1. ABOUT THE DATASET -------------------- Title: Simulation data from the publication - Guffick et al., “Native-like substrate induced conformational dynamics of Eukaryotic Transporter UapA probed by HDX-MS” Creator(s): [Pontes, F.; Kalli, A.;] Organisation(s): [University of Leeds.] Rights-holder(s):Unless otherwise stated, Copyright 2023 University of Leeds Publication Year: 2026 Description: [A repository of simulation data from the publication “Native-like substrate induced conformational dynamics of Eukaryotic Transporter UapA probed by HDX-MS”. 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. Here, hydrogen-deuterium exchange mass spectrometry (HDX-MS) was used to explore substrate binding to UapA within native-like lipid nanodiscs. Computer simulation data supports the different dynamics among wild-type and mutant species.] Cite as: [ Pontes, F.; Kalli, A.; (2026) Dataset for 'Native-like substrate induced conformational dynamics of Eukaryotic Transporter UapA probed by HDX-MS' University of Leeds. [Dataset] https://doi.org/10.5518/1943] Related publication: [Native-like substrate induced conformational dynamics of Eukaryotic Transporter UapA probed by HDX-MS.Native-like substrate induced conformational dynamics of Eukaryotic Transporter UapA probed by HDX-MS. Guffick, C, Gaytán Mondragón, S, Pontes, F, Pyle, E, Kalli, A. C., Byrne, B, Politis, A] Contact: [This is optional. If you wish, enter a contact email or other details for a corresponding Creator.] 2. TERMS OF USE --------------- Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/. 3. PROJECT AND FUNDING INFORMATION ---------------------------------- This study was supported by BBSRC BB/Z517227/1 grant. The computational work was undertaken on AIRE, part of the High Performance Computing facilities at the University of Leeds, UK. This project also made use of time on HPC granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1). 4. CONTENTS ----------- The data has been divided into 2 dataset zip files: [dataset] [name] [description] 1 AA.tar.gz All-atom MD simulation data for the wildtype and mutants simulated in a membrane environment. 3 replicas for each system. 2 CG.tar.gz Coarse grain MD simulation data for the wildtype and mutants simulated in a membrane environment.5 replicas for each system. .tpr files are GROMACS binary input run files for a simulation .gro files are the coordinates from the final frame of a simulation .xtc files are the GROMACS simulation trajectories, thinned to 10% and 4% of their original size (due to memory limitations) by only writing every 10th/40th frame from the original for coarse grain and all-atom trajectories, respectivelly. 5. METHODS ---------- - The simulation data were generated using all-atom and coarse grained molecular dynamics simulations of a full-length structural model of wild-type eukaryotic purine/H+ symporter, UapA (PDB ID: 5I6C) with and its mutants G411V and Q408E insert in a lipid bilayer.