Lattice models of peptide aggregation: evaluation of conformational search algorithms

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.     

A Titration Microcalorimetric Study of the Effects of Halide Counterions on Vesicle-Forming Aggregation in Aqueous Solution of Branched-Chain Alkylpyridinium Surfactants

Titration microcalorimetry is used to study the influences of iodide, bromide, and chloride counterions on the aggregation of vesicle-forming 1-methyl-4-(2-pentylheptyl)pyridinium halide surfactants. Formation of vesicles by these surfactants was characterised using transmission electron microscopy. When the counterion is changed at 303 K through the series iodide, bromide, to chloride, the critical vesicular concentration (cvc) increases and the enthalpy of vesicle formation changes from exo- to endothermic. With increase in temperature to 333 K, vesicle formation becomes strongly exothermic. Increasing the temperature leads to a decrease in enthalpy and entropy of vesicle formation for all three surfactants. However the standard Gibbs energy for vesicle formation is, perhaps surprisingly, largely unaffected by an increase in temperature, as a consequence of a compensating change in both standard entropy and standard enthalpy of vesicle formation. Interestingly, standard isobaric heat capacities of vesicle formation are negative, large in magnitude but not strikingly dependent on the counterion. We conclude that the driving force for vesicle formation can be understood in terms of overlap of the thermally labile hydrophobic hydration shells of the alkyl chains. Copyright 2000 Academic Press.