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Many protein-protein interactions are mediated by short linear peptide motifs binding to cognate proteins or protein domains. Such interactions often display affinities in the mid-micromolar range that are challenging to quantify accurately, especially when the motifs harbor single-point mutations. Here, we present a manual benchtop assay for determining affinities of weak interactions between a purified protein and a peptide array representing mutants of a target motif. The assay is based on the "holdup" principle, a chromatographic approach allowing sensitive detection of weak interactions at equilibrium and accurate estimation of their binding free energy. We tested two alternative setups using, as a readout, either capillary electrophoresis or fluorescence. Using this approach, we studied the amino acid sequence determinants of the interactions between HPV16 E6 viral oncoprotein and single-point mutants of its prototypical target LXXLL motif from the E3 ubiquitin ligase E6AP. Comparing SPOT peptide array and holdup approaches revealed a good agreement for most interactions except the weakest ones, which were only detected by holdup assay. In addition, the strongest interactions were validated by Surface-Plasmon Resonance. The manual holdup procedure proposed here can be readily adapted for accurate evaluation of a wide variety of protein-motif interactions displaying low to medium affinities. Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.


Anna Bonhoure, Anne Forster, Khaled Ould Babah, Gergő Gógl, Pascal Eberling, Camille Kostmann, Rudolf Volkmer, Victor Tapia Mancilla, Gilles Travé, Yves Nominé. Benchtop holdup assay for quantitative affinity-based analysis of sequence determinants of protein-motif interactions. Analytical biochemistry. 2020 Aug 15;603:113772

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PMID: 32428443

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