Estimation of the parameters of the Smoluchowski equation describing the occurrence of pores in a bilayer lipid membrane under soft poration

The conductive lipid pores occurring in planar bilayer membranes are known to manifest themselves experimentally as current fluctuations. Reliable recording of such fluctuations during phase transitions, as well as in membranes with various additives (for example, SDS), allows one to determine the characteristics of hypothetical hydrophilic pores, namely, their number, sizes, lifetimes, and duration of time intervals between pores. Because, in contrast with electroporation, the emergence of pores in a membrane does not require high voltages, this process is called soft poration. Studying the characteristics of pores under soft poration allows us to estimate the parameters of the Smoluchowski equation and compare them with the corresponding parameters used to describe electroporation. In this work, the experimental characteristics of current fluctuations in the membrane with the addition of SDS to the bulk solution were used to estimate the parameters of the Smoluchowski equation: the pore edge tension, the energy of the hydrophobic pore/hydrophilic pore barrier, the coefficient of pore diffusion in the radius space, the initial distribution density of the number of pores, and the attempt rate density of the lipids in a membrane. The obtained estimates are close to the parameter values used in studies of electroporation.

Survival probability of a lazy prey on lattices and complex networks

We develop a framework to analyse the survival probability of a prey following a minimal effort evasion strategy, that is being chased by N predators on finite lattices or complex networks. The predators independently perform random walks if the prey is not within their sighting radius, whereas, the prey only moves when a predator moves onto a node within its sighting radius. We verify the proposed framework on three different finite lattices with periodic boundaries through numerical simulations and find that the survival probability (P_sur) decays exponentially with a decay rate proportional to P(N, k) (number of permutations), where k is the minimum number of predators required to capture a prey. We then extend the framework onto complex networks and verify its robustness on the networks generated by the Watts-Strogatz (W-S), Barabási-Albert (B-A) models and a few real-world networks. Our analysis predicts that, for the considered lattices, P_sur reduces as the degree of the nodes of the lattice is increased. However, for networks, P_sur initially increases with the average degree of the nodes, reaches a maximum, and then decreases. Furthermore, we analyse the effect of the long-range connections in networks on P_sur in W-S networks. The proposed framework enables one to study the survival probability of such a prey being hunted by multiple predators on any given structure.

Mechanical mechanism for the translocation of hexameric and nonstructural helicases: Dependence on physical parameters

Three recently observed facts of the translocation of actual hexameric and nonstructural (NS) helicases are related to the various physical quantities and are in accordance with the recently proposed mechanical mechanism: a) the translocation of hexameric helicases might be led by either the N-terminal domain (NTD) or C-terminal domain (CTD) depending on which domain has a smaller central pore, b) the translocation speed (v_t) of the ring-shaped helicases and NS helicases decreased with decreasing applied tension, and c) a large difference in the v_t of the NS helicase was observed for the helicase translocating on DNA and RNA. These findings are the effects of the physical quantities of the helicase/nuclei acid strands on the translocation of helicases and are difficult to explain with biochemical models. We predict that a similar behavior as described in b) and c) is also shown by hexameric helicases. The validity of the mechanical mechanism is demonstrated in simulation experiments.

Pixantrone anticancer drug as a DNA ligand: Depicting the mechanism of action at single molecule level

In this work we use single molecule force spectroscopy performed with optical tweezers in order to characterize the complexes formed between the anticancer drug Pixantrone (PIX) and the DNA molecule, at two very different ionic strengths. Firstly, the changes of the mechanical properties of the DNA-PIX complexes were studied as a function of the drug concentration in the sample. Then, a quenched-disorder statistical model of ligand binding was used in order to determine the physicochemical (binding) parameters of the DNA-PIX interaction. In particular, we have found that the PIX molecular mechanism of action involves intercalation into the double helix, followed by a significant compaction of the DNA molecule due to partial neutralization of the phosphate backbone. Finally, this scenario of interaction was quantitatively compared to that found for the related drug Mitoxantrone (MTX), which binds to DNA with a considerably higher equilibrium binding constant and promotes a much stronger DNA compaction. The comparison performed between the two drugs can bring clues to the development of new (and more efficient) related compounds.

