Trajectory SP951

Force field: martini_v2.2P
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: 45430
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P265 AP01010
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
MWSGMWRRKLKKLRNALKKKLKGE
Total charge (e): +9
Number of residues: 24
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 11
  Polar: 2
Electrostatic Dipolar Moment (e nm): 5.4
Longitudinal (e nm): 4.98
Transversal (e nm): 2.08
Hydrophobic Dipolar Moment (nm): 10.69
Longitudinal (nm): 10.41
Transversal (nm): 2.43
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): 0.64979300 ± 0.00109192
Upper leaflet (nm2): 0.64979300 ± 0.00109192
Lower leaflet (nm2): 0.64979300 ± 0.00109192
Average Z coordinate
Peptide (nm): 8.6590400 ± 0.0393058
First Residue (nm): 8.5518200 ± 0.0499072
Last Residue (nm): 8.7536000 ± 0.0508734
Membrane (nm): 6.5606100 ± 0.0109312
Upper leaflet Head Group (nm): 8.5268400 ± 0.0128929
Lower leaflet Head Group (nm): 4.59501000 ± 0.00872514
Bilayer Thickness (nm): 3.9318300 ± 0.0155677
Peptide insertion (nm): 0.1322010 ± 0.0413663
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 14.707500 ± 0.298812
Peptide - Tail groups: 12.54250 ± 0.30505
Tilt (°): 84.342700 ± 0.930135
PepDF:
5(ns):  CVS
Displacement (nm): 0.6106320 ± 0.0253103
Precession(°): -0.383839 ± 1.063400
50(ns)  CVS
Displacement (nm): 1.6249700 ± 0.0893617
Precession(°): -4.04639 ± 3.65113
100(ns)  CVS
Displacement(nm): 2.225270 ± 0.117102
Precession(°): -10.38280 ± 5.15233
200(ns)  CVS
Displacement(nm): 3.710350 ± 0.139381
Precession(°): -27.73360 ± 7.62668

  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.