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AutoDock Vina calculations of the µ-Opioid Receptor Complexed with Carfentanil Analogs
Borealis
Wiebe, Heather — 2024-05-30 AutoDock Vina 1.2.3 was used to calculate binding poses and binding energies for carfentanil and its structural analogs inside the binding site of the µ-opioid receptor. All structural analogues exhibited identical binding poses to carfentanil with similar binding energies, indicating that the analogs may be biologically active. This dataset contains AutoDock Vina input files, final docked structures and binding energies, and instructions for running the calculations.
Vancouver Island University Dataverse Translation missing: fr.blacklight.search.logo
The origin of pressure resistance in deep-sea lactate dehydrogenase
Borealis
Wiebe, Heather — 2024-07-16 High hydrostatic pressure has a dramatic effect on biochemical systems, as exposure to high pressure can result in structural perturbations ranging from dissociation of protein complexes to complete denaturation. The deep ocean presents an interesting paradox since it is teeming with life despite the high-pressure environment. This is due to evolutionary adaptations in deep-sea organisms, such as amino acid substitutions in their proteins, which aid in resisting the denaturing effects of pressure. However, the physico-chemical mechanism by which these substitutions can induce pressure resistance remains unknown. Here, we use molecular dynamics simulations to study pressure-adapted lactate dehydrogenase from the deep-sea abyssal grenadier (C. armatus), in comparison with that of the shallow-water Atlantic cod (G. morhua). Alchemical thermodynamic integration and the Archimedean Displacement Method were used to determine whether pressure resistance is due to a thermodynamic stabilization of the native state of the protein or to an increase in the volume of the denatured state. We report that the amino acid substitutions destabilize the folded protein, but pressure resistance is achieved through an increase in compressibility for the pressure-adapted protein. This dataset contains input files and run scripts for the alchemical free energy calculations and the volume calculations. See README.txt files within each archive for specific details on how to run and analyze the calculations.

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(auteur : Wiebe, Heather)

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