PXD039520

PXD039520 is an original dataset announced via ProteomeXchange.

Title	Limited proteolysis–mass spectrometry detects protein–protein interactions of integral membrane proteins
Description	Integral membrane proteins (IMPs) are permanently embedded within the plasma membrane and execute multiple cellular functions. IMPs constitute important targets, but development of drugs that target IMPs to modulate protein–protein interactions, which mediate their functions, has been challenging. Characterizing the structural and functional properties of IMPs as well as their regulatory PPIs is a key step toward new or improved therapeutics. Functional and structural studies of IMPs are hindered by their hydrophobicity, low expression levels in cells, flexibility, and the need to use detergents to solubilize these proteins. Representative examples of IMPs are mammalian adenylyl cyclases that play a pivotal role in the 3',5'-cyclic adenosine monophosphate signaling pathway. The activity of membrane-bound adenylyl cyclases can be regulated by direct and/or indirect binding of calcium ions, for example, via calmodulin. Unstructured and highly flexible regions of adenylyl cyclases engage in PPIs. However, the principles of classical proteomics methods do not allow mapping interactions involving regions without a defined three-dimensional structure. To address this limitation, we used limited proteolysis–mass spectrometry (LiP–MS) to study the known interaction between the adenylyl cyclases AC8 and calmodulin by probing protein structural alterations in crude membrane suspensions treated with calmodulin. The LiP–MS analysis pinpointed putative binding site regions of AC8 previously shown to participate in the interaction with calmodulin, demonstrating that this method can be used to identify interaction domains in membrane proteins in a physiologically relevant context.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:29:04.802.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Aleš Holfeld
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-17 01:30:21	ID requested
1	2024-02-10 17:05:27	announced
⏵ 2	2024-10-22 06:29:05	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: LC-MSMS, Membrane proteins, Interactome, Mass spectrometry,Limited proteolysis, Structural proteomics, Protein-protein interactions, Proteomics, Crude membranes

Paola Picotti
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
contact email	picotti@imsb.biol.ethz.ch
lab head
Aleš Holfeld
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
contact email	holfeld@imsb.biol.ethz.ch
dataset submitter

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/2024/02/PXD039520

PRIDE project URI

• PRIDE
  1. PXD039520
     1. Label: PRIDE project
     2. Name: Limited proteolysis–mass spectrometry detects protein–protein interactions of integral membrane proteins