Modular recognition domains: The mechanism of PDZ and L27 domains and their role in signal transduction.

摘要

Chapter 1 introduces the field by focusing on a well-understood domain that has been a primary focus of my thesis work, the PDZ domain. PDZ domains specifically recognize short amino acid sequence (peptide) motifs with a required C-terminal carboxylate (as well as internal sequences in certain secondary structures, see below). These domains utilize high specificity-low affinity interactions to coordinate several well-known signaling complexes in metazoan organisms.; Chapter 2 describes the recognition by PDZ domains of internal amino acid sequence motifs. The previously solved structure of nNOS 1–130 bound to the Syntrophin PDZ domain showed that PDZ domains can recognize internal peptide motifs in very similar mechanism to that of C-terminal peptides. Our experiments demonstrate that this is accomplished by presentation of the internal sequence motif in an appropriate structural context. PDZ domains can therefore recognize internal sequence motifs, as well as C-terminal ones, if they are accompanied by specific structural elements.; Chapter 3 describes the role of electrostatics in the recognition by PDZ domains of diverse ligand types, and specific recognition of the required C-terminal carboxylate by a non-electrostatic mechanism. Even though PDZ domains recognize ligands with a required carboxylate, they appear to do so by a non-electrostatic (i.e. coulombic) mechanism. The evidence supports recognition of the peptide ligand using balanced hydrogen bonding and hydrophobic interactions—also, as a consequence, allowing the recognition of internal peptide motifs.; Chapter 4 describes the initial characterization of a new protein-protein interaction domain, the LIN-2, -7 homology (L27) domain. This domain associates with a 1:1 stoichiometry to assemble a wide variety of dimeric signaling, transport and localization complexes in the cell. Strikingly, folding and association in these domains is coupled—the domains are only folded when in a heterodimer, implying that folding in this case is an important factor in the regulation of assembly.; The diversity of molecular mechanisms used by these protein-protein interaction domains help to explain how signaling complexes achieve such high specificity in the face of dynamic changes in signaling requirements. Specifically, these domains seem to balance a wide variety of forces; any known factor in protein-protein interactions from electrostatics to protein folding is “fair game”. The reasons for use of particular mechanisms in particular cases in vivo, and the structural basis for some of these mechanisms, remains to be elucidated. (Abstract shortened by UMI.)