Research Data Leeds Repository

Citation

Pontes, Federico and Kalli, Antreas (2026) UapA MD Simulations. University of Leeds. [Dataset] https://doi.org/10.5518/1943

Dataset description

Understanding the mechanism of substrate profiles within the ubiquitous Nucleobase-Ascorbate Transporter (NAT) family is of interest from both an evolutionary and a biomedical angle. The xanthine/uric acid-H+-symporter UapA, is a defining member of the NAT family. Conformational heterogeneity remains elusive, as the transporter strongly favours the inward-facing (IF) state. Here, we utilise hydrogen-deuterium exchange mass spectrometry (HDX-MS) to explore substrate binding to UapA within native-like lipid nanodiscs. We reveal that xanthine induces stability across the wild-type (WT) protein, including into the dimerisation domain and the dynamic N-tail domain. Additionally, characterisation of the NAT signature motif mutant, Q408E, with both native and non-native substrates reveals heterogeneous conformational dynamics relative to the inward-facing stabilised mutant. HDX-MS additionally highlights apparent localised intrinsic unfolding above the substrate binding site, modulated by global protein stability. HDX-MS of UapA puts context to historical genetic and functional study that could not be probed with current structures.

Keywords:	eukaryotic membrane protein; nucleobase ascorbate transporter; hydrogen deuterium exchange mass spectrometry; nanodiscs; EX1 kinetics; conformational dynamics; protein dynamic
Divisions:	Faculty of Medicine and Health > School of Medicine > Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM)
License:	Creative Commons Attribution 4.0 International (CC BY 4.0)
Date deposited:	23 Oct 2026 20:05
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/1653
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Pontes, Federico https://orcid.org/0000-0002-3938-6866 University of Leeds https://ror.org/024mrxd33 ror Kalli, Antreas https://orcid.org/0000-0001-7156-9403 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: BBSRC Grant numbers: BB/Z517227/1 Publication date: 2026 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: medfpo@leeds.ac.uk Last Modified: 23 Oct 2026 20:08

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Documentation

readme [3kB] readme [3kB] readme [3kB] Security: Anyone File name: readme_pontes_2026.txt Content type: Documentation Mime-Type: text/plain License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3kB

Data

AA.tar.gz [6GB] AA.tar.gz [6GB] AA.tar.gz [6GB] Security: Anyone File name: AA.tar.gz Content type: Data Description: All-atom MD Simulations for UapA_WT, UapA_UapA_G411V and UapA_UapA_Q408E embedded in a lipid bilayer. Mime-Type: application/x-gzip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB

CG.tar.gz [6GB] CG.tar.gz [6GB] CG.tar.gz [6GB] Security: Anyone File name: CG.tar.gz Content type: Data Description: Coarse-grained MD Simulations for UapA_WT, UapA_UapA_G411V and UapA_UapA_Q408E embedded in a lipid bilayer. Mime-Type: application/x-gzip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 6GB