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The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis–mass spectrometry (LiP–MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP–MS detects well-characterized PPIs, including antibody–target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states. Synopsis: A structural proteomics approach for identifying candidate interactors of any protein within a complex lysate is presented. It is applied to identify conformation-specific interactors of Rab GTPases and of the monomeric and fibrillar forms of the disease-associated protein alpha-synuclein. A method is presented for identifying candidate interactors of any bait protein within a complex lysate. It is applicable to the identification of conformation-specific interactors and pinpoints interaction sites. A resource of candidate interactors of monomeric and fibrillar forms of alpha-synuclein is presented. Candidate interactors of GTP- and GDP-bound forms of Rab GTPases are identified. A structural proteomics approach for identifying candidate interactors of any protein within a complex lysate is presented. It is applied to identify conformation-specific interactors of Rab GTPases and of the monomeric and fibrillar forms of the disease-associated protein alpha-synuclein. [ABSTRACT FROM AUTHOR]

While several computational methods have been developed to predict the functional relevance of phosphorylation sites, experimental analysis of the interdependency between protein phosphorylation and Protein–Protein Interactions (PPIs) remains challenging. Here, we describe an experimental strategy to establish interdependencies between protein phosphorylation and complex formation. This strategy is based on three main steps: (i) systematically charting the phosphorylation landscape of a target protein; (ii) assigning distinct proteoforms of the target protein to different protein complexes by native complex separation (AP‐BNPAGE) and protein correlation profiling; and (iii) analyzing proteoforms and complexes in cells lacking regulators of the target protein. We applied this strategy to YAP1, a transcriptional co‐activator for the control of organ size and tissue homeostasis that is highly phosphorylated and among the most connected proteins in human cells. We identified multiple YAP1 phosphosites associated with distinct complexes and inferred how both are controlled by Hippo pathway members. We detected a PTPN14/LATS1/YAP1 complex and suggest a model how PTPN14 inhibits YAP1 via augmenting WW domain‐dependent complex formation and phosphorylation by LATS1/2. Synopsis: A novel approach is proposed to study the functional relationships between two critical mechanisms in cell signaling: PTMs and complex formation. This proteomic workflow is applied to investigate YAP1, a major signal integrator and effector of the Hippo pathway. Modules of YAP1 phospho‐proteoforms and their interactors were identified via AP‐BNPAGE.A causal relationship between site phosphorylation and complex formation was established.The control of YAP1 phosphorylation and complex formation was studied in cells lacking known pathway effectors.A model was developed to demonstrate how PTPN14 could inhibit YAP1 co‐transcriptional activity via augmenting ternary complex formation and phosphorylation by LATS1/2. [ABSTRACT FROM AUTHOR]