Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays.

ABSTRACT: One of the principal challenges in systems biology is to uncover the networks of protein-protein interactions that underlie most biological processes. To date, experimental efforts directed at this problem have largely produced only qualitative networks that are replete with false positives and false negatives. Here, we describe a domain-centered approach--compatible with genome-wide investigations--that enables us to measure the equilibrium dissociation constant (K(D)) of recombinant PDZ domains for fluorescently labeled peptides that represent physiologically relevant binding partners. Using a pilot set of 22 PDZ domains, 4 PDZ domain clusters, and 20 peptides, we define a gold standard dataset by determining the K(D) for all 520 PDZ-peptide combinations using fluorescence polarization.

SUBMITTER: Stiffler MA 

PROVIDER: S-EPMC2533859 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature