Trajectory SP1336

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: 19208
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P457 AP03721
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LWKSILKNAGKAALNEINQIV
Total charge (e): +2
Number of residues: 21
By amino acid:
  Basic: 3
  Acidic: 1
  Hydrophobic: 12
  Polar: 5
Electrostatic Dipolar Moment (e nm): 6.72
Longitudinal (e nm): 6.38
Transversal (e nm): 2.12
Hydrophobic Dipolar Moment (nm): 1.88
Longitudinal (nm): 1.55
Transversal (nm): 1.06
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): 0.64996300 ± 0.00102997
Upper leaflet (nm2): 0.64996300 ± 0.00102997
Lower leaflet (nm2): 0.64996300 ± 0.00102997
Average Z coordinate
Peptide (nm): 9.105880 ± 0.156186
First Residue (nm): 8.7115900 ± 0.0541597
Last Residue (nm): 9.573060 ± 0.391739
Membrane (nm): 6.8207300 ± 0.0108181
Upper leaflet Head Group (nm): 8.7597300 ± 0.0128246
Lower leaflet Head Group (nm): 4.88150000 ± 0.00891016
Bilayer Thickness (nm): 3.878230 ± 0.015616
Peptide insertion (nm): 0.346156 ± 0.156712
Contacts
Peptide - Water: 50.23250 ± 5.86063
Peptide - Head groups: 9.82750 ± 1.18118
Peptide - Tail groups: 9.13000 ± 1.59107
Tilt (°): 72.09760 ± 8.06296
PepDF:
5(ns):  CVS
Displacement (nm): 0.868240 ± 0.036964
Precession(°): -0.581342 ± 4.424440
50(ns)  CVS
Displacement (nm): 2.692840 ± 0.123275
Precession(°): -9.26131 ± 17.86980
100(ns)  CVS
Displacement(nm): 3.999000 ± 0.165097
Precession(°): -28.9380 ± 21.1573
200(ns)  CVS
Displacement(nm): 5.45867 ± 0.26797
Precession(°): -43.7950 ± 22.6126

  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.