PXD054550

PXD054550 is an original dataset announced via ProteomeXchange.

Title	PIGEON-FEATHER datasets, extracting site-resolved energetic information from HX/MS experiments
Description	We present PIGEON-FEATHER, a method for calculating free energies of opening (∆Gop) at single- or near-single-amino acid resolution for protein ensembles of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data. PIGEON-FEATHER disambiguates and reconstructs all experimentally measured isotopic mass envelopes using a Bayesian Monte Carlo sampling approach. We applied PIGEON-FEATHER to reveal how E. coli and human dihydrofolate reductase (ecDHFR, hDHFR) have evolved distinct conformational ensembles tuned to their catalytic cycles. We showed how two competitive inhibitors of ecDHFR arrest its ensemble in different ways, only one of which is compatible with vertebrate DHFR orthologs. Finally, we uncovered how the lac repressor (LacI) ensemble responds to binding its inducer molecule and operator DNA to regulate transcriptional activation.
HostingRepository	PRIDE
AnnounceDate	2024-08-06
AnnouncementXML	Submission_2024-08-06_02:00:20.028.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chenlin Lu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	maXis

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-02 19:39:31	ID requested
⏵ 1	2024-08-06 02:00:20	announced

10.1101/2024.08.04.606547;

submitter keyword: ecDHFR, hDHFR, LacI, HX/MS

Anum Glasgow
contact affiliation	Columbia University, Dept. of Biochemistry and Molecular Biophysics
contact email	ag4522@cumc.columbia.edu
lab head
Chenlin Lu
contact affiliation	Columbia University Irving Medical Center
contact email	lucltsinghua@gmail.com
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/2024/08/PXD054550

PRIDE project URI

• PRIDE
  1. PXD054550
     1. Label: PRIDE project
     2. Name: PIGEON-FEATHER datasets, extracting site-resolved energetic information from HX/MS experiments