A Specificity Map for the PDZ Domain Family

PLoS Biology, Sep 2008

PDZ domains are protein–protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides, we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenorhabditis elegans proteomes. The domains recognize features of the last seven ligand positions, and we find 16 distinct specificity classes conserved from worm to human, significantly extending the canonical two-class system based on position −2. Thus, most PDZ domains are not promiscuous, but rather are fine-tuned for specific interactions. Specificity profiling of 91 point mutants of a model PDZ domain reveals that the binding site is highly robust, as all mutants were able to recognize C-terminal peptides. However, many mutations altered specificity for ligand positions both close and far from the mutated position, suggesting that binding specificity can evolve rapidly under mutational pressure. Our specificity map enables the prediction and prioritization of natural protein interactions, which can be used to guide PDZ domain cell biology experiments. Using this approach, we predicted and validated several viral ligands for the PDZ domains of the SCRIB polarity protein. These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth.

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A Specificity Map for the PDZ Domain Family

Citation: Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh J-H, et al. ( A Specificity Map for the PDZ Domain Family Raffi Tonikian 0 1 2 Yingnan Zhang 0 1 2 Stephen L. Sazinsky 0 1 2 Bridget Currell 0 1 2 Jung-Hua Yeh 0 1 2 Boris Reva 0 1 2 Heike A. Held 0 1 2 Brent A. Appleton 0 1 2 Marie Evangelista 0 1 2 Yan Wu 0 1 2 Xiaofeng Xin 0 1 2 Andrew C. Chan 0 1 2 Somasekar Seshagiri 0 1 2 Laurence A. Lasky 0 1 2 Chris Sander 0 1 2 Charles Boone 0 1 2 Gary D. Bader 0 1 2 Sachdev S. Sidhu sachdev.sidhu@utoronto 0 1 2 0 Current address: Terrence Donnelly Center for Cellular and Biomolecular Research and Banting and Best Department of Medical Research, University of Toronto , Toronto, Ontario , Canada 1 Academic Editor: Sean R. Eddy, Howard Hughes Medical Institute , Janelia Farm , United States of America 2 1 Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto , Toronto, Ontario , Canada , 2 Department of Molecular Genetics, University of Toronto , Toronto, Ontario , Canada , 3 Department of Protein Engineering , Genentech, South San Francisco , California, United States of America, 4 Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts , United States of America, 5 Department of Molecular Biology, Genentech , South San Francisco , California, United States of America, 6 Department of Immunology, Genentech South San Francisco, California, United States of America, 7 Computational Biology Center, Memorial Sloan-Kettering Cancer Center , New York , New York, United States of America, 8 Department of Antibody Engineering , Genentech, South San Francisco, California , United States of America PDZ domains are protein-protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides, we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenorhabditis elegans proteomes. The domains recognize features of the last seven ligand positions, and we find 16 distinct specificity classes conserved from worm to human, significantly extending the canonical two-class system based on position 2. Thus, most PDZ domains are not promiscuous, but rather are fine-tuned for specific interactions. Specificity profiling of 91 point mutants of a model PDZ domain reveals that the binding site is highly robust, as all mutants were able to recognize Cterminal peptides. However, many mutations altered specificity for ligand positions both close and far from the mutated position, suggesting that binding specificity can evolve rapidly under mutational pressure. Our specificity map enables the prediction and prioritization of natural protein interactions, which can be used to guide PDZ domain cell biology experiments. Using this approach, we predicted and validated several viral ligands for the PDZ domains of the SCRIB polarity protein. These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth. - Modular proteinprotein recognition domains are involved in the assembly of numerous intracellular complexes that mediate diverse cellular functions. Thousands of recognition domains are contained within the human proteome, and these have been classified into over 70 distinct families [1]. The PDZ (PSD-95/Discs-large/ZO-1) domain family is particularly interesting because it plays a key role in the development of multicellular organisms, in which PDZ domains are often found as components of multidomain scaffolding proteins involved in cell polarity and intercellular interactions [2,3]. PDZ domains are often embedded in proteins that assemble specialized subcellular sites, such as epithelial junctions [4], neuronal postsynaptic densities [5], and immunological synapses of T cells [6]. The biological importance of PDZ domains is further underscored by the identification of various PDZ-containing proteins as human disease and pathogen effector targets [4,715]. Although the human genome encodes over 250 PDZ domains in over 100 proteins, most studies to date have focused on individual family members or a handful of domains [1620]. Nevertheless, these studies uncovered general features of PDZ domain structure and function. Aside from unusual cases in which phospholipids [21,22] or internal motifs [23,24] are recognized, PDZ domains assemble intracellular complexes principally by recognition of C-terminal sequences in which specificity is mediated by interactions between ligand side chains and the PDZ domain binding surface [2]. Early studies grouped PDZ domains into two main specificity classes based on two ligand positions: class 1 (X[T/ S]X/COOH) and class 2 (X/X/COOH), where X is any residue and / is a hydrophobe [1 (...truncated)


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Raffi Tonikian, Yingnan Zhang, Stephen L Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A Held, Brent A Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C Chan, Somasekar Seshagiri, Laurence A Lasky, Chris Sander, Charles Boone, Gary D Bader, Sachdev S Sidhu. A Specificity Map for the PDZ Domain Family, PLoS Biology, 2008, 9, DOI: 10.1371/journal.pbio.0060239