A specificity map for the PDZ domain family.
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.
Tonikian
Raffi
R
Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
Zhang
Yingnan
Y
Sazinsky
Stephen L
SL
Currell
Bridget
B
Yeh
Jung-Hua
JH
Reva
Boris
B
Held
Heike A
HA
Appleton
Brent A
BA
Evangelista
Marie
M
Wu
Yan
Y
Xin
Xiaofeng
X
Chan
Andrew C
AC
Seshagiri
Somasekar
S
Lasky
Laurence A
LA
Sander
Chris
C
Boone
Charles
C
Bader
Gary D
GD
Sidhu
Sachdev S
SS
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000032:analysis* / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D054731:PDZ Domains; D010455:Peptides / Q000032:analysis / Q000235:genetics; D010802:Phylogeny; D017433:Protein Structure, Secondary; D020543:Proteome / Q000032:analysis*; D025521:Tumor Suppressor Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
D029742:Caenorhabditis elegans Proteins; D008565:Membrane Proteins; D010455:Peptides; D020543:Proteome; C480591:SCRIB protein, human; D025521:Tumor Suppressor Proteins; D014764:Viral Proteins