Trajectory SP1262

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: P420 AP02143
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
SLQMGATAIKQVKKLFKKKGG
Total charge (e): +6
Number of residues: 21
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 11
  Polar: 4
Electrostatic Dipolar Moment (e nm): 1.73
Longitudinal (e nm): 1.28
Transversal (e nm): 1.16
Hydrophobic Dipolar Moment (nm): 6.09
Longitudinal (nm): 6.02
Transversal (nm): 0.9
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): 0.64761300 ± 0.00102668
Upper leaflet (nm2): 0.64761300 ± 0.00102668
Lower leaflet (nm2): 0.64761300 ± 0.00102668
Average Z coordinate
Peptide (nm): 7.17265 ± 2.02434
First Residue (nm): 7.16142 ± 1.99483
Last Residue (nm): 7.17438 ± 2.06622
Membrane (nm): 6.84173 ± 0.01058
Upper leaflet Head Group (nm): 8.7864100 ± 0.0126863
Lower leaflet Head Group (nm): 4.89759000 ± 0.00875991
Bilayer Thickness (nm): 3.8888200 ± 0.0154168
Peptide insertion (nm): -1.61376 ± 2.02438
Contacts
Peptide - Water: 85.727500 ± 0.738461
Peptide - Head groups: 0.530000 ± 0.376857
Peptide - Tail groups: 0.0425000 ± 0.0543218
Tilt (°): 86.79970 ± 8.12041
PepDF:
5(ns):  CVS
Displacement (nm): 1.7204900 ± 0.0791389
Precession(°): -10.2953 ± 10.8521
50(ns)  CVS
Displacement (nm): 5.444460 ± 0.269719
Precession(°): -113.0930 ± 32.9935
100(ns)  CVS
Displacement(nm): 7.439440 ± 0.417208
Precession(°): -230.3540 ± 50.5416
200(ns)  CVS
Displacement(nm): 9.707360 ± 0.454471
Precession(°): -422.9060 ± 79.0345

  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.