Thermodynamics of Protein Folding and Design

Abstract: The protein folding and protein design problems are addressed, using coarse-grained models with only two types of amino acids, hydrophobic and hydrophilic. In addition to hydrophobicity forces, the models contain sequence-independent local interactions which are found to strongly influence the thermodynamics of these models. The models are studied using the dynamical-parameter Monte Carlo method. A Monte Carlo approach to protein design based on this method is developed, and the usefulness of the method for another difficult problem in computational biology, sequence assembly, is explored. Finally, the statistical distribution of hydrophobicity in real and model protein sequences is studied.