Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation

• Published in: The journal of physical chemistry letters 2024-02, Vol.15 (4), p.940-946
• Main Authors: Samuel Russell, Premila P., Maytin, Andrew K., Rickard, Meredith M., Russell, Matthew C., Pogorelov, Taras V., Gruebele, Martin
• Format: Article
• Language: English
• Subjects: Physical Insights into Materials and Molecular Properties
• ISSN: 1948-7185; 1948-7185
• DOI: 10.1021/acs.jpclett.3c03134

Many enzymes undergo major conformational changes to function in cells, particularly when they bind to more than one substrate. We quantify the large-amplitude hinge-bending landscape of human phosphoglycerate kinase (PGK) in a human cytoplasm. Approximately 70 μs of all-atom simulations, upon coarse graining, reveal three metastable states of PGK with different hinge angle distributions and additional substates. The “open” state was more populated than the “semi-open” or “closed” states. In addition to free energies and barriers within the landscape, we characterized the average transition state passage time of ≈0.3 μs and reversible substrate and product binding. Human PGK in a dilute solution simulation shows a transition directly from the open to closed states, in agreement with previous SAXS experiments, suggesting that the cell-like model environment promotes stability of the human PGK semi-open state. Yeast PGK also sampled three metastable states within the cytoplasm model, with the closed state favored in our simulation.