Trajectory SP692

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: 19187
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P136 AP01259
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
WKIFKKIEKVGQNIRDGIVKAGPAVAVVGQAATI
Total charge (e): +4
Number of residues: 34
By amino acid:
  Basic: 6
  Acidic: 2
  Hydrophobic: 22
  Polar: 4
Electrostatic Dipolar Moment (e nm): 11.32
Longitudinal (e nm): 11.08
Transversal (e nm): 2.36
Hydrophobic Dipolar Moment (nm): 3.99
Longitudinal (nm): 3.48
Transversal (nm): 1.95
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: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

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): 0.645742000 ± 0.000930817
Upper leaflet (nm2): 0.645742000 ± 0.000930817
Lower leaflet (nm2): 0.645742000 ± 0.000930817
Average Z coordinate
Peptide (nm): 8.5133500 ± 0.0335312
First Residue (nm): 8.7027300 ± 0.0418979
Last Residue (nm): 8.5863200 ± 0.0545776
Membrane (nm): 6.79181000 ± 0.00971165
Upper leaflet Head Group (nm): 8.7515800 ± 0.0117554
Lower leaflet Head Group (nm): 4.83685000 ± 0.00775203
Bilayer Thickness (nm): 3.9147300 ± 0.0140813
Peptide insertion (nm): -0.2382300 ± 0.0355321
Contacts
Peptide - Water: 37.547500 ± 0.838646
Peptide - Head groups: 20.072500 ± 0.326176
Peptide - Tail groups: 19.387500 ± 0.355178
Tilt (°): 91.984600 ± 0.836274
PepDF:
5(ns):  CVS
Displacement (nm): 0.5809230 ± 0.0245267
Precession(°): 1.479580 ± 0.963063
50(ns)  CVS
Displacement (nm): 1.6151700 ± 0.0893772
Precession(°): 17.79200 ± 3.58742
100(ns)  CVS
Displacement(nm): 2.048560 ± 0.107824
Precession(°): 36.47930 ± 5.60517
200(ns)  CVS
Displacement(nm): 2.787580 ± 0.122178
Precession(°): 71.49720 ± 7.46563

  Download JSON File.

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.