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Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation
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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley & Sons, Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601872/ https://www.ncbi.nlm.nih.gov/pubmed/36173167 http://dx.doi.org/10.1002/pro.4420 |
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author | El‐Sayed, Sherihan Freeman, Sally Bryce, Richard A. |
author_facet | El‐Sayed, Sherihan Freeman, Sally Bryce, Richard A. |
author_sort | El‐Sayed, Sherihan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-9601872 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley & Sons, Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-96018722022-10-27 Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation El‐Sayed, Sherihan Freeman, Sally Bryce, Richard A. Protein Sci Full‐length Papers 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. John Wiley & Sons, Inc. 2022-09-21 2022-10 /pmc/articles/PMC9601872/ /pubmed/36173167 http://dx.doi.org/10.1002/pro.4420 Text en © 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Full‐length Papers El‐Sayed, Sherihan Freeman, Sally Bryce, Richard A. Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title | Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title_full | Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title_fullStr | Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title_full_unstemmed | Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title_short | Probing the effect of NEK7 and cofactor interactions on dynamics of NLRP3 monomer using molecular simulation |
title_sort | probing the effect of nek7 and cofactor interactions on dynamics of nlrp3 monomer using molecular simulation |
topic | Full‐length Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601872/ https://www.ncbi.nlm.nih.gov/pubmed/36173167 http://dx.doi.org/10.1002/pro.4420 |
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