| Protein folding is described as a dynamic process of an ensemble of molecules reaching well-defined three dimensional structures to achieve biological activity from linear amino acids sequences. Many human diseases result from protein misfolding or aggregation. Enormous effort has been made both experimentally and theoretically for nearly 40 years to explain the basic principle and mechanism of protein folding and unfolding. Nonetheless, many of them are still unknown or incompletely understood, mainly due to the complexity of the systems and the fast folding time scale. Experimental and theoretical approaches are complementary with each other for the protein folding studies and hence, combination of the two is required to have better understanding.;One of the most popular experimental methods for the protein folding studies is laser-induced temperature-jump (T-jump), because it has nanosecond resolution. In the first project, the T-jump on the polyalanine peptides (Ala 20) was simulated as a proof-of-principle system to mimic the experimental measurements. Replica exchange molecular dynamics (REMD) were performed to obtain equilibrated ensembles as a proper conformational sampling, which was combined with multiplexed molecular dynamics to extract kinetic properties in line with experiments.;In the second project, the same methodology used in the first project was applied to real proteins. Effect of frictional coefficient in the solvent model was approximated using Langevin dynamics. Computationall results on the two related 14-residue peptides were chosen and compared with experimental results. A ratio of relaxation time of the two peptides was determined by calculated Circular Dichroism (CD) spectra by a factor of ∼1.2, while the experimental results were ∼1.1. |
