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Journal Articles Nature Methods Year : 2015

Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

Katja Luck

Abstract

Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-throughput holdup assay, a chromatographic approach that can measure up to 1,000 domain-motif equilibrium binding affinities per day. After benchmarking the approach on 210 PDZ-peptide pairs with known affinities, we determined the affinities of two viral PDZ-binding motifs derived from human papillomavirus E6 oncoproteins for 209 PDZ domains covering 79% of the human 'PDZome'. We obtained sharply sequence-dependent binding profiles that quantitatively describe the PDZome recognition specificity of each motif. This approach, applicable to many categories of domain-ligand interactions, has wide potential for quantifying the specificities of interactomes.
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Dates and versions

pasteur-02883959 , version 1 (19-06-2023)

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Renaud Vincentelli, Katja Luck, Juline Poirson, Jolanta Polanowska, Julie Abdat, et al.. Quantifying domain-ligand affinities and specificities by high-throughput holdup assay. Nature Methods, 2015, 12 (8), pp.787-793. ⟨10.1038/nmeth.3438⟩. ⟨pasteur-02883959⟩
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