ArticleProtein science : a publication of the Protein Society2022
Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 10 citations in OpenAlex.
- Nose-brain axis: A bridge from the nasal cavity to the central nervous system.Neural regeneration research · 2026Article
- Stage-dependent role of NEK7 in the inactive-to-active conformational transition of NLRP3 monomer.PLoS computational biology · 2026Article
- A derivative of PD156707 selectively inhibits NLRP3 inflammasome activation by directly binding to NLRP3.Scientific reports · 2026Article
- HOXA5 Suppresses NEK7-Mediated Alveolar Epithelial Pyroptosis in Acute Lung Injury by Transcriptionally Inhibiting KAT2A.The Kaohsiung journal of medical sciences · 2026Article
- Structural dynamics, pathogenic mechanisms, and therapeutic targeting of the NLRP3 inflammasome in lupus nephritis.Frontiers in immunology · 2026Review
- Structural Insight into the Binding Pattern and Interaction Mechanism of Antagonist MCC950 and Agonist BMS986299 with NLRP3 by Molecular Dynamics Simulation.Current computer-aided drug design · 2025Article
- Article
- Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants.Frontiers in molecular biosciences · 2024Article
- Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation.Protein science : a publication of the Protein Society · 2022Article
- A Selective Review and Virtual Screening Analysis of Natural Product Inhibitors of the NLRP3 Inflammasome.Molecules (Basel, Switzerland) · 2022Review
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Authors and funding
3 authors at 2 institutions in 2 countries.
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Abstract
The NLRP3 inflammasome is a cytoplasmic complex that regulates the activation of inflammatory cytokines and, given its implication in a range of diseases, is an important therapeutic target. The cofactor ATP and the centrosomal kinase NEK7 are important for NLRP3 activation. Here we have constructed and simulated computational models of full-length monomeric NLRP3 to shed light on the importance of NEK7 and cofactor interactions for its conformation and dynamics in aqueous solution. We find that molecular dynamics simulation reproduces well the features of the recently published cryo-EM structure of the ADP-bound NLRP3-NEK7 complex; on the removal of NEK7, the NLRP3 molecule adopts a more compact closed form during simulations. Replacement of ADP by ATP promotes a rearrangement of hydrogen-bonding interactions, domain interfaces, and a degree of opening of the NLRP3 conformation. We also examine the dynamics of an acidic loop of the LRR domain of NLRP3, which samples in a region observed in the NEK7-bound cryo-EM structure but not in an oligomeric form of inactive NLRP3. During the molecular dynamics simulations of NLRP3, we find some plasticity in its topology that suggests access routes for ATP to the cofactor pocket not immediately evident from the existing NEK7-bound cryo-EM structure. These computed dynamical trajectories of NLRP3 provide insight into coordinates of deformation that may be key for cofactor binding and inflammasome activation.
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