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Showing 1–9 of 9 results
Advanced filters: Author: Mrinal Shekhar Clear advanced filters

  • This protocol combines hydrogen–deuterium exchange mass spectrometry (HDX-MS) of membrane proteins in nanodiscs with molecular dynamics (MD) simulations to identify lipid–protein interactions that modulate conformational changes.

    • Chloe Martens
    • Mrinal Shekhar
    • Argyris Politis
    Protocols
    Nature Protocols
    Volume: 14, P: 3183-3204

  • The EMDataResource Ligand Model Challenge aimed at assessing the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryo-EM maps determined at near-atomic resolution. This analysis presents the results and recommends best practices for assessing cryo-EM structures of liganded macromolecules.

    • Catherine L. Lawson
    • Andriy Kryshtafovych
    • Wah Chiu
    Research
    Nature Methods
    Volume: 21, P: 1340-1348

  • A multi-laboratory study in the form of a community challenge assesses the quality of models that can be produced from cryo-EM maps using different software tools, the reproducibility of models generated by different users and the performance of metrics used for model validation.

    • Catherine L. Lawson
    • Andriy Kryshtafovych
    • Wah Chiu
    ResearchOpen Access
    Nature Methods
    Volume: 18, P: 156-164

  • XylE is a bacterial xylose transporter and homologue of human glucose transporters GLUTs 1-4. HDX-MS, mutagenesis and MD simulations suggest that protonation of a conserved aspartate triggers conformational transition from outward- to inward facing state only in the presence of substrate xylose. In contrast, inhibitor glucose locks the transporter in the outward facing state.

    • Ruyu Jia
    • Chloe Martens
    • Argyris Politis
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-10

  • There is a great interest in retrieving functional pathways from cryo-EM single-particle data. Here, the authors present an approach that combines cryo-EM with advanced data-analytical methods and molecular dynamics simulations to reveal the functional pathways traversed on experimentally derived energy landscapes using the ryanodine receptor type 1 as an example.

    • Ali Dashti
    • Ghoncheh Mashayekhi
    • Abbas Ourmazd
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-14

  • Secondary transporters catalyse substrate translocation across the cell membrane but the role of lipids during the transport cycle remains unclear. Here authors used hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations to understand how lipids regulate the conformational dynamics of secondary transporters.

    • Chloe Martens
    • Mrinal Shekhar
    • Argyris Politis
    ResearchOpen Access
    Nature Communications
    Volume: 9, P: 1-12