Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

Ruyu Jia, Chloe Martens, Mrinal Shekhar , Shashank Pant, Grant Pellowe, Andy M. Lau, Heather Findlay, Nicola Harris, Emad Tajkhorshid, Paula Booth, Argyris Politis

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)
152 Downloads (Pure)

Abstract

Proton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.
Original languageEnglish
Article number6162
JournalNature Communications
Volume11
Early online date2 Dec 2020
DOIs
Publication statusPublished - 2 Dec 2020

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