Trajectory SP937

Force field: martini_v2.2P
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: 45470
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P258 AP00492
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
QRVEELSKFSKKGAAARRRK
Total charge (e): +6
Number of residues: 20
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 7
  Polar: 3
Electrostatic Dipolar Moment (e nm): 1.16
Longitudinal (e nm): 1.04
Transversal (e nm): 0.51
Hydrophobic Dipolar Moment (nm): 4.72
Longitudinal (nm): 4.51
Transversal (nm): 1.38
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): 0.64667900 ± 0.00108351
Upper leaflet (nm2): 0.64667900 ± 0.00108351
Lower leaflet (nm2): 0.64667900 ± 0.00108351
Average Z coordinate
Peptide (nm): 5.46517 ± 1.35745
First Residue (nm): 5.44680 ± 1.33392
Last Residue (nm): 5.45698 ± 1.39614
Membrane (nm): 6.5960100 ± 0.0107346
Upper leaflet Head Group (nm): 8.5687900 ± 0.0131054
Lower leaflet Head Group (nm): 4.62402000 ± 0.00829149
Bilayer Thickness (nm): 3.944770 ± 0.015508
Peptide insertion (nm): -0.841154 ± 1.357480
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 0.060000 ± 0.101572
Peptide - Tail groups: 0.00250000 ± 0.00845298
Tilt (°): 85.76100 ± 6.01269
PepDF:
5(ns):  CVS
Displacement (nm): 1.8116400 ± 0.0829394
Precession(°): -9.92849 ± 14.07400
50(ns)  CVS
Displacement (nm): 5.90744 ± 0.30775
Precession(°): -140.4020 ± 37.0785
100(ns)  CVS
Displacement(nm): 8.158590 ± 0.363623
Precession(°): -289.9810 ± 54.9163
200(ns)  CVS
Displacement(nm): 10.498900 ± 0.572466
Precession(°): -651.4860 ± 98.8207

  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.