study the effect of the driving force on Brownian motion of a point particle in a tube formed by identical spherical compartments, which create periodic entropy potential for the motion along the tube axis. The focus is on (i) the effective mobility and diffusion coefficient of the particle as functions of the driving force, (ii) localization of the particle in the central part of the tube induced by the driving force, and (iii) transit time of the particle between the openings connecting neighboring compartments. Some of the results at very small and large driving force are obtained analytically, while the majority of the results are obtained from Brownian dynamics simulations