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

Version 1.1
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
Learn about Data Citation Standards.
Dataset Metrics
288 Downloads
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 2023doi: 10.1038/s41586-023-05991-z
License/Data Use Agreement

CC BY 4.0

Filter by
1 to 10 of 11 Files
45-ring_CG_resid39-152_cryoEM.tar.gz
Gzip Archive - 44.8 MB
Published Mar 9, 2023
28 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
45-ring_CG_resid79-152.tar.gz
Gzip Archive - 30.9 MB
Published Mar 9, 2023
39 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
charmm36-jul2017.ff.tar.gz
Gzip Archive - 390.5 KB
Published Mar 9, 2023
26 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
doublefil_CG_noDMP.tar.gz
Gzip Archive - 4.8 MB
Published Mar 9, 2023
25 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
doublefil_CG_withDMP.tar.gz
Gzip Archive - 4.4 MB
Published Mar 9, 2023
26 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
endlessmembranepatch_singlefilament_AA.tar.gz
Gzip Archive - 23.2 MB
Published Mar 9, 2023
28 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
endlessmembranepatch_singlefilament_CG.tar.gz
Gzip Archive - 14.3 MB
Published Mar 9, 2023
23 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
resolution_conversion_5B.tar.gz
Gzip Archive - 5.0 MB
Published Mar 9, 2023
25 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
singlefil_AA_resid39-152_alphafoldstructure.tar.gz
Gzip Archive - 2.3 MB
Published Mar 9, 2023
29 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.
singlefil_AA_resid39-152_cryoEMstructure.tar.gz
Gzip Archive - 1.6 MB
Published Mar 9, 2023
18 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.
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue
Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

You may request access to any restricted file(s) by clicking the Request Access button.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

You may request access to any restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 1.9 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Preview URL

Preview URL can only be used with unpublished versions of datasets.

Unpublished Dataset Preview URL

Are you sure you want to disable the Preview URL? If you have shared the Preview URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

CC BY 4.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://darus.uni-stuttgart.de/api/access/datafile/

Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

Please use the publication checklist for authors ( https://www.izus.uni-stuttgart.de/en/fokus/darus/publication/ ) to ensure publication readiness. You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until PN 3-11 is published by its administrator.

Publish Dataset

This dataset cannot be published until PN 3-11 and PN 3 are published.

Return to Author

Return this dataset to contributor for modification. The reason for return entered below will be sent by email to the author.

Add/Edit a Version Note

Enter the reason this version was created. To learn more about Version Notes, visit the Version Notes section of the User Guide.

Styled Citation