Global profiling of protein complex dynamics with an experimental library of protein interaction markers
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Date
2025-09
Publication Type
Journal Article
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yes
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Abstract
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.
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published
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Journal / series
Volume
43 (9)
Pages / Article No.
1562 - 1576
Publisher
Nature
Event
Edition / version
Methods
Software
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Date collected
Date created
Subject
Organisational unit
03927 - Picotti, Paola / Picotti, Paola
03532 - Barral, Yves / Barral, Yves
Notes
Funding
866004 - Three-dimensional dynamic views of proteomes as a novel readout for physiolgical and pathological alterations (EC)
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