Computational studies of protein stability and folding kinetics

Proteins are some of the most complex systems known, hence to gain a fundamental understanding of their structure and processes will greatly increase our basic knowledge of molecular biology. Computational tools provide a detailed analysis on the atomic scale, though current computers only allow us to study the shortest time-scales. Simplified protein models along with efficient algorithms are currently the best choice for studying protein stability and folding kinetics.; In our studies of protein stability we employ the multicanonical Monte Carlo algorithm and a coarse-grain protein model to study the protein phase-diagram. We find that the model protein denaturates above the pressure where water freezes to the dense ice phase, in agreement with experiments on bovine pancreatic ribonuclease A. We employ the discrete molecular dynamics algorithm and a series of coarse-grain protein models to study the folding transition at equilibrium conditions. We find that the Src-homology-3 (SH3) proteins resemble a system with only two stable states, mediated by a first-order like transition. In another study, we calculate the stability and structure of the intermediates and the ground state of a designed-peptide by mutating the amino acid sequence. We also study the relevance of electrostatics interactions and the hydrophobic effect in the stability of the decapeptide Abeta(21--30), which has been suggested by recent experiments to be the nucleating site for the formation of the fibrils observed in Alzheimer's disease patients. We find that Abeta(21--30) adopts a loop-like conformation in solution and undergoes partial rearrangement of structure upon aggregation.; In our studies of folding kinetics we find that the transition state of the SH3 proteins features a set of amino acid contacts that drive the protein to the ground state. Such amino acid contacts are the folding nucleus. We investigate the kinetics of the folding transition of the SH3 proteins over a broad range of temperatures and identify three distinct folding pathways below a specific temperature, the kinetic partition temperature. Our findings suggest the hypothesis that the SH3 proteins, for which only two-state folding kinetics was observed in previous experiments, may exhibit intermediate states under conditions that strongly stabilize the ground state.