Trajectory SP788

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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P184 AP03745
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
WKIFKRIEKVGRNVRDGVIKAGPAVAVLGQAKALG-
K
Total charge (e): +7
Number of residues: 36
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 23
  Polar: 2
Electrostatic Dipolar Moment (e nm): 8.3
Longitudinal (e nm): 8.12
Transversal (e nm): 1.72
Hydrophobic Dipolar Moment (nm): 2.71
Longitudinal (nm): 2.12
Transversal (nm): 1.68
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): 0.645891000 ± 0.000899449
Upper leaflet (nm2): 0.645891000 ± 0.000899449
Lower leaflet (nm2): 0.645891000 ± 0.000899449
Average Z coordinate
Peptide (nm): 8.5669000 ± 0.0348996
First Residue (nm): 8.6524000 ± 0.0435093
Last Residue (nm): 8.7108300 ± 0.0525024
Membrane (nm): 6.78970000 ± 0.00937984
Upper leaflet Head Group (nm): 8.748720 ± 0.010855
Lower leaflet Head Group (nm): 4.83632000 ± 0.00799434
Bilayer Thickness (nm): 3.9124000 ± 0.0134811
Peptide insertion (nm): -0.1818250 ± 0.0365488
Contacts
Peptide - Water: 44.150000 ± 0.992207
Peptide - Head groups: 21.870000 ± 0.360051
Peptide - Tail groups: 18.920000 ± 0.440819
Tilt (°): 88.088400 ± 0.717595
PepDF:
5(ns):  CVS
Displacement (nm): 0.5902080 ± 0.0265458
Precession(°): -0.539223 ± 0.843966
50(ns)  CVS
Displacement (nm): 1.6379900 ± 0.0854906
Precession(°): -5.32567 ± 3.50269
100(ns)  CVS
Displacement(nm): 2.128170 ± 0.116375
Precession(°): -9.42013 ± 5.00590
200(ns)  CVS
Displacement(nm): 2.610630 ± 0.176205
Precession(°): -7.94767 ± 6.03378

  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.