Dynamics of cooperative cargo transport by two elastically coupled kinesin motors

Intracellular transport is performed often by multiple motor proteins bound to the same cargo. Here, we study theoretically collective transport of the cargo by two kinesin motors. We propose that the motor has only the elastic interaction with the cargo via the linker connecting them and has no interaction with another motor. With parameters values for single motors from the available single-molecule data, we show that at linker's elastic strength [Formula: see text] pN/nm the theoretical data of both velocity and run length of the two-motor assembly under no load are identical to the available experimental data. The run length distribution is single exponential. The single-motor-bound state of the assembly dominates the transport. Both the force dependence of the velocity of the cargo driven by single load-bearing motor and that by two load-bearing motors in the assembly are consistent with the experimental data. The stall force of the assembly is larger than the sum of stall forces of two uncoupled motors. Moreover, we predict that the stall force increases with the increase of K and becomes saturated at large K, with the saturated value being 1.5-fold larger than the sum of stall forces of the two uncoupled motors.

Fluctuation-induced hydrodynamic coupling in an asymmetric, anisotropic dumbbell

We recently introduced a model of an asymmetric dumbbell made of two hydrodynamically coupled subunits as a minimal model for a macromolecular complex, in order to explain the observation of enhanced diffusion of catalytically active enzymes. It was shown that internal fluctuations lead to a negative contribution to the overall diffusion coefficient and that the fluctuation-induced contribution is controlled by the strength of the interactions between the subunits and their asymmetry. We develop the model by studying the effect of anisotropy on the diffusion properties of a modular structure. Using a moment expansion method we derive an analytic form for the long-time diffusion coefficient of an asymmetric, anisotropic dumbbell and show systematically its dependence on internal and external symmetry. The method provides a tractable, analytical route for studying the stochastic dynamics of dumbbell models. The present work opens the way to more detailed descriptions of the effect of hydrodynamic interactions on the diffusion and transport properties of biomolecules with complex structures.

The effect of pH on the dynamics of natural membranes

Pure phospholipids and membrane fragments from bacterial cells living under various conditions were studied against the influence of the surrounding acidity on the internal dynamics. For that we compared mean square displacements extracted from elastic incoherent neutron scattering data, measured both at low and at neutral pH, of the phospholipids 1,2-dimyristoyl-sn-glycero-3-phosphocholine and of samples from neutralophilic and acidophilic micro-organisms (some being hyperthermophilic and others mesophilic). The lipids showed a slight shift in the phase transition temperature of about 4 degrees under pH variation and became slightly more mobile at lower pH. The membrane fragments not used to extreme acidic conditions were significantly more sensitive to variations in the pH values, whereas the acidophilic and -tolerant samples were much less influenced by this parameter. They presented the higher softness at low pH, which was closer to their native condition. Such findings might be a hint for adaptation mechanisms to different acidity conditions.

The role of DNA sequence in nucleosome breathing

Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.

Neuronal avalanches: Where temporal complexity and criticality meet

The model of the current paper is an extension of a previous publication, wherein we have used the leaky integrate-and-fire model on a regular lattice with periodic boundary conditions, and introduced the temporal complexity as a genuine signature of criticality. In that work, the power-law distribution of neural avalanches was a manifestation of supercriticality rather than criticality. Here, however, we show that the continuous solution of the model and replacing the stochastic noise with a Gaussian zero-mean noise leads to the coincidence of power-law display of temporal complexity, and spatiotemporal patterns of neural avalanches at the critical point. We conclude that the source of inconsistency may be a numerical artifact originated by the discrete description of the model which may imply a slow numerical convergence of the avalanche distribution compared to temporal complexity.

On the different sources of cooperativity in pH titrating sites of a membrane protein channel

Cooperative interactions play a central role in the regulation of protein functions. Here we show that in multi-site systems like ion channels the application of the Hill formalism could require a combination of different experiments, even involving site-directed mutagenesis, to identify the different sources of cooperativity and to discriminate between genuine and apparent cooperativity. We discuss the implications for the channel function in the bacterial porins PorA (N. meningitidis) and OmpF (E. coli) and the viroporin SARS-CoV E.