Broz, P., Pelegrín, P. & Shao, F. The gasdermins, a protein family executing cell death and inflammation. Nat. Rev. Immunol. 20, 143–157 (2020).
Google Scholar
Lieberman, J., Wu, H. & Kagan, J. C. Gasdermin D activity in inflammation and host defense. Sci. Immunol. 4, eaav1447 (2019).
Google Scholar
Shi, J., Gao, W. & Shao, F. Pyroptosis: gasdermin-mediated programmed necrotic cell death. Trends Biochem. Sci 42, 245–254 (2017).
Google Scholar
Liu, X. et al. Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores. Nature 535, 153–158 (2016).
Google Scholar
Ding, J. et al. Pore-forming activity and structural autoinhibition of the gasdermin family. Nature 535, 111–116 (2016).
Google Scholar
Ruan, J., Xia, S., Liu, X., Lieberman, J. & Wu, H. Cryo-EM structure of the gasdermin A3 membrane pore. Nature 557, 62–67 (2018).
Google Scholar
Xia, S. et al. Gasdermin D pore structure reveals preferential release of mature interleukin-1. Nature 593, 607–611 (2021).
Google Scholar
Wang, C. et al. Structural basis for GSDMB pore formation and its targeting by IpaH7.8. Nature 616, 590–597 (2023).
Google Scholar
Zhong, X. et al. Structural mechanisms for regulation of GSDMB pore-forming activity. Nature 616, 598–605 (2023).
Google Scholar
Rogers, C. et al. Gasdermin pores permeabilize mitochondria to augment caspase-3 activation during apoptosis and inflammasome activation. Nat. Commun. 10, 1–17 (2019).
Google Scholar
Hansen, J. M. et al. Pathogenic ubiquitination of GSDMB inhibits NK cell bactericidal functions. Cell 184, 3178–3191.e18 (2021).
Google Scholar
Jiang, S., Zhou, Z., Sun, Y., Zhang, T. & Sun, L. Coral gasdermin triggers pyroptosis. Sci. Immunol. 5, eabd2591 (2020).
Google Scholar
Daskalov, A., Mitchell, P. S., Sandstrom, A., Vance, R. E. & Glass, N. L. Molecular characterization of a fungal gasdermin-like protein. Proc. Natl Acad. Sci. USA 117, 18600–18607 (2020).
Google Scholar
Clavé, C. et al. Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proc. Natl Acad. Sci. USA 119, e2109418119 (2022).
Google Scholar
Johnson, A. G. et al. Bacterial gasdermins reveal an ancient mechanism of cell death. Science 375, 221–225 (2022).
Google Scholar
Pang, S. S. et al. The cryo-EM structure of the acid activatable pore-forming immune effector macrophage-expressed gene 1. Nat. Commun. 10, 4288 (2019).
Google Scholar
Dudkina, N. V. et al. Structure of the poly-C9 component of the complement membrane attack complex. Nat. Commun. 7, 10588 (2016).
Google Scholar
Tilley, S. J., Orlova, E. V., Gilbert, R. J. C., Andrew, P. W. & Saibil, H. R. Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 121, 247–256 (2005).
Google Scholar
van Pee, K. et al. CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin. eLife 6, e23644 (2017).
Google Scholar
Sborgi, L. et al. GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death. EMBO J. 35, 1766–1778 (2016).
Google Scholar
Schaefer, S. L. & Hummer, G. Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022).
Google Scholar
Gilbert, R. J. C. et al. Two structural transitions in membrane pore formation by pneumolysin, the pore-forming toxin of Streptococcus pneumoniae. Cell 97, 647–655 (1999).
Google Scholar
Holm, L. Dali server: structural unification of protein families. Nucleic Acids Res. 50, W210–W215 (2022).
Google Scholar
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2023).
Google Scholar
Mari, S. A. et al. Gasdermin-A3 pore formation propagates along variable pathways. Nat. Commun. 13, 2609 (2022).
Google Scholar
Johnson, A. G. & Kranzusch, P. J. What bacterial cell death teaches us about life. PLoS Pathog. 18, e1010879 (2022).
Google Scholar
Peraro, M. D. & Van Der Goot, F. G. Pore-forming toxins: ancient, but never really out of fashion. Nat. Rev. Microbiol. 14, 77–92 (2016).
Google Scholar
Strahl, H. & Errington, J. Bacterial membranes: structure, domains, and function. Annu. Rev. Microbiol. 71, 519–538 (2017).
Google Scholar
Du, G. et al. ROS-dependent palmitoylation is an obligate licensing modification for GSDMD pore formation. Preprint at bioRxiv https://doi.org/10.1101/2023.03.07.531538 (2023).
Balasubramanian, A. et al. Palmitoylation of gasdermin D directs its membrane translocation and pore formation in pyroptosis. Preprint at bioRxiv https://doi.org/10.1101/2023.02.21.529402 (2023).
Tan, B. K. et al. Discovery of a cardiolipin synthase utilizing phosphatidylethanolamine and phosphatidylglycerol as substrates. Proc. Natl Acad. Sci. USA 109, 16504–16509 (2012).
Google Scholar
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Google Scholar
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Google Scholar
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Google Scholar
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
Google Scholar
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Google Scholar
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Google Scholar
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
Google Scholar
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Google Scholar
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865 (2008).
Google Scholar
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
Google Scholar
Abraham, M. J. et al. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
Google Scholar
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017).
Google Scholar
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
Google Scholar
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: A linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).
Google Scholar
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
Google Scholar
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984).
Google Scholar
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996). 27–8.
Google Scholar
Gowers, R. et al. in Proc. 15th Python in Science Conference (eds Benthall, S. & Rostrup, S.) 98–105 (2016).
Michaud‐Agrawal, N., Denning, E. J., Woolf, T. B. & Beckstein, O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J. Comput. Chem. 32, 2319–2327 (2011).
Google Scholar
Schaefer, S. L. & Hummer, G. Raw data for: Structure and assembly of a bacterial gasdermin pore. Zenodo https://doi.org/10.5281/zenodo.7828403 (2023).
Schaefer, S. L. & Hummer, G. Additional raw data for: Structure and assembly of a bacterial gasdermin pore. Zenodo https://doi.org/10.5281/zenodo.8272143 (2023).