Broz, P., Pelegrín, P. & Shao, F. The gasdermins, a protein family executing cell death and inflammation. Nat. Rev. Immunol. 20, 143–157 (2020).
Lieberman, J., Wu, H. & Kagan, J. C. Gasdermin D activity in inflammation and host defense. Sci. Immunol. 4, eaav1447 (2019).
Shi, J., Gao, W. & Shao, F. Pyroptosis: gasdermin-mediated programmed necrotic cell death. Trends Biochem. Sci 42, 245–254 (2017).
Liu, X. et al. Inflammasome-activated gasdermin D causes pyroptosis by forming membrane pores. Nature 535, 153–158 (2016).
Ding, J. et al. Pore-forming activity and structural autoinhibition of the gasdermin family. Nature 535, 111–116 (2016).
Ruan, J., Xia, S., Liu, X., Lieberman, J. & Wu, H. Cryo-EM structure of the gasdermin A3 membrane pore. Nature 557, 62–67 (2018).
Xia, S. et al. Gasdermin D pore structure reveals preferential release of mature interleukin-1. Nature 593, 607–611 (2021).
Wang, C. et al. Structural basis for GSDMB pore formation and its targeting by IpaH7.8. Nature 616, 590–597 (2023).
Zhong, X. et al. Structural mechanisms for regulation of GSDMB pore-forming activity. Nature 616, 598–605 (2023).
Rogers, C. et al. Gasdermin pores permeabilize mitochondria to augment caspase-3 activation during apoptosis and inflammasome activation. Nat. Commun. 10, 1–17 (2019).
Hansen, J. M. et al. Pathogenic ubiquitination of GSDMB inhibits NK cell bactericidal functions. Cell 184, 3178–3191.e18 (2021).
Jiang, S., Zhou, Z., Sun, Y., Zhang, T. & Sun, L. Coral gasdermin triggers pyroptosis. Sci. Immunol. 5, eabd2591 (2020).
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).
Clavé, C. et al. Fungal gasdermin-like proteins are controlled by proteolytic cleavage. Proc. Natl Acad. Sci. USA 119, e2109418119 (2022).
Johnson, A. G. et al. Bacterial gasdermins reveal an ancient mechanism of cell death. Science 375, 221–225 (2022).
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).
Dudkina, N. V. et al. Structure of the poly-C9 component of the complement membrane attack complex. Nat. Commun. 7, 10588 (2016).
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).
van Pee, K. et al. CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin. eLife 6, e23644 (2017).
Sborgi, L. et al. GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death. EMBO J. 35, 1766–1778 (2016).
Schaefer, S. L. & Hummer, G. Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022).
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).
Holm, L. Dali server: structural unification of protein families. Nucleic Acids Res. 50, W210–W215 (2022).
van Kempen, M. et al. Fast and accurate protein structure search with Foldseek. Nat. Biotechnol. 42, 243–246 (2023).
Mari, S. A. et al. Gasdermin-A3 pore formation propagates along variable pathways. Nat. Commun. 13, 2609 (2022).
Johnson, A. G. & Kranzusch, P. J. What bacterial cell death teaches us about life. PLoS Pathog. 18, e1010879 (2022).
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).
Strahl, H. & Errington, J. Bacterial membranes: structure, domains, and function. Annu. Rev. Microbiol. 71, 519–538 (2017).
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).
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).
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
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).
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).
Abraham, M. J. et al. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).
Huang, J. et al. CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat. Methods 14, 71–73 (2017).
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
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).
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
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).
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.
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).
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).