PXD015275

PXD015275 is an original dataset announced via ProteomeXchange.

Title	Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations
Description	We have studied both the Spy and the FKBP protein-ligand systems by structural proteomics and molecular -dynamics simulations. We have used hydrogen/deuterium exchange, differential crosslinking, and surface modification to characterize the conformational changes that occur upon both peptide binding (Im7 with Spy) and small molecule binding (rapamycin with FKBP) to the protein. We have shown that, in both cases, the proteins are considerably disordered but their structures are different from the unfolded structure obtained with 8M urea in solution, and both proteins undergo a dramatic increase in secondary structure content upon ligand binding.
HostingRepository	PRIDE
AnnounceDate	2021-09-08
AnnouncementXML	Submission_2021-09-08_11:35:57.067.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Makepeace
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-09-02 01:17:28	ID requested
⏵ 1	2021-09-08 11:35:57	announced

Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH, Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. J Proteomics, 211():103544(2020) [pubmed]

submitter keyword: Structural proteomics

mass spectrometry

discrete molecular dynamics simulations

protein-ligand interaction

hydrogen/deuterium exchange

crosslinking/mass spectrometry

surface modification

conformational change

quantitative protein structure

intrinsically disordered protein

protein folding

Christoph H. Borchers
contact affiliation	1. University of Victoria Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada 2. Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada 3. Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada 4. Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada
contact email	christoph.borchers@mcgill.ca
lab head
Karl Makepeace
contact affiliation	University of Victoria
contact email	karlm@uvic.ca
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/2021/09/PXD015275

PRIDE project URI

• PRIDE
  1. PXD015275
     1. Label: PRIDE project
     2. Name: Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations