Computational Study of Allosteric Switch of NLRP3: How ATP Binding Unlocks the NACHT Domain

Abstract

The NLRP3 inflammasome acts as a central mediator of innate immunity, yet how ATP binding to the NACHT domain allosterically activates the NLRP3 inflammasome remains a critical open question. Here, we employ μs-scale molecular dynamics simulations to characterize the conformational landscapes of the NLRP3 NACHT domain in both ADP- (inactive) and ATP-bound (active) states. Our results reveal that ATP binding initiates a cascade of structural events, beginning with the local unwinding of the FISNA helix. This steric release facilitates a global domain expansion, characterized by the coordinated separation of the NBD from the WHD. ARG351 is dynamically recruited to coordinate the ATP γ-phosphate, thereby stabilizing the active conformation through a rearranged hydrogen-bond network at the NBD-HD2 hinge interface. These findings offer crucial insights into the ATP-induced allosteric mechanism of NLRP3, providing a theoretical foundation for the design of selective NLRP3 modulators as potential therapeutic agents for related diseases.