Trajectory SP1272

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: 19204
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P425 AP02379
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
LLRPLLQLLKQKLR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.17
Longitudinal (e nm): 1.9
Transversal (e nm): 1.04
Hydrophobic Dipolar Moment (nm): 4.52
Longitudinal (nm): 4.43
Transversal (nm): 0.88
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): 0.64956100 ± 0.00105524
Upper leaflet (nm2): 0.64956100 ± 0.00105524
Lower leaflet (nm2): 0.64956100 ± 0.00105524
Average Z coordinate
Peptide (nm): 8.8696700 ± 0.0407324
First Residue (nm): 8.6733100 ± 0.0453222
Last Residue (nm): 9.0913800 ± 0.0580545
Membrane (nm): 6.8267500 ± 0.0110658
Upper leaflet Head Group (nm): 8.767820 ± 0.013141
Lower leaflet Head Group (nm): 4.88610000 ± 0.00907214
Bilayer Thickness (nm): 3.8817200 ± 0.0159684
Peptide insertion (nm): 0.1018460 ± 0.0427997
Contacts
Peptide - Water: 32.455000 ± 0.654839
Peptide - Head groups: 9.035000 ± 0.235045
Peptide - Tail groups: 8.427500 ± 0.281851
Tilt (°): 83.08230 ± 1.91289
PepDF:
5(ns):  CVS
Displacement (nm): 0.830346 ± 0.033045
Precession(°): 1.07851 ± 2.95000
50(ns)  CVS
Displacement (nm): 2.322300 ± 0.117945
Precession(°): 15.46500 ± 8.81839
100(ns)  CVS
Displacement(nm): 3.380260 ± 0.197487
Precession(°): 35.7393 ± 11.9818
200(ns)  CVS
Displacement(nm): 5.431600 ± 0.344938
Precession(°): 72.3198 ± 12.2759

  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.