Trajectory SP1454

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: 19211
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P516 NC03705
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
HIQLSPFSQSWR
Total charge (e): +1
Number of residues: 12
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 5
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.45
Longitudinal (e nm): 1.27
Transversal (e nm): 0.7
Hydrophobic Dipolar Moment (nm): 1.46
Longitudinal (nm): 1.33
Transversal (nm): 0.59
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): 0.649303000 ± 0.000969306
Upper leaflet (nm2): 0.649303000 ± 0.000969306
Lower leaflet (nm2): 0.649303000 ± 0.000969306
Average Z coordinate
Peptide (nm): 8.922920 ± 0.164541
First Residue (nm): 8.972550 ± 0.167315
Last Residue (nm): 9.219110 ± 0.169489
Membrane (nm): 6.8314900 ± 0.0099834
Upper leaflet Head Group (nm): 8.773530 ± 0.011829
Lower leaflet Head Group (nm): 4.88948000 ± 0.00804906
Bilayer Thickness (nm): 3.8840500 ± 0.0143078
Peptide insertion (nm): 0.149384 ± 0.164966
Contacts
Peptide - Water: 31.9325 ± 2.2226
Peptide - Head groups: 8.305000 ± 0.707273
Peptide - Tail groups: 6.472500 ± 0.569115
Tilt (°): 82.36990 ± 2.18975
PepDF:
5(ns):  CVS
Displacement (nm): 0.9991560 ± 0.0523861
Precession(°): 1.02346 ± 7.10220
50(ns)  CVS
Displacement (nm): 3.177250 ± 0.166137
Precession(°): 14.3430 ± 16.3492
100(ns)  CVS
Displacement(nm): 4.511740 ± 0.267646
Precession(°): 41.5124 ± 21.9212
200(ns)  CVS
Displacement(nm): 6.918370 ± 0.428029
Precession(°): 133.8760 ± 21.8553

  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.