PN 3

SimTech EXC 2075 Project Network 3 "Data-integrated model reduction for particles and continua"

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41 to 50 of 327 Results

45-ring_CG_resid39-152_cryoEM.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 44.8 MB - 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 marti...
45-ring_CG_resid79-152.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 30.9 MB - 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-...
charmm36-jul2017.ff.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 390.5 KB - 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:10.1080/00268978500103...
doublefil_CG_noDMP.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 4.8 MB - 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 polariza...
doublefil_CG_withDMP.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 4.4 MB - 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 pa...
endlessmembranepatch_singlefilament_AA.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 23.2 MB - 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 Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 14.3 MB - 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 f...
resolution_conversion_5B.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 5.0 MB - 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 Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 2.3 MB - 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...
singlefil_AA_resid39-152_cryoEMstructure.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 1.6 MB - 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...

45-ring_CG_resid39-152_cryoEM.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 44.8 MB -

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 marti...

45-ring_CG_resid79-152.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 30.9 MB -

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-...

charmm36-jul2017.ff.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 390.5 KB -

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:10.1080/00268978500103...

doublefil_CG_noDMP.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 4.8 MB -

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 polariza...

doublefil_CG_withDMP.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 4.4 MB -

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 pa...

endlessmembranepatch_singlefilament_AA.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 23.2 MB -

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

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 14.3 MB -

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 f...

resolution_conversion_5B.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 5.0 MB -

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

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 2.3 MB -

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...

singlefil_AA_resid39-152_cryoEMstructure.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 1.6 MB -

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...

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