Most eukaryotic proteins that receive and process signals are constructed from a combination of interaction and catalytic domains. Among the many interaction domains identified in the past decade, PDZ's are one of the most frequently encountered. They are often found in combination with other interaction modules and play a role in directing the specificity of receptor tyrosine kinase-mediated signaling, in establishing cell polarity, in directing protein trafficking, and in coordinating synaptic signaling. Their importance is underscored by the severe neuronal and developmental phenotypes observed in PDZ knockout mice and by their implication in human congenital diseases like Usher syndrome and Dejerine-Sottas neuropathy. The enormous diversity of PDZ function is manifest in their abundance;there are over 250 PDZ's encoded in the mouse genome. To understand their individual roles, it is necessary first to define their recognition properties in a comprehensive and relevant fashion. Previous efforts to define PDZ selectivity have focused on only a few domains and have relied on collections of randomized peptides, rather than on physiological ligands. In order to provide a genome-wide understanding of PDZ function, the selectivity of every PDZ encoded in the mouse genome will be investigated relative to a large collection of genomically-encoded ligands using protein microarray technology.
The aims of this proposal are: (1) to clone, express, and purify every mouse PDZ domain;(2) to screen every PDZ with every PDZ to reveal putative PDZ-PDZ interactions;(3) to screen every PDZ with 222 genomically-encoded peptide ligands to identify putative PDZ-protein interactions;(4) to investigate the physiological relevance of a subset of predicted interactions biochemically;and (5) to construct a relational database that integrates protein microarray data with published information on PDZ domains. Collectively, these efforts should provide the necessary foundation to understand PDZ function on a genome-wide level and aid future efforts to intervene appropriately when PDZ function goes awry.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM072872-05
Application #
7579117
Study Section
Physiological Chemistry Study Section (PC)
Program Officer
Edmonds, Charles G
Project Start
2005-02-01
Project End
2010-07-31
Budget Start
2009-02-01
Budget End
2010-07-31
Support Year
5
Fiscal Year
2009
Total Cost
$295,452
Indirect Cost
Name
Harvard University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138
AlQuraishi, Mohammed; Koytiger, Grigoriy; Jenney, Anne et al. (2014) A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks. Nat Genet 46:1363-1371
Gujral, Taranjit S; Chan, Marina; Peshkin, Leonid et al. (2014) A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell 159:844-56
Koytiger, Grigoriy; Kaushansky, Alexis; Gordus, Andrew et al. (2013) Phosphotyrosine signaling proteins that drive oncogenesis tend to be highly interconnected. Mol Cell Proteomics 12:1204-13
Gujral, Taranjit S; Karp, Ethan S; Chan, Marina et al. (2013) Family-wide investigation of PDZ domain-mediated protein-protein interactions implicates ?-catenin in maintaining the integrity of tight junctions. Chem Biol 20:816-27
Chang, Bryan H; Gujral, Taranjit S; Karp, Ethan S et al. (2011) A systematic family-wide investigation reveals that ~30% of mammalian PDZ domains engage in PDZ-PDZ interactions. Chem Biol 18:1143-52
Kaushansky, Alexis; Allen, John E; Gordus, Andrew et al. (2010) Quantifying protein-protein interactions in high throughput using protein domain microarrays. Nat Protoc 5:773-90
Wolf-Yadlin, Alejandro; Sevecka, Mark; MacBeath, Gavin (2009) Dissecting protein function and signaling using protein microarrays. Curr Opin Chem Biol 13:398-405
Kaushansky, Alexis; Gordus, Andrew; Budnik, Bogdan A et al. (2008) System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties. Chem Biol 15:808-17
Chen, Jiunn R; Chang, Bryan H; Allen, John E et al. (2008) Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol 26:1041-5
Stiffler, Michael A; Chen, Jiunn R; Grantcharova, Viara P et al. (2007) PDZ domain binding selectivity is optimized across the mouse proteome. Science 317:364-9

Showing the most recent 10 out of 11 publications