Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules
Nat Commun. 2019-10-04; 10(1):
DOI: 10.1038/s41467-019-12528-4
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Rimbault C(1)(2), Maruthi K(3)(4), Breillat C(1)(2), Genuer C(1)(2), Crespillo S(1)(2), Puente-Muñoz V(1)(2), Chamma I(1)(2), Gauthereau I(1)(2), Antoine
S(1)(2), Thibaut C(1)(2), Tai FWJ(5), Dartigues B(5), Grillo-Bosch D(1)(2), Claverol S(6), Poujol C(7), Choquet D(1)(2)(7), Mackereth CD(8)(9), Sainlos M(10)(11).
Author information:
(1)Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique, F-33076, Bordeaux, France.
(2)Interdisciplinary Institute for Neuroscience, University of Bordeaux, F-33076, Bordeaux, France.
(3)Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607, Pessac, France.
(4)Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076, Bordeaux, France.
(5)University of Bordeaux, CBiB-LaBRI, F-33000, Bordeaux, France.
(6)Proteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076, Bordeaux, France.
(7)Bordeaux Imaging Center, UMS 3420 Centre National de la Recherche Scientifique, University of Bordeaux, US 4 INSERM, F-33076, Bordeaux, France.
(8)Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607, Pessac, France. .
(9)Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076, Bordeaux, France. .
(10)Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique, F-33076, Bordeaux, France. .
(11)Interdisciplinary Institute for Neuroscience, University of Bordeaux, F-33076, Bordeaux, France. .
Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved
interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces. We report here a strategy that uses a semi-rational approach to separate the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by using phage display selection coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to contact the target interface. We apply this approach to specifically bind a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides a paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules.