Trajectory SP722

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: 19193
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P151 AP02379
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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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): 2.1
Longitudinal (e nm): 1.82
Transversal (e nm): 1.03
Hydrophobic Dipolar Moment (nm): 4.43
Longitudinal (nm): 4.34
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)
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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): 0.64329900 ± 0.00097048
Upper leaflet (nm2): 0.64329900 ± 0.00097048
Lower leaflet (nm2): 0.64329900 ± 0.00097048
Average Z coordinate
Peptide (nm): 5.0869700 ± 0.0352359
First Residue (nm): 5.2729000 ± 0.0440817
Last Residue (nm): 4.916110 ± 0.037217
Membrane (nm): 6.8297800 ± 0.0103043
Upper leaflet Head Group (nm): 8.7896200 ± 0.0121681
Lower leaflet Head Group (nm): 4.86777000 ± 0.00836466
Bilayer Thickness (nm): 3.9218500 ± 0.0147658
Peptide insertion (nm): -0.2192050 ± 0.0362151
Contacts
Peptide - Water: 21.492500 ± 0.611761
Peptide - Head groups: 10.950000 ± 0.256108
Peptide - Tail groups: 9.927500 ± 0.246031
Tilt (°): 85.25750 ± 1.13761
PepDF:
5(ns):  CVS
Displacement (nm): 0.7369770 ± 0.0323009
Precession(°): 1.32033 ± 2.57937
50(ns)  CVS
Displacement (nm): 2.420510 ± 0.128868
Precession(°): 13.55220 ± 8.22195
100(ns)  CVS
Displacement(nm): 3.620390 ± 0.220176
Precession(°): 24.592 ± 10.532
200(ns)  CVS
Displacement(nm): 5.300920 ± 0.335731
Precession(°): 51.5322 ± 12.9822

  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.