Denaturation of firefly luciferase at heat shock temperatures captured in silico

Firefly luciferase (Fluc) is a bioluminescent protein that is widely used in cell and molecular biology research. Specifically, it is a gold standard substrate in chaperone protein studies because its bioluminescence decrease and recovery are related to Fluc misfolding and chaperone-assisted refolding, respectively. Fluc is moderately stable at room temperature but quickly loses bioluminescent activity at elevated temperatures as a stable, misfolded conformation is induced, which persists upon cooling Fluc to room temperature. The heat shock protein 70 chaperone system can revert such structural changes, restoring bioluminescent activity. Although thermal denaturation of Fluc is often used in chaperone-assisted refolding reactions, little is known about the specific structural alterations that occur in Fluc at heat shock temperatures. In this study, we use comprehensive all-atom molecular dynamics simulations to investigate the structural dynamics of Fluc at room (∼25°C) and heat shock temperatures (∼42°C). We conduct simulations totaling over 100 µs across replicates, which allows a misfolded equilibrium to be approached. We find that at heat shock temperatures, Fluc undergoes subtle but long-lasting and reproducible conformational changes, namely the complete and irreversible denaturation of the α-helix at residues 405-411. We show the potential for this discrete change to inhibit Fluc bioluminescent activity. This consistent α-helix denaturation along with other small secondary structure changes outlined in this work are potential targets for chaperone systems known to restore Fluc activity after thermal denaturation. Therefore, our results inform a refined mechanism for chaperone-assisted refolding in which chaperone proteins may restore protein function by fixing localized structural perturbations as opposed to refolding an entirely denatured polypeptide chain.