PXD063040-1

PXD063040 is an original dataset announced via ProteomeXchange.

Title	MAPK Pathway Inhibition Reshapes Kinase Chemoproteomic Ligandability Reporting on Cellular Activation States
Description	Despite the pivotal role of oncogenic kinases in cancer initiation, progression, and resistance, functional profiling of their conformational states within cells remains challenging. Current methodologies often struggle to capture the dynamic structural features and inhibitor-bound conformations of these kinases, particularly in clinically relevant scenarios such as treatment response and relapse, where genomic characterization alone is insufficient.  Chemoproteomic techniques, including activity-based protein profiling (ABPP), offer a powerful means to assess amino acid reactivity in situ as a proxy for protein structure and function. Here, we report that treatment of BRAF mutation positive melanoma cell lines with the BRAF and MEK1/2 inhibitors, vemurafenib and trametinib respectively, results in a significant decrease in cysteine and lysine residue accessibility, consistent with inhibitor-induced conformational changes. Comparison of two ATP-competitive BRAF inhibitors, vemurafenib and dabrafenib, revealed distinct labelling patterns at the DFG-motif aspartate, demonstrating the ability of ABPP to resolve functional residue accessibility within kinase active sites. In melanoma cell lines with acquired resistance to BRAF or MEK inhibition, ABPP identified altered residue specific probe reactivity consistent with mutation-driven conformational shifts. Mass spectrometry validation further revealed similar accessibility changes in MAPK pathway components, including KSR2, suggesting broader pathway-level remodelling. These findings support the utility of ABPP for probing conformational dynamics, ligandability, and resistance-associated structural adaptations in kinases and related signalling proteins.
HostingRepository	PRIDE
AnnounceDate	2026-05-13
AnnouncementXML	Submission_2026-05-13_09:34:31.234.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	George M Burslem
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-16 13:51:16	ID requested
⏵ 1	2026-05-13 09:34:32	announced

Jarvis AF, Bhat MY, Maujean T, Abreu AL, Toy K, Burslem GM, Brady DC, MAPK Pathway Inhibition Reshapes Kinase Chemical Probe Reactivity Reflecting Cellular Activation States. ACS Bio Med Chem Au, 6(2):178-191(2026) [pubmed]

10.1021/acsbiomedchemau.5c00231;

submitter keyword: IA-alkyne, TMT, BRAF, Trametinib, chemoproteomics, Mass spectrometry, MEK1/2, Vemurafenib, ArSq-alkyne, Cysteine and lysine ligandability,ABPP, Click chemistry

George Burslem
contact affiliation	University of Pennsylvania
contact email	George.Burslem@pennmedicine.upenn.edu
lab head
George M Burslem
contact affiliation	University of Pennsylvania
contact email	george.burslem@pennmedicine.upenn.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063040
     1. Label: PRIDE project
     2. Name: MAPK Pathway Inhibition Reshapes Kinase Chemoproteomic Ligandability Reporting on Cellular Activation States