PXD044415

PXD044415 is an original dataset announced via ProteomeXchange.

Title	A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts
Description	Chemical activators and inhibitors are useful probes to identify substrates and downstream effects of enzymes; however, due to the complex signaling environment within cells, it is challenging to distinguish between direct and indirect effects. This is particularly the case for phosphorylation, where a single (de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additional complication arises when a single catalytic entity, which acts in form of many different holoenzymes with different substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turn which of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to study targets of drugs do not address these challenges. Here, we tackle this by studying the modulation of protein phosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, by using a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDP with in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and begin to separate direct and indirect effects. Together with experiments analyzing which holoenzymes are particularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complex network of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1 in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemical modulators with complex mode of action in general.
HostingRepository	PRIDE
AnnounceDate	2024-01-12
AnnouncementXML	Submission_2024-01-12_01:01:23.699.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christina Ludwig
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-07 09:09:07	ID requested
⏵ 1	2024-01-12 01:01:24	announced

10.1039/D3SC04746F;

submitter keyword: Protein phosphatase-1

enzyme activators

enzyme inhibitors

phosphoproteomics

mode of action

Christina Ludwig
contact affiliation	Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University Munich (TUM) Gregor-Mendel-Strasse 4 85354 Freising GERMANY
contact email	tina.ludwig@tum.de
lab head
Christina Ludwig
contact affiliation	TU Munich
contact email	tina.ludwig@tum.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044415
     1. Label: PRIDE project
     2. Name: A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts