Molecular Electroporation and the Transduction of Oligoarginines

Certain short polycations, such as TAT and polyarginine, rapidly pass through the plasma membranes of mammalian cells by an unknown mechanism called transduction as well as by endocytosis and macropinocytosis. These cell-penetrating peptides (CPPs) promise to be medically useful when fused to biologically active peptides. I offer a simple model in which one or more CPPs and the phosphatidylserines of the inner leaflet form a kind of capacitor with a voltage in excess of 180 mV, high enough to create a molecular electropore. The model is consistent with an empirical upper limit on the cargo peptide of 40--60 amino acids and with experimental data on how the transduction of a polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of arginines in the CPP and on the CPP concentration. The model makes three testable predictions.Comment: 15 pages, 5 figure

Unifying model of driven polymer translocation

We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.Comment: 7 pages, 3 figure

Membrane fluctuations near a plane rigid surface

We use analytical calculations and Monte Carlo simulations to determine the thermal fluctuation spectrum of a membrane patch of a few tens of nanometer in size, whose corners are located at a fixed distance $d$ above a plane rigid surface. Our analysis shows that the surface influence on the bilayer fluctuations can be effectively described in terms of a uniform confining potential that grows quadratically with the height of the membrane $h$ relative to the surface: $V=(1/2)\gamma h^2$. The strength $\gamma$ of the harmonic confining potential vanishes when the corners of the membrane patch are placed directly on the surface ($d=0$), and achieves its maximum value when $d$ is of the order of a few nanometers. However, even at maximum strength the confinement effect is quite small and has noticeable impact only on the amplitude of the largest bending mode.Comment: Accepted for publication in Phys. Rev.

Correlated dynamics of inclusions in a supported membrane

The hydrodynamic theory of heterogeneous fluid membranes is extended to the case of a membrane adjacent to a solid substrate. We derive the coupling diffusion coefficients of pairs of membrane inclusions in the limit of large separation compared to the inclusion size. Two-dimensional compressive stresses in the membrane make the coupling coefficients decay asymptotically as $1/r^2$ with interparticle distance $r$. For the common case, where the distance to the substrate is of sub-micron scale, we present expressions for the coupling between distant disklike inclusions, which are valid for arbitrary inclusion size. We calculate the effect of inclusions on the response of the membrane and the associated corrections to the coupling diffusion coefficients to leading order in the concentration of inclusions. While at short distances the response is modified as if the membrane were a two-dimensional suspension, the large-distance response is not renormalized by the inclusions.Comment: 15 page

Solid domains in lipid vesicles and scars

The free energy of a crystalline domain coexisting with a liquid phase on a spherical vesicle may be approximated by an elastic or stretching energy and a line tension term. The stretching energy generally grows as the area of the domain, while the line tension term grows with its perimeter. We show that if the crystalline domain contains defect arrays consisting of finite length grain boundaries of dislocations (scars) the stretching energy grows linearly with a characteristic length of the crystalline domain. We show that this result is critical to understand the existence of solid domains in lipid-bilayers in the strongly segregated two phase region even for small relative area coverages. The domains evolve from caps to stripes that become thinner as the line tension is decreased. We also discuss the implications of the results for other experimental systems and for the general problem that consists in finding the ground state of a very large number of particles constrained to move on a fixed geometry and interacting with an isotropic potential.Comment: 7 pages, 6 eps figure

Discreteness-induced Transition in Catalytic Reaction Networks

Drastic change in dynamics and statistics in a chemical reaction system, induced by smallness in the molecule number, is reported. Through stochastic simulations for random catalytic reaction networks, transition to a novel state is observed with the decrease in the total molecule number N, characterized by: i) large fluctuations in chemical concentrations as a result of intermittent switching over several states with extinction of some molecule species and ii) strong deviation of time averaged distribution of chemical concentrations from that expected in the continuum limit, i.e., $N \to \infty$. The origin of transition is explained by the deficiency of molecule leading to termination of some reactions. The critical number of molecules for the transition is obtained as a function of the number of molecules species M and that of reaction paths K, while total reaction rates, scaled properly, are shown to follow a universal form as a function of NK/M

Steady-state simulations using weighted ensemble path sampling

We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. The straightforward steady-state implementation of WE is directly practical for simple landscapes, but not when significant metastable intermediates states are present. We therefore develop an enhanced WE scheme, building on existing ideas, which accelerates attainment of steady state in complex systems. We apply both WE approaches to several model systems confirming their correctness and efficiency by comparison with brute-force results. The enhanced version is significantly faster than the brute force and straightforward WE for systems with WE bins that accurately reflect the reaction coordinate(s). The new WE methods can also be applied to equilibrium sampling, since equilibrium is a steady state

Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

The mechanical response of semiflexible networks to localized perturbations

Previous research on semiflexible polymers including cytoskeletal networks in cells has suggested the existence of distinct regimes of elastic response, in which the strain field is either uniform (affine) or non-uniform (non-affine) under external stress. Associated with these regimes, it has been further suggested that a new fundamental length scale emerges, which characterizes the scale for the crossover from non-affine to affine deformations. Here, we extend these studies by probing the response to localized forces and force dipoles. We show that the previously identified nonaffinity length [D.A. Head et al. PRE 68, 061907 (2003).] controls the mesoscopic response to point forces and the crossover to continuum elastic behavior at large distances.Comment: 16 pages, 18 figures; substantial changes to text and figures to clarify the crossover to continuum elasticity and the role of finite-size effect

Load fluctuations drive actin network growth

The growth of actin filament networks is a fundamental biological process that drives a variety of cellular and intracellular motions. During motility, eukaryotic cells and intracellular pathogens are propelled by actin networks organized by nucleation-promoting factors, which trigger the formation of nascent filaments off the side of existing filaments in the network. A Brownian ratchet (BR) mechanism has been proposed to couple actin polymerization to cellular movements, whereby thermal motions are rectified by the addition of actin monomers at the end of growing filaments. Here, by following actin--propelled microspheres using three--dimensional laser tracking, we find that beads adhered to the growing network move via an object--fluctuating BR. Velocity varies with the amplitude of thermal fluctuation and inversely with viscosity as predicted for a BR. In addition, motion is saltatory with a broad distribution of step sizes that is correlated in time. These data point to a model in which thermal fluctuations of the microsphere or entire actin network, and not individual filaments, govern motility. This conclusion is supported by Monte Carlo simulations of an adhesion--based BR and suggests an important role for membrane tension in the control of actin--based cellular protrusions.Comment: To be published in PNA