Trajectory SP1398

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: 19209
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P488 NC01521
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LVVGDQLCYRVLIKCLMNK
Total charge (e): +2
Number of residues: 19
By amino acid:
  Basic: 3
  Acidic: 1
  Hydrophobic: 10
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.45
Longitudinal (e nm): 0.95
Transversal (e nm): 1.09
Hydrophobic Dipolar Moment (nm): 3.15
Longitudinal (nm): 3.1
Transversal (nm): 0.52
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): 0.64783900 ± 0.00102454
Upper leaflet (nm2): 0.64783900 ± 0.00102454
Lower leaflet (nm2): 0.64783900 ± 0.00102454
Average Z coordinate
Peptide (nm): 6.70546 ± 1.82075
First Residue (nm): 6.77066 ± 1.68285
Last Residue (nm): 6.60846 ± 2.01166
Membrane (nm): 6.8445000 ± 0.0113368
Upper leaflet Head Group (nm): 8.7880800 ± 0.0137067
Lower leaflet Head Group (nm): 4.90079000 ± 0.00897472
Bilayer Thickness (nm): 3.8872900 ± 0.0163835
Peptide insertion (nm): -1.80467 ± 1.82077
Contacts
Peptide - Water: 68.46750 ± 5.71845
Peptide - Head groups: 3.03750 ± 1.96803
Peptide - Tail groups: 1.93250 ± 1.37771
Tilt (°): 79.3172 ± 14.5374
PepDF:
5(ns):  CVS
Displacement (nm): 1.5791200 ± 0.0892565
Precession(°): 1.39169 ± 9.39753
50(ns)  CVS
Displacement (nm): 5.403680 ± 0.358619
Precession(°): 17.6794 ± 32.3764
100(ns)  CVS
Displacement(nm): 7.968200 ± 0.460869
Precession(°): 45.7391 ± 41.6815
200(ns)  CVS
Displacement(nm): 10.634900 ± 0.635173
Precession(°): 171.2400 ± 47.4414

  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.