Author: Rehman Fazeem

Publisher:

Published: 2013

Total Pages: 185

ISBN-13:

"Metropolis Monte Carlo (MC) simulations were performed with positively charged peptides in aqueous solution to study changes in peptide conformations at solid/liquid interface, and its effects on protein aggregation. Intermediate-resolution diblock model peptide, comprising of 10 units of ALA (non-polar) and LYS (polar) amino acid residues, was used for the simulations. In the first approach to modeling, solvent effects were considered explicitly. The explicit model was then used to study two peptide molecules, in helical structure, at solid/liquid interface. In order to increase the number of peptide molecules in the simulation box, with reduced computational cost, an implicit solvent model was developed with nonadditive hydrogen bonding and hydrophobic interaction potentials. The implicit model was used to simulate two peptides of helical structure at charged surfaces (to compare with the explicit model), and ten peptides of random coil structure with and without charged surfaces. The peptides were observed to always move towards the negatively charged surface and orient with residues of complimentary charge settling close to the surface, maximizing the electrostatic interactions. On reaching the surface, the peptides partially lose their secondary structure and clusters around the hydrophobic ends; this restructuring and dehydration of the peptides provides the entropic drive for adsorption and subsequent misfolding events. The 2- peptide-water-surface system in explicit model was also simulated with periodic switching of surface charge polarity, to induce a "shaking effect" in order to observe possible peptide configurational changes"--Abstract, page iii.