Membranes


N.B.: If you use the following files in your work, please cite the primary source. (see Description field)

Name:mammalian plasma membrane
Lipids: CHOL, PIPC, POPE, POPC, PAPE, PAPS, PIPE, DAPE, DPSM, POPS, DOPE, PUPE, PUPS, PNSM, POPI, PAPC, PAPI, XNSM, PIPI, DXSM, DUPE, PQPE, BNSM, PIPS, DBSM, PUPI, DOPC, POPA, POI7, POI6, POI1, PAPA, PIPA, PQPS, PEPC, PUPC, PADG, DUPS, DAPS, POSM, PIDG, PGSM, PUPA, DAPC, DPCE, PODG, XNCE, PUDG, PNCE, DXCE, DPG1, DPG3, PNG3, PNG1, P0PC, DXG1, DXG3, XNG3, XNG1, O0PC, A0PC, I0PC, U0PC
Forcefield: martini 2.0
Software:Gromacs 4.5
Files: LIM1_mammalian_plasma_membrane.gro, LIM1_mammalian_plasma_membrane.txt
Parameters and other files
md-production.mdp
Simulation files
Number:6664 lipids
Temperature:310 °K
Equilibration:10000 ns
Tags:mammalian, plasma membrane
Proteins:
Description:

Primary source: http://www.cgmartini.nl/index.php/plasma-membrane

Simulations have been performed using the GROMACS simulation package version 4.5.x and 4.6.x.

POPC and PIPC (version Ingolfsson2014) have position restrains on the z-axes on the PO4 bead that can be controled with POS_Z_AXES

