Specificity, Structure and Dynamics of Tiam1 PDZ Domain Ligand-Bound Complexes

Abstract

PSD-95/DlgA/ZO-1 (PDZ) domains are among the most abundant protein-protein interaction domains in the human proteome and typically bind the 4-10 C-terminal residues of its interaction partner with exquisite specificity. We used two homologous PDZ domains from the Tiam-family of guanine nucleotide exchange factors to investigate PDZ specificity. The Tiam1 and Tiam2 PDZ domains have overlapping but distinct ligand binding specificity, and this is exemplified by their unique preferences for C-terminal peptides derived from the syndecan1, Caspr4 and neurexin1 adhesion proteins. The Tiam1 PDZ domain binds syndecan1 and Caspr4 but not neurexin1, while the Tiam2 PDZ domain binds Caspr4 and neurexin1 but not syndecan1. Amino acid sequence comparison of Tiam-family PDZ domains revealed that four residues critical for ligand specificity are not conserved. Remarkably, substitution of these four residues in the Tiam1 PDZ for those found in the Tiam2 PDZ domain switched ligand specificity. To understand the structural and dynamic basis for this change in specificity we used X-ray crystallography and solution NMR methods, respectively. We determined the crystal structures of wild type Tiam1 PDZ domain bound to syndecan1 and phosphorylated syndecan1 peptides and the Tiam1 PDZ quadruple mutant (QM) bound to Caspr4 and neurexin1 peptides. Comparison of the crystal structures of the Tiam1 PDZ-syndecan1 and PDZ-phosphorylated syndecan1 showed that a distinct specificity pocket is used to accommodate the phosphoryl group. The crystal structure of the Tiam1 QM PDZ domain showed a unique side chain stacking interaction between aromatic residues in the PDZ domain and the Caspr4 ligand. Side chain methyl relaxation experiments revealed distinct patterns of dynamics in the Tiam1 PDZ-syndecan1 and PDZ-Caspr4 complexes. Collectively, the structures and dynamics of physiologically-based PDZ domain complexes are contributing to understanding the origin of PDZ specificity and function of Tiam-family PDZ domains.