PXD018145

PXD018145 is an original dataset announced via ProteomeXchange.

Title	Distinct dynamics upon substrate and inhibitor binding to a secondary transporter
Description	The bacterial sugar transporter XylE is a proton-coupled symporter from the Major Facilitator Family (MFS) that has been crystalized in multiple conformations, and with both substrate xylose and inhibitor glucose bound. However, this series of static pictures does not capture the coupling between ligand binding and conformational changes required for transport. Furthermore, the ability for the transporter to discriminate between substrate and inhibitor is puzzling in light of the similarity of the bound structures. Here, we combine differential HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of transport in XylE. We show that protonation of D27 is a key event for conformational transition from outward-facing (OF) to inward-facing (IF). Strikingly, this transition only occurs in the presence of substrate xylose, while inhibitor glucose locks the transporter in the OF state. We corroborate our experimental findings with MD simulations by showing that D27 protonation in the presence of xylose, but not glucose, leads to unstable substrate binding, increased solvent accessibility, and correlated motions between the N- and C- lobes of the transporter, effectively setting the transporter up for the conformational transition. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding to XylE and propose that the allosteric coupling between ligand binding and protonation is a key step to initiate transport.
HostingRepository	PRIDE
AnnounceDate	2021-03-23
AnnouncementXML	Submission_2021-03-23_11:22:12.662.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ruyu Jia
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-23 03:49:15	ID requested
⏵ 1	2021-03-23 11:22:13	announced

Jia R, Martens C, Shekhar M, Pant S, Pellowe GA, Lau AM, Findlay HE, Harris NJ, Tajkhorshid E, Booth PJ, Politis A, Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. Nat Commun, 11(1):6162(2020) [pubmed]

submitter keyword: Hydrogen-deuterium exchange mass spectrometry (HDX-MS), membrane proteins, conformational dynamics, molecular dynamics simulations, secondary transporters, molecular transport, major facilitator superfamily

Argyris Politis
contact affiliation	Chemistry Department, King's College London
contact email	argyris.politis@kcl.ac.uk
lab head
Ruyu Jia
contact affiliation	King's College London
contact email	ruyu.jia@kcl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD018145
     1. Label: PRIDE project
     2. Name: Distinct dynamics upon substrate and inhibitor binding to a secondary transporter