Cell membrane as a model for the design of ion-active nanostructured supramolecular systems

Confined self-assembly of toric focal conic domains (the effects of confined geometry on the feature size of toric focal conic domains)

A smectic liquid crystal (LC) containing a rigid biphenyl group and semifluorinated chains exhibits a high density of toric focal conic domains (TFCDs) arranged in an ordered array when confined within a microchannel. The formation of the TFCDs is strongly influenced by the width (W) and depth (h) of the confined microchannels, most importantly, by the channel depth. We studied a broad variety of microchannels, with varying width in the range of 3-200 mum and depth in the range of 2-10 mum. The radius of the TFCDs increases with increases in the width until the saturated radius is achieved, which is determined by the depth of the channel. We used the elastic-anchoring model of TFCD formation to explain the experimental observations. The model allows one to trace the dependence of the TFCD radius on the channel depth h, to explain why the TFCDs do not form in channels that are too shallow or too narrow.

Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics

The ion channel protein alpha-hemolysin (alphaHL) forms supramolecular complexes with the polysaccharide beta-cyclodextrin (betaCD). This system has potential uses in nanoscale device engineering. It has been found recently that betaCD formed longer- or shorter-lived complexes with some engineered alphaHL mutants then with a wild type protein (Gu et al. J. Gen. Physiol. 2001, 118, 481-493). However, how changes in the protein sequence affect complex lifetime was not completely understood in part due to the lack of knowledge of structures of these metastable complexes. In this paper, we present an extensive molecular modeling study of the betaCD-alphaHL and selected mutant complexes to gain insights into the betaCD-alphaHL interaction mechanisms and to predict possible structures and energetics of the complexes. Thermodynamic integration (TI) and umbrella sampling (US) techniques (with the weighted histogram analysis method (WHAM)) were used to calculate the relative binding affinities of the complexes formed with the wild type alphaHL and the M113N, M113E, M113A, and M113V mutants. Our results are in excellent agreement with experiment. While betaCD-M113N and betaCD-M113A complexes were stable in the configuration of the wild type complex, the equilibrium configuration of the betaCD-M113V and betaCD-M113E complexes was significantly different. In these cases, TI alone was insufficient to accurately calculate the corresponding free energy differences. By utilizing a TI/US combination in a novel manner, we were able to accurately calculate free energy changes in these flexible systems. The betaCD-M113A and betaCD-M113E complexes, which exhibited shorter lifetimes than other complexes in an experiment, in simulations exhibited greater flexibility and higher water solvation of the betaCD adapter. MD simulations of the betaCD-M113N complex with betaCD in a downward orientation were also performed.