Permeation and gating in proteins: kinetic Monte Carlo reaction path following

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC). This approach permits navigation among potential minima on an energy surface, finding the minimum-energy paths and determining their associated free-energy profiles. The methodological and algorithmic strategies underlying the kMCRPF method are described. We have tested it using an analytical model and applied it to study permeation through the curvilinear ClC chloride and aquaporin pores and to gating in the gramicidin A channel. These studies of permeation and gating in real proteins provide extensive procedural tests of the method.     

Membrane inclusions as coupled harmonic oscillators: effects due to anisotropic membrane slope relaxation

Membrane-mediated interaction between membrane-spanning peptides or protein segments plays an important role in their function and stability. Our rigorous "coupled harmonic oscillators" representation is extended to account for the complex boundary conditions permitting anisotropic relaxation of the membrane slope along the contours of the inclusions. Using this representation and applying a highly efficient finite-difference algorithm, we have analyzed the membrane-mediated interaction triggered by deformation of the hydrophobic tails of lipid molecules to match the lipophilic exterior of the inserted peptide. We establish that anisotropic relaxation crucially affects the interaction energy, leading to a short-range attraction between two inclusions, while conventional isotropic boundary conditions result in their strong repulsion. In a multi-inclusion cluster, this attraction is further enhanced and modified due to nonpairwise interactions. The results for dimyristoyl phosphatidylcholine and glyceryl monooleate membranes are compared, and the effects of the inclusion radius are considered. The possible role of slope relaxation in the reported stabilization of linked gramicidin channels and in proteins' functional cooperativity is outlined.     

Structural characteristics of different types of nanoparticles synthesised in mesomorphic metal alkanoates

The class of thermotropic ionic liquid crystals (LCs) of the metal alkanoates possesses a number of unique properties, such as intrinsic ionic conductivity, high dissolving ability and ability to form time-stable mesomorphic glasses. These ionic LCs can be used as nanoreactors for the synthesis and stabilisation of different types of nanoparticles (NPs). Thus, some semiconductors, metals and core/shell NPs were chemically synthesised in the thermotropic ionic liquid crystalline phase (smectic A) of the cadmium octanoate (CdC₈) and of the cobalt octanoate (CoC₈). By applying the scanning electron microscopy, the cadmium and cobalt octanoate composites containing CdS, Au, Ag and core/shell Au/CdS NPs have been studied. NPs’ sizes and dispersion distribution of the NPs’ size in the nanocomposites have been obtained.