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March 8, 20260 citationsOpen Access

Structural basis for pH-responsive amino acid transport via SLC7A4

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DKDimitrios Kolokouris

Key Points

  • The research aims to elucidate the structural mechanisms by which SLC7A4 transports amino acids in response to pH changes.
  • Conducted molecular dynamics simulations on SLC7A4
  • Collected and analyzed initial and final structure coordinates
  • Generated parameter and topology files for simulations
  • Detailed system equilibration process over several steps
  • Provided essential molecular dynamics data for understanding SLC7A4 functionality
  • Demonstrated pH dependency in amino acid transport mechanisms
  • Included comprehensive files necessary for replication and open-science

Abstract

MD datafiles of SLC7A4 to go with the Nat Commun (Volume 17) 2026 manuscript: Structural basis for pH-responsive amino acid transport via SLC7A4. Dimitrios Kolokouris1,2,3, Anuja Bothra1,2, Takafumi Kato1,2, Yi C. Zeng1,2, Simon Lichtinger1,3, Joanne L. Parker1,2, Philip Biggin1,3, Simon Newstead1,2*. 1 Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK. 2 Kavli Institute of Nanoscience Discovery, University of Oxford, Oxford. 3Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, United Kingdom. This deposition provides the essential Molecular Dynamics data required for open-science and replication. Included are initial and final coordinates (GROMACS .gro/.pdb), parameter files (.mdp), topology (.top), index (.ndx), run input (.tpr), ligand parameterization files, and the system equilibration protocol (step 1–8 .mdp). Full details of data generation are described in the published manuscript.

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Cite This Study

Dimitrios Kolokouris (2025) studied this question.

synapsesocial.com/papers/69ada885bc08abd80d5bb8d5https://doi.org/10.5281/zenodo.17184929
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