Trajectory SP814

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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P197 AP04628
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
RRLSKVLGKLRDKIATWRQRLLTK
Total charge (e): +8
Number of residues: 24
By amino acid:
  Basic: 9
  Acidic: 1
  Hydrophobic: 10
  Polar: 4
Electrostatic Dipolar Moment (e nm): 7.82
Longitudinal (e nm): 7.77
Transversal (e nm): 0.84
Hydrophobic Dipolar Moment (nm): 3.68
Longitudinal (nm): 3.26
Transversal (nm): 1.7
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): 0.64411900 ± 0.00101666
Upper leaflet (nm2): 0.64411900 ± 0.00101666
Lower leaflet (nm2): 0.64411900 ± 0.00101666
Average Z coordinate
Peptide (nm): 4.9191700 ± 0.0304557
First Residue (nm): 4.8549500 ± 0.0392195
Last Residue (nm): 4.81585 ± 0.04331
Membrane (nm): 6.8169600 ± 0.0104125
Upper leaflet Head Group (nm): 8.7737100 ± 0.0123692
Lower leaflet Head Group (nm): 4.85679000 ± 0.00854026
Bilayer Thickness (nm): 3.9169200 ± 0.0150311
Peptide insertion (nm): -0.0623807 ± 0.0316304
Contacts
Peptide - Water: 38.170000 ± 0.779811
Peptide - Head groups: 17.220000 ± 0.313003
Peptide - Tail groups: 12.675000 ± 0.271567
Tilt (°): 86.875300 ± 0.885237
PepDF:
5(ns):  CVS
Displacement (nm): 0.644344 ± 0.027827
Precession(°): -0.0629012 ± 1.2263800
50(ns)  CVS
Displacement (nm): 1.9353700 ± 0.0956015
Precession(°): -0.839275 ± 3.675730
100(ns)  CVS
Displacement(nm): 2.936210 ± 0.143156
Precession(°): -1.08878 ± 5.65228
200(ns)  CVS
Displacement(nm): 4.438290 ± 0.257392
Precession(°): 2.15596 ± 8.80950

  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.