| 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.;In chapter 2, the underlying mechanism of the co-evolution of regulatory and protein coding sequences is studied. Regulatory sequences control the expression of a gene. The protein coding sequence determines the probability of a protein folding correctly through thermodynamic stability. Because organismal fitness is determined by both the total protein products and by the probability of a protein folding correctly, we expect there to be co-evolution between regulatory sequences and protein coding sequences. We provide support for our hypothesis using a molecular-level evolutionary simulation. The results of our simulation are consistent with previous findings demonstrating that highly expressed genes are stable and evolve relatively slowly. Our simulation also shows that the number of substitutions in a regulatory sequence is positively correlated with the rate of evolution in the coding sequence and that highly expressed genes have low upstream regulatory sequence substitution rates. We then analyze sequence data from yeast; the results of this analysis confirm those of our simulation.;In chapter 3, we study how recombination and mutation act together to shape protein evolution. We use a biophysical model of protein folding with explicit sequences and protein structures. The biophysical model allows us to consider the roles of mutation and recombination in the context of a realistic biophysical fitness landscape. Our model naturally includes epistasis and sequence depletion effects. In addition, our explicit sequence model permits intragenic recombination. We find that mutation and recombination have different effects on the adaptation process, protein stability and the origin and fixation of recombinant alleles during protein evolution. |
