Trajectory SP784

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: 19185
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P182 AP03679
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LPLLAGLAANFLPQIICKIARKC
Total charge (e): +3
Number of residues: 23
By amino acid:
  Basic: 3
  Acidic: 0
  Hydrophobic: 16
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.7
Longitudinal (e nm): 0.84
Transversal (e nm): 1.48
Hydrophobic Dipolar Moment (nm): 6.67
Longitudinal (nm): 6.62
Transversal (nm): 0.84
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): 0.64501700 ± 0.00101892
Upper leaflet (nm2): 0.64501700 ± 0.00101892
Lower leaflet (nm2): 0.64501700 ± 0.00101892
Average Z coordinate
Peptide (nm): 5.1416200 ± 0.0289574
First Residue (nm): 5.2143000 ± 0.0354478
Last Residue (nm): 5.0602300 ± 0.0406681
Membrane (nm): 6.8066300 ± 0.0105298
Upper leaflet Head Group (nm): 8.7637200 ± 0.0122699
Lower leaflet Head Group (nm): 4.84639000 ± 0.00873473
Bilayer Thickness (nm): 3.9173400 ± 0.0150614
Peptide insertion (nm): -0.2952360 ± 0.0302461
Contacts
Peptide - Water: 26.180000 ± 0.634466
Peptide - Head groups: 13.332500 ± 0.300595
Peptide - Tail groups: 14.075000 ± 0.247886
Tilt (°): 86.109100 ± 0.852606
PepDF:
5(ns):  CVS
Displacement (nm): 0.658877 ± 0.027244
Precession(°): 2.02736 ± 1.43119
50(ns)  CVS
Displacement (nm): 2.342670 ± 0.118998
Precession(°): 15.63860 ± 5.52339
100(ns)  CVS
Displacement(nm): 3.66749 ± 0.19014
Precession(°): 34.33570 ± 7.94315
200(ns)  CVS
Displacement(nm): 5.13826 ± 0.30603
Precession(°): 82.1614 ± 11.6243

  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.