Trajectory SP1226

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: 19210
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P402 AP01010
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
MWSGMWRRKLKKLRNALKKKLKGE
Total charge (e): +9
Number of residues: 24
By amino acid:
  Basic: 10
  Acidic: 1
  Hydrophobic: 11
  Polar: 2
Electrostatic Dipolar Moment (e nm): 5.29
Longitudinal (e nm): 4.66
Transversal (e nm): 2.5
Hydrophobic Dipolar Moment (nm): 10.73
Longitudinal (nm): 10.48
Transversal (nm): 2.33
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): 0.648804 ± 0.001127
Upper leaflet (nm2): 0.648804 ± 0.001127
Lower leaflet (nm2): 0.648804 ± 0.001127
Average Z coordinate
Peptide (nm): 9.525840 ± 0.170179
First Residue (nm): 8.8067200 ± 0.0522505
Last Residue (nm): 10.386700 ± 0.381203
Membrane (nm): 6.8256900 ± 0.0120096
Upper leaflet Head Group (nm): 8.7664200 ± 0.0145267
Lower leaflet Head Group (nm): 4.8843400 ± 0.0097959
Bilayer Thickness (nm): 3.882070 ± 0.017521
Peptide insertion (nm): 0.759427 ± 0.170798
Contacts
Peptide - Water: 80.53750 ± 5.33443
Peptide - Head groups: 9.17250 ± 1.33514
Peptide - Tail groups: 7.48250 ± 1.08742
Tilt (°): 59.70180 ± 7.45595
PepDF:
5(ns):  CVS
Displacement (nm): 0.8836710 ± 0.0351227
Precession(°): 1.85077 ± 3.99696
50(ns)  CVS
Displacement (nm): 2.564130 ± 0.132783
Precession(°): 14.4026 ± 12.6675
100(ns)  CVS
Displacement(nm): 3.61121 ± 0.20603
Precession(°): 16.1783 ± 18.0190
200(ns)  CVS
Displacement(nm): 4.740880 ± 0.270957
Precession(°): -21.7572 ± 25.7008

  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.