Global profiling of protein complex dynamics with an experimental library of protein interaction markers.

Autor: Dörig C; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Marulli C; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Peskett T; Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland., Volkmar N; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Pantolini L; Biozentrum, University of Basel, Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland., Studer G; Biozentrum, University of Basel, Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland., Paleari C; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Frommelt F; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Schwede T; Biozentrum, University of Basel, Basel, Switzerland.; SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland., de Souza N; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland., Barral Y; Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland., Picotti P; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland. picotti@imsb.biol.ethz.ch.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2024 Oct 16. Date of Electronic Publication: 2024 Oct 16.
DOI: 10.1038/s41587-024-02432-8
Abstrakt: Methods to systematically monitor protein complex dynamics are needed. We introduce serial ultrafiltration combined with limited proteolysis-coupled mass spectrometry (FLiP-MS), a structural proteomics workflow that generates a library of peptide markers specific to changes in PPIs by probing differences in protease susceptibility between complex-bound and monomeric forms of proteins. The library includes markers mapping to protein-binding interfaces and markers reporting on structural changes that accompany PPI changes. Integrating the marker library with LiP-MS data allows for global profiling of protein-protein interactions (PPIs) from unfractionated lysates. We apply FLiP-MS to Saccharomyces cerevisiae and probe changes in protein complex dynamics after DNA replication stress, identifying links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes. FLiP-MS enables protein complex dynamics to be probed on any perturbation, proteome-wide, at high throughput, with peptide-level structural resolution and informing on occupancy of binding interfaces, thus providing both global and molecular views of a system under study.
(© 2024. The Author(s).)
Databáze: MEDLINE
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