Trajectory SP1412

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: 19214
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P495 NC02046
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
HPTWPQKSVWHGSDPNGRRLTESY
Total charge (e): +1
Number of residues: 24
By amino acid:
  Basic: 9
  Acidic: 2
  Hydrophobic: 9
  Polar: 8
Electrostatic Dipolar Moment (e nm): 5.16
Longitudinal (e nm): 5.14
Transversal (e nm): 0.38
Hydrophobic Dipolar Moment (nm): 5.45
Longitudinal (nm): 5.36
Transversal (nm): 0.96
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): 0.647764 ± 0.001048
Upper leaflet (nm2): 0.647764 ± 0.001048
Lower leaflet (nm2): 0.647764 ± 0.001048
Average Z coordinate
Peptide (nm): 4.057210 ± 0.225811
First Residue (nm): 4.629700 ± 0.274942
Last Residue (nm): 3.410270 ± 0.271104
Membrane (nm): 6.8409900 ± 0.0108948
Upper leaflet Head Group (nm): 8.785460 ± 0.012928
Lower leaflet Head Group (nm): 4.89648000 ± 0.00877211
Bilayer Thickness (nm): 3.8889800 ± 0.0156232
Peptide insertion (nm): 0.839268 ± 0.225982
Contacts
Peptide - Water: 77.93000 ± 4.38245
Peptide - Head groups: 9.29500 ± 1.49459
Peptide - Tail groups: 4.71000 ± 1.04565
Tilt (°): 69.82420 ± 4.68884
PepDF:
5(ns):  CVS
Displacement (nm): 0.9548200 ± 0.0423727
Precession(°): -0.493639 ± 3.630400
50(ns)  CVS
Displacement (nm): 3.00009 ± 0.17170
Precession(°): -2.7419 ± 10.3349
100(ns)  CVS
Displacement(nm): 4.304420 ± 0.277097
Precession(°): 4.71631 ± 14.73100
200(ns)  CVS
Displacement(nm): 5.950420 ± 0.356341
Precession(°): 25.1077 ± 19.3599

  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.