Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

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Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/darus-3373, DaRUS, V1

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Description	Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether the newly resolved cryo-electron microscopy NINJ1 filaments are capable to cap membrane edges by multiscaling molecular dynamics simulations. Site-directed mutagenesis was employed to validate the function of the resulting supramolecular arrangement. The membrane protein NINJ1 is thus an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.
Subject	Medicine, Health and Life Sciences
Keyword	Molecular Dynamics Simulation, GROMACS, Filaments
Related Publication	Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, "Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death", Nature 2023 doi: 10.1038/s41586-023-05991-z
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	45-ring_CG_resid39-152_cryoEM.tar.gz Gzip Archive - 44.8 MB Published Mar 9, 2023 21 Downloads MD5: ece893fb0e4c783553ef62e82ca31fb2 simulations of ninjurin-1 rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains residues 39-152 in the cryoEM shape the dynamics of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was chosen as our initial test as well as literature https://pubs.acs.org/doi/10.1021/acs.jctc.1c00257 have shown that martini2.2p well reproduces filament structures Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10.1021/ct300646g martini2 (lipids): doi:10.1021/jp071097f	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	45-ring_CG_resid79-152.tar.gz Gzip Archive - 30.9 MB Published Mar 9, 2023 26 Downloads MD5: 198f9c7dfe0019557d4c4f05eed30837 control simulations of ninjurin-1 mutant rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains only the two transmembrane helices- i.e residues 79-152 the collapse of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was chosen as our initial test as well as literature https://pubs.acs.org/doi/10.1021/acs.jctc.1c00257 have shown that martini2.2p well reproduces filament structures Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10.1021/ct300646g martini2 (lipids): doi:10.1021/jp071097f	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	charmm36-jul2017.ff.tar.gz Gzip Archive - 390.5 KB Published Mar 9, 2023 18 Downloads MD5: 2465d1691943b03ccb7893d39f54fbdc charmm36m force field directory for GROMACS Please cite following papers if you use charmm36 parameters for protein: doi:10.1038/nmeth.4067 lipids: doi:10.1021/jp101759q cholesterol: doi:10.1021/jp207925m charmm-gui: doi:10.1002/jcc.20945 tip4p water: doi:10.1080/00268978500103111	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	doublefil_CG_noDMP.tar.gz Gzip Archive - 4.8 MB Published Mar 9, 2023 20 Downloads MD5: f73995912be7f84b7e0b939735a90abe ninjurin-1 double filaments coarse-grained simulations using Martini2 polarizable force field. the protein structure after simulation 1 was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10.1021/ct300646g martini2 (lipids): doi:10.1021/jp071097f	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	doublefil_CG_withDMP.tar.gz Gzip Archive - 4.4 MB Published Mar 9, 2023 20 Downloads MD5: ff1c621b0291dda0010f459c3721140c ninjurin-1 double filaments filled with dodecylmaltopyranoside coarse-grained simulations using Martini2 polarizable force field the protein structure after simulations was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10.1021/ct300646g martini2 (lipids): doi:10.1021/jp071097f	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	endlessmembranepatch_singlefilament_AA.tar.gz Gzip Archive - 23.2 MB Published Mar 9, 2023 21 Downloads MD5: 7f4c6b23f12e1fdd5e1da6928146e460 here are two 1 µs-long all-atom simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 5 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	endlessmembranepatch_singlefilament_CG.tar.gz Gzip Archive - 14.3 MB Published Mar 9, 2023 16 Downloads MD5: fcfbc234143822286b87b31ae761929f two 20 µs-long Martini2P simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 10 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10.1021/ct300646g martini2 (lipids): doi:10.1021/jp071097f	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	resolution_conversion_5B.tar.gz Gzip Archive - 5.0 MB Published Mar 9, 2023 21 Downloads MD5: 0a0c3474e575280bb3af6b5888ae2fc9 backwarding files for martini lipids containing 5 beads in the oleoyl chain to charmm36 force field please cite backward: doi:10.1021/ct400617g	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	singlefil_AA_resid39-152_alphafoldstructure.tar.gz Gzip Archive - 2.3 MB Published Mar 9, 2023 17 Downloads MD5: 9dd0e348234886fd5780f1153d8f2060 this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the structure that resulted from the alphafold prediction in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX
