COMPUTATIONAL STUDIES ON THE STRUCTURAL ASPECTS OF PROTEIN-PEPTIDE INTERACTIONS

Abstract

Proteins mediate biological important processes by interacting with other biomolecules, namely, proteins, peptides, sugars, lipids or nucleic acids. This thesis presents my works on proteinpeptide interactions, and more specifically on protein- polyproline type II helix (PPII) peptide interaction. These interactions are crucial to several processes such as signaling pathways, localization, immune response, post-translational modifications etc. Three different aspects of protein-PPII interaction have been studied to decipher the specificity of these interactions, including refining two X-ray crystal structures of protein-PPII complex, applying molecular dynamics simulation on protein-PPII complex to understand the peptide editing mechanism, and predicting the binding sites of PPII peptide. One other aspect, pKa prediction of ionizable residues in proteins, which is important to understanding protein functions as well as protein-peptide interactions is also presented in this thesis.