Trajectory SP1220

Force field: martini_v3
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: 19208
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P399 AP00890
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
DWKKVDWKKVSKKTCKVMLKACKFLG
Total charge (e): +7
Number of residues: 26
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 11
  Polar: 4
Electrostatic Dipolar Moment (e nm): 4.33
Longitudinal (e nm): 3.92
Transversal (e nm): 1.85
Hydrophobic Dipolar Moment (nm): 8.04
Longitudinal (nm): 7.92
Transversal (nm): 1.41
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): 0.64848300 ± 0.00110101
Upper leaflet (nm2): 0.64848300 ± 0.00110101
Lower leaflet (nm2): 0.64848300 ± 0.00110101
Average Z coordinate
Peptide (nm): 7.78760 ± 1.57838
First Residue (nm): 7.91004 ± 1.74108
Last Residue (nm): 7.74642 ± 1.54246
Membrane (nm): 6.8282900 ± 0.0112823
Upper leaflet Head Group (nm): 8.770840 ± 0.013394
Lower leaflet Head Group (nm): 4.88558000 ± 0.00922489
Bilayer Thickness (nm): 3.8852700 ± 0.0162634
Peptide insertion (nm): -0.983245 ± 1.578430
Contacts
Peptide - Water: 96.2850 ± 10.4658
Peptide - Head groups: 6.52750 ± 3.45242
Peptide - Tail groups: 4.15500 ± 2.33618
Tilt (°): 95.90890 ± 7.29292
PepDF:
5(ns):  CVS
Displacement (nm): 1.1325600 ± 0.0622533
Precession(°): 5.59073 ± 4.45635
50(ns)  CVS
Displacement (nm): 3.466710 ± 0.198031
Precession(°): 65.3818 ± 16.9589
100(ns)  CVS
Displacement(nm): 5.540540 ± 0.268922
Precession(°): 138.5710 ± 22.7932
200(ns)  CVS
Displacement(nm): 8.796440 ± 0.507337
Precession(°): 275.444 ± 26.298

  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.