POPX, PIPX, POP1, POP2, POP3, PPC, OPC, IPC, APC and UPC have been renamed POPC, PIPC, POI1, POI6, POI7, P0PC, O0PC, I0PC, A0PC and U0PC.
ION residues have been renamed NA+ and CL- and CP atoms of PAPI and PIPI residues have been renamed PO4
References: Ingólfsson2014 Journal of the American Chemical Society, 136. Lipid Organization of the Plasma Membrane
Composition:
Upper leaflet 1
912 CHOL (Melo2015) ( 28.4%)
281 PIPC (Wassenaar2015) ( 8.7%)
198 POPE (Ingólfsson2014) ( 6.2%)
191 POPC (Ingólfsson2014) ( 5.9%)
181 PAPE (Wassenaar2015) ( 5.6%)
160 PAPS (Wassenaar2015) ( 5.0%)
132 PIPE (Wassenaar2015) ( 4.1%)
115 DAPE (Wassenaar2015) ( 3.6%)
97 DPSM (Wassenaar2015) ( 3.0%)
69 POPS (Ingólfsson2014) ( 2.1%)
66 DOPE (Ingólfsson2014) ( 2.1%)
66 PUPE (Ingólfsson2014) ( 2.1%)
62 PUPS (Ingólfsson2014) ( 1.9%)
60 PNSM (Wassenaar2015) ( 1.9%)
47 POPI (Ingólfsson2014) ( 1.5%)
45 PAPC (Wassenaar2015) ( 1.4%)
42 PAPI (López2013) ( 1.3%)
42 XNSM (Wassenaar2015) ( 1.3%)
42 PIPI (López2013) ( 1.3%)
39 DXSM (Wassenaar2015) ( 1.2%)
33 DUPE (Ingólfsson2014) ( 1.0%)
33 PQPE (Wassenaar2015) ( 1.0%)
30 BNSM (Wassenaar2015) ( 0.9%)
27 PIPS (Wassenaar2015) ( 0.8%)
21 DBSM (Wassenaar2015) ( 0.7%)
17 PUPI (Ingólfsson2014) ( 0.5%)
17 DOPC (Ingólfsson2014) ( 0.5%)
16 POPA (Ingólfsson2014) ( 0.5%)
16 POI7 (Ingólfsson2014) ( 0.5%)
16 POI6 (Ingólfsson2014) ( 0.5%)
16 POI1 (Ingólfsson2014) ( 0.5%)
13 PAPA (Wassenaar2015) ( 0.4%)
13 PIPA (Wassenaar2015) ( 0.4%)
13 PQPS (Wassenaar2015) ( 0.4%)
11 PEPC (Ingólfsson2014) ( 0.3%)
11 PUPC (Ingólfsson2014) ( 0.3%)
7 PADG (Wassenaar2015) ( 0.2%)
7 DUPS (Ingólfsson2014) ( 0.2%)
7 DAPS (Wassenaar2015) ( 0.2%)
6 POSM (Ingólfsson2014) ( 0.2%)
6 PIDG (Wassenaar2015) ( 0.2%)
6 PGSM (Wassenaar2015) ( 0.2%)
6 PUPA (Ingólfsson2014) ( 0.2%)
5 DAPC (Wassenaar2015) ( 0.2%)
5 DPCE (Wassenaar2015) ( 0.2%)
3 PODG (Ingólfsson2014) ( 0.1%)
3 XNCE (Wassenaar2015) ( 0.1%)
1 PUDG (Ingólfsson2014) ( 0.0%)
1 PNCE (Wassenaar2015) ( 0.0%)
1 DXCE (Wassenaar2015) ( 0.0%)
Lower leaflet 1
1093 CHOL (Melo2015) ( 31.7%)
617 PIPC (Ingólfsson2014_Z) ( 17.9%)
419 POPC (Ingólfsson2014_Z) ( 12.1%)
212 DPSM (Wassenaar2015) ( 6.1%)
132 PNSM (Wassenaar2015) ( 3.8%)
98 PAPC (Wassenaar2015) ( 2.8%)
92 XNSM (Wassenaar2015) ( 2.7%)
86 DXSM (Wassenaar2015) ( 2.5%)
66 BNSM (Wassenaar2015) ( 1.9%)
47 POPE (Ingólfsson2014) ( 1.4%)
46 DBSM (Wassenaar2015) ( 1.3%)
43 PAPE (Wassenaar2015) ( 1.2%)
36 DOPC (Ingólfsson2014) ( 1.0%)
31 PIPE (Wassenaar2015) ( 0.9%)
31 DPG1 (Ingólfsson2014) ( 0.9%)
31 DPG3 (Ingólfsson2014) ( 0.9%)
27 DAPE (Wassenaar2015) ( 0.8%)
24 PEPC (Ingólfsson2014) ( 0.7%)
24 PUPC (Ingólfsson2014) ( 0.7%)
22 PNG3 (Ingólfsson2014) ( 0.6%)
22 PNG1 (Ingólfsson2014) ( 0.6%)
22 P0PC (Ingólfsson2014) ( 0.6%)
17 DXG1 (Ingólfsson2014) ( 0.5%)
17 DXG3 (Ingólfsson2014) ( 0.5%)
17 XNG3 (Ingólfsson2014) ( 0.5%)
17 XNG1 (Ingólfsson2014) ( 0.5%)
15 DOPE (Ingólfsson2014) ( 0.4%)
15 PUPE (Ingólfsson2014) ( 0.4%)
13 POSM (Ingólfsson2014) ( 0.4%)
13 PGSM (Wassenaar2015) ( 0.4%)
12 DAPC (Wassenaar2015) ( 0.3%)
11 PODG (Ingólfsson2014) ( 0.3%)
10 DPCE (Wassenaar2015) ( 0.3%)
9 PNCE (Wassenaar2015) ( 0.3%)
7 DUPE (Ingólfsson2014) ( 0.2%)
7 PQPE (Wassenaar2015) ( 0.2%)
7 PIDG (Wassenaar2015) ( 0.2%)
7 DXCE (Wassenaar2015) ( 0.2%)
7 O0PC (Ingólfsson2014) ( 0.2%)
6 PADG (Wassenaar2015) ( 0.2%)
6 A0PC (Ingólfsson2014) ( 0.2%)
6 I0PC (Ingólfsson2014) ( 0.2%)
5 XNCE (Wassenaar2015) ( 0.1%)
3 PUDG (Ingólfsson2014) ( 0.1%)
2 U0PC (Ingólfsson2014) ( 0.1%)
Curator: Jean-Marc Crowet on Dec. 11, 2020

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