	singlefil_AA_resid39-152_cryoEMstructure.tar.gz Gzip Archive - 1.6 MB Published Mar 9, 2023 12 Downloads MD5: c102e5587521a452aedef9a84cff0958 this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the cryoEM structure in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.	Access File File Access Public Download Options Gzip Archive Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/darus-3373
Publication Date	2023-03-09
Title	Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'
Author	Degen, Morris (Biozentrum, University of Basel) - ORCID: 0000-0003-3762-5779 Santos, José Carlos (Department of Immunobiology, University of Lausanne) - ORCID: 0000-0002-3446-4001 Pluhackova, Kristyna (SC SimTech, University of Stuttgart) - ORCID: 0000-0002-7498-6584 Cebrero, Gonzalo (Biozentrum, University of Basel) - ORCID: 0000-0001-7171-0921 Ramos, Saray (Department of Immunobiology, University of Lausanne) - ORCID: 0000-0001-6015-9310 Jankevicius, Gytis (Biozentrum, University of Basel) - ORCID: 0000-0002-0212-3923 Hartenian, Ella (Department of Immunobiology, University of Lausanne) - ORCID: 0000-0001-9277-2152 Guillerm, Undina (Institute of Science and Technology Austria) Mari, Stefania A. (Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich) - ORCID: 0000-0002-6420-8578 Kohl, Bastian (Biozentrum, University of Basel) - ORCID: 0000-0001-6601-8340 Müller, Daniel J. (Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich) - ORCID: 0000-0003-3075-0665 Schanda, Paul (Institute of Science and Technology Austria) - ORCID: 0000-0002-9350-7606 Maier, Timm (Biozentrum, University of Basel) - ORCID: 0000-0002-7459-1363 Perez, Camilo (Biozentrum, University of Basel) - ORCID: 0000-0002-5800-0084 Sieben, Christian (Institute for Genetics, Technische Universität Braunschweig; Nanoscale Infection Biology Group, Department of Cell Biology, Helmholtz Centre for Infection Research) - ORCID: 0000-0002-2836-2623 Broz, Petr (Department of Immunobiology, University of Lausanne) - ORCID: 0000-0002-2334-7790 Hiller, Sebastian (Biozentrum, University of Basel) - ORCID: 0000-0002-6709-4684
Point of Contact	Use email button above to contact. Pluhackova, Kristyna (University of Stuttgart)
Description	Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether the newly resolved cryo-electron microscopy NINJ1 filaments are capable to cap membrane edges by multiscaling molecular dynamics simulations. Site-directed mutagenesis was employed to validate the function of the resulting supramolecular arrangement. The membrane protein NINJ1 is thus an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.
Subject	Medicine, Health and Life Sciences
Keyword	Molecular Dynamics Simulation https://www.wikidata.org/wiki/Q901663 (Wikidata) GROMACS https://www.wikidata.org/wiki/Q905302 (Wikidata) Filaments https://www.wikidata.org/wiki/Q1340591 (Wikidata)
Related Publication	Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, "Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death", Nature 2023 doi: 10.1038/s41586-023-05991-z https://doi.org/10.1038/s41586-023-05991-z
Language	English
Funding Information	DFG: EXC 2075 - 390740016 Ministry of Science, Research and the Arts Baden-Württemberg: HoreKa supercomputer Federal Ministry of Education and Research: HoreKa supercomputer
Depositor	Pluhackova, Kristyna
Deposit Date	2023-03-06
Data Type	Files and structures for molecular dynamics simulations
Software	GROMACS, Version: 2020 and 2021

Process Metadata

Software

GROMACS Version: 2020 and 2021 (https://www.gromacs.org/) LGPL-2.1-or-later (1: B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, “GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation”, J. Chem. Theory Comput., 4 [3] 435-447 (2008), doi: 10.1021/ct700301q. 2: S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, and J.C. Smith et al., “GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit", Bioinformatics, 29 [7] 845-854 (2013), doi: 10.1093/bioinformatics/btt055. 3: S. Páll, M.J. Abraham, C. Kutzner, B. Hess, and E. Lindahl, “Tackling exascale software challenges in molecular dynamics simulations with GROMACS”; pp. 3-27 in Solving software challenges for exascale. Edited by S. Markidis and E. Laure. Springer International Publishing Switzerland, London, 2015, doi: 10.1007/978-3-319-15976-8_1. 4: M.J. Abraham, T. Murtola, R. Schulz, S. Páll, J.C. Smith, B. Hess, and E. Lindahl, “GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers,” SoftwareX, 1-2 19-25 (2015), doi: 10.1016/j.softx.2015.06.001.)

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Force Field	CHARMM36 force field Martini force field

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