Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes

作者：Ylva Ivarsson, Roland Arnold, Megan McLaughlin, Satra Nim, Rakesh Kumar Joshi, Debashish Ray, Bernard A. Liu, Joan Teyra, Tony Pawson, Jason Moffat, Shawn S.‐C. Li, Sachdev S. Sidhu, Philip M. Kim · 发表于：Proceedings of the National Academy of Sciences · 年份：2014 · DOI：10.1073/pnas.1312296111 · 被引用次数：154 · 研究领域：Viral Infectious Diseases and Gene Expression in Insects、vaccines and immunoinformatics approaches、Ubiquitin and proteasome pathways

The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, proteomic peptide-phage display (ProP-PD), to identify domain-SLiM interactions. Specifically, we generated phage libraries containing all human and viral C-terminal peptides using custom oligonucleotide microarrays. With these libraries we screened the nine PSD-95/Dlg/ZO-1 (PDZ) domains of human Densin-180, Erbin, Scribble, and Disks large homolog 1 for peptide ligands. We identified several known and putative interactions potentially relevant to cellular signaling pathways and confirmed interactions between full-length Scribble and the target proteins β-PIX, plakophilin-4, and guanylate cyclase soluble subunit α-2 using colocalization and coimmunoprecipitation experiments. The affinities of recombinant Scribble PDZ domains and the synthetic peptides representing the C termini of these proteins were in the 1- to 40-μM range. Furthermore, we identified several well-established host-virus protein-protein interactions, and confirmed that PDZ domains of Scribble interact with the C terminus of Tax-1 of human T-cell leukemia virus with micromolar affinity. Previously unknown putative viral protein ligands for the PDZ domains of Scribble and Erbin were also identified...