PXD050770

PXD050770 is an original dataset announced via ProteomeXchange.

Title	Affinity-based protein profiling (AfBPP) using different Callyaerin probes in M. tuberculosis H37Rv
Description	The natural cyclopeptide Callyaerin B (CalB) exhibits highly specific antitubercular activity. The aim of this project is to study the protein binding partner of this compound using either activity-based protein profiling (ABPP) (ACE_0721) or affinity-based protein profiling (AfBPP) (ACE_0682 & ACE_0721). To enable a two-step enrichment protocol, CalB probes modified with an alkyne group (CalB_C4Pra) and optionally additional photoleucine (CalB_R5phLeu) or 4-benzoyl-phenylalanine (CalB_R3Bpa) as photoactive groups were used. For this purpose, M. tuberculosis H37Rv cells were treated with the respective probe for three hours at 37 °C and then exposed to UV light (λ = 365 nM) for 20 minutes at room temperature. The cells were lysed, and biotin was attached to probe-labeled proteins using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). These proteins were subsequently enriched with an avidin-matrix, which was thoroughly washed with a 1% SDS solution. Furthermore, a competitive AfBPP approach was chosen, to distinguish specific protein labeling from background labeling (ACE_0721). For this, the cells were treated with excess of unmodified CalB for 30 minutes prior to the addition of the respective photoprobe. In addition, it has been shown, that the susceptibility of M. tuberculosis H37Rv to CalB is highly dependent on the expression of the putative membrane protein Rv2113. A gene deletion mutation of this protein (Δrv2113) was used to identify further unspecific labeling of the AfBPP approach (ACE_0740).
HostingRepository	PRIDE
AnnounceDate	2024-07-25
AnnouncementXML	Submission_2024-07-25_10:27:55.077.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Farnusch Kaschani
SpeciesList	scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: 83332;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-19 09:05:20	ID requested
⏵ 1	2024-07-25 10:27:55	announced

10.1016/j.chembiol.2024.06.002;

Podlesainski D, Adeniyi ET, Gr, ö, ner Y, Schulz F, Krisilia V, Rehberg N, Richter T, Sehr D, Xie H, Simons VE, Kiffe-Delf AL, Kaschani F, Ioerger TR, Kaiser M, Kalscheuer R, The anti-tubercular callyaerins target the Mycobacterium tuberculosis-specific non-essential membrane protein Rv2113. Cell Chem Biol, ():(2024) [pubmed]

submitter keyword: Callyaerin

Mycobacterium tuberculosis

cyclopeptide

natural product

antibiotic action

anti-TB drug development

photoaffinity labelling

Farnusch Kaschani
contact affiliation	Farnusch Kaschani, Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany
contact email	farnusch.kaschani@uni-due.de
lab head
Farnusch Kaschani
contact affiliation	University Duisburg-Essen
contact email	farnusch.kaschani@uni-due.de
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/2024/07/PXD050770

PRIDE project URI

• PRIDE
  1. PXD050770
     1. Label: PRIDE project
     2. Name: Affinity-based protein profiling (AfBPP) using different Callyaerin probes in M. tuberculosis H37Rv