Computer Simulations of Protein Folding and Evolution
Contributors: Shakhnovich, Eugene; Xie, Sunney; Verdine, Gregory
Published: 2013
Language: eng
Description: Computer simulations for investigating protein folding and evolution are presented. In chapter 1, an all-atom model with a knowledge-based potential is used to study the folding kinetics of Formin-Binding protein. We study the folding kinetics by performing Monte Carlo simulations. We examine the order of formation of two beta-hairpins, the folding mechanism of each individual beta-hairpin, and transition state ensemble (TSE) and compare our results with experimental data and previous computational studies. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated phi values.
Notes: Thesis Ph.D. Harvard University 2013