Trajectory SP1328

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: 19210
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P453 AP03517
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
VVNVLVKVLPPPVV
Total charge (e): +1
Number of residues: 14
By amino acid:
  Basic: 1
  Acidic: 0
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.58
Longitudinal (e nm): 2.49
Transversal (e nm): 0.66
Hydrophobic Dipolar Moment (nm): 0.96
Longitudinal (nm): 0.49
Transversal (nm): 0.83
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): 0.64944700 ± 0.00102949
Upper leaflet (nm2): 0.64944700 ± 0.00102949
Lower leaflet (nm2): 0.64944700 ± 0.00102949
Average Z coordinate
Peptide (nm): 8.7202500 ± 0.0461327
First Residue (nm): 8.6822100 ± 0.0530923
Last Residue (nm): 8.8382600 ± 0.0630013
Membrane (nm): 6.8305500 ± 0.0106581
Upper leaflet Head Group (nm): 8.772150 ± 0.012469
Lower leaflet Head Group (nm): 4.89005000 ± 0.00857768
Bilayer Thickness (nm): 3.8821000 ± 0.0151345
Peptide insertion (nm): -0.0518999 ± 0.0477881
Contacts
Peptide - Water: 22.75250 ± 0.79835
Peptide - Head groups: 8.250000 ± 0.248728
Peptide - Tail groups: 8.452500 ± 0.248459
Tilt (°): 91.42170 ± 2.10027
PepDF:
5(ns):  CVS
Displacement (nm): 0.9429370 ± 0.0389441
Precession(°): -3.89488 ± 3.34129
50(ns)  CVS
Displacement (nm): 2.477150 ± 0.137696
Precession(°): -36.8637 ± 10.3438
100(ns)  CVS
Displacement(nm): 3.65301 ± 0.21531
Precession(°): -70.0347 ± 15.3880
200(ns)  CVS
Displacement(nm): 5.944130 ± 0.291351
Precession(°): -130.4430 ± 24.0563

  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.