PXD020434-1

PXD020434 is an original dataset announced via ProteomeXchange.

Title	Allosteric priming of E. coli CheY by the flagellar motor protein FliM
Description	We detail simulations and solution measurements to better understand the differences between the native and D13K-Y106W CheY crystal structures. We resolved the complex conformational landscapes by MD simulations with mutual information measures to determine the coupling between protein fragments. Protection experiments with XFMS (X-ray foot-printing with mass spectroscopy), a technique that probed sidechain solvent accessibility in contrast to deuterium exchange of backbone hydrogen atoms, supported the FliMN requirement for D13K-Y106W CheY activation reported by the crystal structures, and the MD allosteric network model. XFMS has a more straight-forward physical rationale than fluorescence quenching for reporting sidechain motions over time-resolved windows and is not limited by the size of the protein assembly. Further analysis of the MD trajectories resolved multiple CheY Y106 rotamer states. Inward orientation was temporally coupled to stabilization of both the CheY fold and the FliMN interface in the CheY·FliMN complex, but not in CheY alone. The coupling increased in D13K-Y106WCheY·FliMN. The formation of a distinct module that orchestrates CheY dynamicsto stabilize new surface topologies for possible second-stage binding to FliN was the signature of the fully activated D13K-Y106W CheY·FliMN state.
HostingRepository	PRIDE
AnnounceDate	2020-09-21
AnnouncementXML	Submission_2020-09-20_22:45:27.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020434
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Escherichia coli BL21(DE3); NCBI TaxID: 469008;
ModificationList	dihydroxylated residue; monohydroxylated residue
Instrument	6550 iFunnel Q-TOF LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-19 22:01:26	ID requested
⏵ 1	2020-09-20 22:45:28	announced
2	2024-10-22 05:12:32	announced	2024-10-22: Updated project metadata.

Wheatley P, Gupta S, Pandini A, Chen Y, Petzold CJ, Ralston CY, Blair DF, Khan S, coli CheY by the Flagellar Motor Protein FliM. Biophys J, 119(6):1108-1122(2020) [pubmed]

submitter keyword: CheY, FliM, XFMS, Atomistic simulation, Flagellar

Christopher J. Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
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/2020/09/PXD020434

PRIDE project URI

• PRIDE
  1. PXD020434
     1. Label: PRIDE project
     2. Name: Allosteric priming of E. coli CheY by the flagellar motor protein FliM