4NNM

Tax-Interacting Protein-1 (TIP-1) PDZ domain bound to Y-iCAL36 (YPTSII) peptide

Summary for 4NNM

• Entry DOI: 10.2210/pdb4nnm/pdb
• Related: 4NNL
• Descriptor: Tax1-binding protein 3, TIP-1 PDZ domain, GLYCEROL, ... (4 entities in total)
• Functional Keywords: tax-interacting protein-1, tip-1, pdz, pdz-peptide, protein binding
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: O14907
• Total number of polymer chains: 4
• Total formula weight: 26488.11

Authors

Amacher, J.F.,Madden, D.R. (deposition date: 2013-11-18, release date: 2015-01-21, Last modification date: 2026-01-21)

Primary citation

Amacher, J.F.,Cushing, P.R.,Vouilleme, L.,Cullati, S.N.,Deng, B.,Gerber, S.A.,Boisguerin, P.,Madden, D.R.
Sequence Engineering at Non-motif Modulator Residues Yields a Peptide That Effectively Targets a Single PDZ Protein in a Disease-relevant Cellular Context.
J.Mol.Biol., 438:169597-169597, 2026

PubMed Abstract: PDZ interaction networks are finely-tuned products of evolution. These widespread binding domains recognize short linear motifs (SLiMs), usually at the C-terminus of their interacting partners, and are involved in trafficking and signaling pathways, the formation of tight junctions, and scaffolding of the post-synaptic density of neurons, amongst other roles. Typically, a single PDZ domain binds multiple targets; conversely, each PDZ-binding protein engages several PDZ domains, dependent on cellular conditions. Historical PDZ binding motifs rely on two key positions for binding. However, previous insights on modulator, or non-motif, selectivity preferences reveal that these limited motifs are insufficient to describe PDZ-mediated interactomes, consistent with the observation that the degree of promiscuity is much more limited than predicted by defined binding classes. Here, we use these principles to engineer and test a peptide-based inhibitor capable of interacting with a single PDZ domain-containing protein in a disease-relevant cellular system. We first interrogate a previously developed sequence selective for cystic fibrosis transmembrane conductance regulator (CFTR)-Associated Ligand (CAL), one of five PDZ domains known to bind the CFTR C-terminus, probing for off-target PDZ partners. Once identified, we use parallel biochemical and structural refinement to eliminate these interactions and introduce a CAL PDZ inhibitor with unprecedented PDZ domain selectivity. We test and verify specificity using relevant cellular PDZ target networks in a mass spectrometry-based approach. Our resultant selective inhibitor enhances chloride efflux when applied to polarized patient bronchial epithelial cells, as well as confirms that engineering an effectively single-PDZ peptide is possible when modulator preferences are applied.

PubMed: 41419168
DOI: 10.1016/j.jmb.2025.169597

Experimental method

X-RAY DIFFRACTION (1.6 Å)