PDZ domains are highly abundant protein-protein interaction modules and often found in multi-domain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and clustering receptors and ion-channels at defined membrane regions, organizing and targeting signaling complexes at specific cellular compartments, interfacing cytoskeletal structures with membranes, and maintaining various cellular structures. PDZ domains, each with ~90 amino acid residues folding into a highly similar structure, are best known to bind to short carboxyl tail peptides from their target proteins. A series of recent studies have revealed that, in addition to the canonical target binding mode, many PDZ/target interactions involve amino acid resi...[ Read more ]

PDZ domains are highly abundant protein-protein interaction modules and often found in multi-domain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and clustering receptors and ion-channels at defined membrane regions, organizing and targeting signaling complexes at specific cellular compartments, interfacing cytoskeletal structures with membranes, and maintaining various cellular structures. PDZ domains, each with ~90 amino acid residues folding into a highly similar structure, are best known to bind to short carboxyl tail peptides from their target proteins. A series of recent studies have revealed that, in addition to the canonical target binding mode, many PDZ/target interactions involve amino acid residues beyond the regular PDZ domain fold, which we refer to as extensions. Such extension sequences often form an integral structural and functional unit with the attached PDZ domain, which is defined as a PDZ supramodule. Correspondingly, PDZ domain binding sequences from target proteins are frequently found to require extension sequences beyond canonical short carboxyl tail peptides. Formation of PDZ supramodules not only affords necessary binding specificities and affinities demanded by physiological functions of PDZ domain targets, but also provides regulatory switches to be built in the PDZ/target interactions.

Chapter 1 provides an overview introduction of the PDZ domain of the thesis work. I mainly focus on a series of recent studies showing that, in addition to the well-documented, canonical PDZ/target interaction mode, many PDZ domains employ amino acid sequences beyond the canonical PDZ domain fold, which we refer to as “extended PDZ domains”. Such extension sequences often form an integral structural and functional unit with the regular PDZ domains, and we term the “extended PDZ domains” as PDZ supramodules.

In Chapter 2, I found a totally unexpected PDZ/target binding mode observed in the interaction between Drosophila scaffold protein INAD and TRP channel. The C-terminal 15 residues of TRP are required for the potent and specific interaction with INAD PDZ3. The structure of the INAD PDZ3/TRP peptide complex reveals that only the extreme C-terminal Leu of the TRP peptide binds to the canonical carboxyl binding pocket of INAD PDZ3. The rest of the TRP peptide, via forming a β-hairpin structure, binds to a surface that is formed by βB, βC and αA, and located away from the canonical target binding groove of INAD PDZ3. As such, the INAD PDZ3/TRP channel interaction is exquisitely specific and represents a new paradigm for PDZ/target recognitions.

In Chapter 3, I found the second PDZ domain of INAD, PDZ2, adopts a novel structural and functional “supramodule” for binding to eye-PKC, a key component for light adaptation and deactivation in fly visual signaling. Furthermore, an NMR-based real-time study of PDZ2 eye-PKC phosphorylation provides both kinetic and mechanistic insights into the potential regulation mechanisms of INAD NPDZ2/eye-PKC. These results indicate that INAD NPDZ2 is a structural supramodule and plays a regulatory role in the Drosophila visual signaling.