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

Sequence Heterogeneity Accelerates Protein Search for Targets on DNA

The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry and heterogeneity of a genome.Comment: 10 pages, 5 figure

Insight into Resonant Activation in Discrete Systems

The resonant activation phenomenon (RAP) in a discrete system is studied using the master equation formalism. We show that the RAP corresponds to a non-monotonic behavior of the frequency dependent first passage time probability density function (pdf). An analytical expression for the resonant frequency is introduced, which, together with numerical results, helps understand the RAP behavior in the space spanned by the transition rates for the case of reflecting and absorbing boundary conditions. The limited range of system parameters for which the RAP occurs is discussed. We show that a minimum and a maximum in the mean first passage time (MFPT) can be obtained when both boundaries are absorbing. Relationships to some biological systems are suggested.Comment: 5 pages, 5 figures, Phys. Rev. E., in pres

Contractile units in disordered actomyosin bundles arise from F-actin buckling

Bundles of filaments and motors are central to contractility in cells. The classic example is striated muscle, where actomyosin contractility is mediated by highly organized sarcomeres which act as fundamental contractile units. However, many contractile bundles in vivo and in vitro lack sarcomeric organization. Here we propose a model for how contractility can arise in actomyosin bundles without sarcomeric organization and validate its predictions with experiments on a reconstituted system. In the model, internal stresses in frustrated arrangements of motors with diverse velocities cause filaments to buckle, leading to overall shortening. We describe the onset of buckling in the presence of stochastic actin-myosin detachment and predict that buckling-induced contraction occurs in an intermediate range of motor densities. We then calculate the size of the "contractile units" associated with this process. Consistent with these results, our reconstituted actomyosin bundles contract at relatively high motor density, and we observe buckling at the predicted length scale.Comment: 5 pages, 4 figures, Supporting text and movies attache

Fluctuation spectrum of quasispherical membranes with force-dipole activity

The fluctuation spectrum of a quasi-spherical vesicle with active membrane proteins is calculated. The activity of the proteins is modeled as the proteins pushing on their surroundings giving rise to non-local force distributions. Both the contributions from the thermal fluctuations of the active protein densities and the temporal noise in the individual active force distributions of the proteins are taken into account. The noise in the individual force distributions is found to become significant at short wavelengths.Comment: 9 pages, 2 figures, minor changes and addition

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

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

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

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

Segregation of receptor-ligand complexes in cell adhesion zones: Phase diagrams and role of thermal membrane roughness

The adhesion zone of immune cells, the 'immunological synapse', exhibits characteristic domains of receptor-ligand complexes. The domain formation is likely caused by a length difference of the receptor-ligand complexes, and has been investigated in experiments in which T cells adhere to supported membranes with anchored ligands. For supported membranes with two types of anchored ligands, MHCp and ICAM1, that bind to the receptors TCR and LFA1 in the cell membrane, the coexistence of domains of TCR-MHCp and LFA1-ICAM1 complexes in the cell adhesion zone has been observed for a wide range of ligand concentrations and affinities. For supported membranes with long and short ligands that bind to the same cell receptor CD2, in contrast, domain coexistence has been observed for a rather narrow ratio of ligand concentrations. In this article, we determine detailed phase diagrams for cells adhering to supported membranes with a statistical-physical model of cell adhesion. We find a characteristic difference between the adhesion scenarios in which two types of ligands in a supported membrane bind (i) to the same cell receptor or (ii) to two different cell receptors, which helps to explain the experimental observations. Our phase diagrams fully include thermal shape fluctuations of the cell membranes on nanometer scales, which lead to a critical point for the domain formation and to a cooperative binding of the receptors and ligands.Comment: 23 pages, 6 figure