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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\u2013mass spectrometry (LiP\u2013MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins\u00a0in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP\u2013MS detects well-characterized PPIs, including antibody\u2013target 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\u2019s 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.<\/jats:p>","DOI":"10.1038\/s44320-024-00037-6","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T11:01:31Z","timestamp":1714734091000},"page":"651-675","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Systematic identification of structure-specific protein\u2013protein interactions"],"prefix":"10.1038","volume":"20","author":[{"given":"Ale\u0161","family":"Holfeld","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6611-8237","authenticated-orcid":false,"given":"Dina","family":"Schuster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabian","family":"Sesterhenn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3835-2333","authenticated-orcid":false,"given":"Alison K","family":"Gillingham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Stalder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4868-3704","authenticated-orcid":false,"given":"Walther","family":"Haenseler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5686-0451","authenticated-orcid":false,"given":"Inigo","family":"Barrio-Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2087-8075","authenticated-orcid":false,"given":"Dhiman","family":"Ghosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Vowles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0297-6675","authenticated-orcid":false,"given":"Sally A","family":"Cowley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8844-7234","authenticated-orcid":false,"given":"Luise","family":"Nagel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6637-3550","authenticated-orcid":false,"given":"Basavraj","family":"Khanppnavar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetiana","family":"Serdiuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2724-7703","authenticated-orcid":false,"given":"Pedro","family":"Beltrao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0962-9433","authenticated-orcid":false,"given":"Volodymyr M","family":"Korkhov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6160-5773","authenticated-orcid":false,"given":"Sean","family":"Munro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland","family":"Riek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4286-8951","authenticated-orcid":false,"given":"Natalie","family":"de Souza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4109-3552","authenticated-orcid":false,"given":"Paola","family":"Picotti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,3]]},"reference":[{"key":"37_CR1","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.jmb.2019.11.019","volume":"432","author":"K Afitska","year":"2020","unstructured":"Afitska K, Priss A, Yushchenko DA, Shvadchak VV (2020) Structural optimization of inhibitors of \u03b1-synuclein fibril growth: affinity to the fibril end as a crucial factor. 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