PXD034790 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Native holdup (nHU) to measure binding affinities from cell extracts |
Description | Characterizing macromolecular interactions is essential for understanding cellular processes, yet nearly all methods used to detect protein interactions from cells are qualitative. Here, we introduce a native holdup (nHU) approach that requires minimal sample preparation, investigates binding mechanisms, and quantifies equilibrium binding constants of protein interactions from cell extracts. We use nHU coupled with western blotting (nHU-WB) and mass spectrometry (nHU-MS) to explore interactions of SNX27, a cargo adaptor of the retromer complex. We find good agreement between affinities measured using minimal binding fragments and those measured directly from cell extracts using nHU. This challenges the unwritten paradigm stating that biophysical parameters like binding constants cannot be accurately determined from cells or cellular extracts. We discuss the strengths and limitations of nHU and provide simple protocols that can be implemented in most laboratories. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:37:08.733.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Luc Negroni |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-06-21 07:22:37 | ID requested | |
1 | 2023-03-10 20:53:56 | announced | |
⏵ 2 | 2023-11-14 08:37:10 | announced | 2023-11-14: Updated project metadata. |
Publication List
Zambo B, Morlet B, Negroni L, Trave G, Gogl G, Native holdup (nHU) to measure binding affinities from cell extracts. Sci Adv, 8(51):eade3828(2022) [pubmed] |
Keyword List
submitter keyword: protein interaction, mass spectrometry,native holdup |
Contact List
Gilles Travé |
contact affiliation | IGBMC,UMR7104, Illkirch |
contact email | travegi@igbmc.fr |
lab head | |
Luc Negroni |
contact affiliation | CNRS |
contact email | luc.negroni@igbmc.fr |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD034790 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD034790
- Label: PRIDE project
- Name: Native holdup (nHU) to measure binding affinities from cell extracts