Molecular recognition of protein-ligand complexes: Studies of the Src SH3 domain

nteractions involving proteins and other molecules orchestrate the fundamental processes of cellular signal transduction. A common mechanism through which these interactions are regulated is the recognition of specific peptide sequences by a few conserved protein domains. Understanding these recognition events is an important step towards controlling the dissemination of intracellular signals using small molecule ligands. One group of these protein domains, the Src homology 3 (SH3) domains, are a family of homologous protein sequences that mediate the binding interactions of cellular proteins. They are approximately 60 amino acids in length, and have been found in several classes of enzymes, as well as many adaptor and structural proteins that lack catalytic functions.;The research described in this thesis is focused on the structural basis of molecular recognition between the c-Src kinase SH3 domain and several families of peptidic and non-peptidic ligands that were discovered from combinatorial chemistry studies. Chapter 2 describes two distinct binding modes through which peptidic ligands complex with the SH3 domain. As revealed by multidimensional NMR spectroscopy at the atomic level, ligands in both binding modes adopt a left-handed polyproline type II (PPII) helix, yet the peptide backbone orientation of the class I ligand is opposite from that of the class II ligand. The key orientation determinant is an electrostatic interaction between aspartate-99 of the SH3 domain and the terminal arginine residues of the ligands. The results provide a general structural model to analyze SH3-peptide interactions at the core binding site. Chapter 3 addresses in detail the question of ligand specificity outside the core binding region for both classes of peptidic ligands. A large pocket located between two variable regions--the RT and n-Src loops--connecting the...