Trajectory SP223

Force field: martini_v2.2
Simulation length (ns): 5000
Electric field (kJ mol-1 nm-1 e-1): 0
Temperature (K): 300 (v-rescale)
Pressure (bar): 1 (parrinello-rahman semiisotropic)
Number of particles: 11558
Time step (fs) : 25
Software: GROMACS 2020
Supercomputer: Finisterrae II CESGA
Peptides: P38 DRAMP03751
Lipids: DOPC, DOPE, DOPS, DPSM
Heteromolecules: CHOL
Ions: NA
Water model: W

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Sequence :
FFGHLFKLATKIIPSLFQ
Total charge (e): +2
Number of residues: 18
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 12
  Polar: 3
Electrostatic Dipolar Moment (e nm): 3.37
Longitudinal (e nm): 3.17
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 6.61
Longitudinal (nm): 4.04
Transversal (nm): 5.22
Secondary structure: Helix
Activity:

Download Files
  ITP file.
  JSON file.
  PDB file.

Click on any component to highlight it from the plot.
Upper leaflet
Lower leaflet

Lipids


Membrane model for: DOPC:DOPE:DOPS:DPSM:CHOL (3:3:3:2:4) (Cancer)

DOPC
1,2-dioleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See DOPC lipid
  Download ITP File.
  Download PDB File.
DOPE
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Total charge (e): 0

  See DOPE lipid
  Download ITP File.
  Download PDB File.
DOPS
1,2-dioleoyl-sn-glycero-3-phospho-L-serine
Total charge (e): -1

  See DOPS lipid
  Download ITP File.
  Download PDB File.
DPSM
DPSM
Total charge (e): 0

  See DPSM lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
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Contacts per residue
(normalized by number of beads in the residue)
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Molecular Dynamics based descriptors
Average and standard deviation, calculated using the autocorrelation function (for time series) or the width of the distribution, for the last microsecond of the trajectory

Area per lipid
Membrane (nm2): 0.71702 ± 0.00075
Upper leaflet (nm2): 0.71702 ± 0.00075
Lower leaflet (nm2): 0.71702 ± 0.00075
Average Z coordinate
Peptide (nm): 6.679 ± 0.034
First Residue (nm): 6.641 ± 0.033
Last Residue (nm): 6.888 ± 0.053
Membrane (nm): 4.8518 ± 0.0049
Upper leaflet Head Group (nm): 6.8537 ± 0.0061
Lower leaflet Head Group (nm): 2.8592 ± 0.0037
Bilayer Thickness (nm): 3.9945 ± 0.0071
Peptide insertion (nm): -0.175 ± 0.035
Contacts
Peptide - Water: 25.90 ± 0.41
Peptide - Head groups: 10.99 ± 0.17
Peptide - Tail groups: 10.42 ± 0.23
Tilt (°): 90.7 ± 1.1
PepDF:
5(ns):  CVS
Displacement (nm): 0.476 ± 0.027
Precession(°): 0.1 ± 1.9
50(ns)  CVS
Displacement (nm): 1.55 ± 0.35
Precession(°): 3.0 ± 14.0
100(ns)  CVS
Displacement(nm): 2.16 ± 0.71
Precession(°): 5.0 ± 19.0
200(ns)  CVS
Displacement(nm): 3.2 ± 1.1
Precession(°): 15.0 ± 17.0

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Peptide Analyses

Peptide Displacement Fingerprint (PepDF)
Lateral displacement vs Rotational Displacement along the trajectory, for different time windows .

Density maps:
2D-density maps of lipids around the peptide along XY and YZ axis, calculated for each lipid type along the last microsecond.

Lipid-Peptide Analyses:

z-Position
Z-coordinate, averaged for differetn parts of the the system: peptide, membrane, first and last backbone (BB) residues and upper of lower leaflet lipids’ headgroups (HGs).
Minimum distance
Minimum distance (nm) between the peptide backbone and the lipids (headgroups and tailgroups).
Number of contacts
Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm.
Lateral density
Lateral density for the different components of the system: headgroups, tail groups, peptide and water.