Trajectory SP925

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: 45464
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P252 AP00146
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
IGAVLKVLTTGLPALISWIKRKRQQ
Total charge (e): +5
Number of residues: 25
By amino acid:
  Basic: 5
  Acidic: 0
  Hydrophobic: 15
  Polar: 5
Electrostatic Dipolar Moment (e nm): 2.58
Longitudinal (e nm): 2.4
Transversal (e nm): 0.94
Hydrophobic Dipolar Moment (nm): 11.44
Longitudinal (nm): 11.35
Transversal (nm): 1.48
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): 0.649816000 ± 0.000945568
Upper leaflet (nm2): 0.649816000 ± 0.000945568
Lower leaflet (nm2): 0.649816000 ± 0.000945568
Average Z coordinate
Peptide (nm): 4.7198600 ± 0.0324517
First Residue (nm): 4.8853000 ± 0.0384688
Last Residue (nm): 4.3462200 ± 0.0446415
Membrane (nm): 6.56506000 ± 0.00965509
Upper leaflet Head Group (nm): 8.5318500 ± 0.0115292
Lower leaflet Head Group (nm): 4.59587000 ± 0.00792764
Bilayer Thickness (nm): 3.9359800 ± 0.0139918
Peptide insertion (nm): -0.123986 ± 0.033406
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 15.077500 ± 0.295208
Peptide - Tail groups: 14.067500 ± 0.271771
Tilt (°): 83.69040 ± 0.85379
PepDF:
5(ns):  CVS
Displacement (nm): 0.6289210 ± 0.0257902
Precession(°): -0.205393 ± 1.062500
50(ns)  CVS
Displacement (nm): 2.1739600 ± 0.0877161
Precession(°): -1.10859 ± 3.01778
100(ns)  CVS
Displacement(nm): 3.195610 ± 0.140932
Precession(°): -0.854603 ± 3.998660
200(ns)  CVS
Displacement(nm): 4.64691 ± 0.19000
Precession(°): 2.57968 ± 6.10671

  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.