Identifying Stereochemical Preferences that Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Crystallographic and Sequence Analyses

• Published in: Structure (London) 2014-01, Vol.22 (1), p.82-93
• Main Authors: Amacher, J., Cushing, P., Brooks, L., Madden, D.
• Format: Article
• Language: English
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2013.09.019

PDZ domain interactions are involved in signaling and trafficking pathways that coordinate crucial cellular processes. Alignment-based PDZ binding motifs identify the few most favorable residues at certain positions along the peptide backbone. However, sequences that bind the CAL (CFTR-Associated Ligand) PDZ domain reveal only a degenerate motif that overpredicts the true number of high affinity interactors. Here, we combine extended peptide-array motif analysis with biochemical techniques to show that non-motif ‘modulator’ residues influence CAL binding. The crystallographic structures of 13 new CAL:peptide complexes reveal defined, but accommodating stereochemical environments at non-motif positions, which are reflected in modulator preferences uncovered by multi-sequence substitutional arrays. These preferences facilitate the identification of new high-affinity CAL binding sequences and differentially affect CAL and NHERF PDZ binding. As a result, they also help determine the specificity of a PDZ domain network that regulates the trafficking of CFTR at the apical membrane.