Trajectory SP1224

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: 19206
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P401 AP00955
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
IIRPIIQIIKQKIR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.18
Longitudinal (e nm): 1.95
Transversal (e nm): 0.99
Hydrophobic Dipolar Moment (nm): 4.62
Longitudinal (nm): 4.53
Transversal (nm): 0.94
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): 0.64922800 ± 0.00104019
Upper leaflet (nm2): 0.64922800 ± 0.00104019
Lower leaflet (nm2): 0.64922800 ± 0.00104019
Average Z coordinate
Peptide (nm): 4.7851500 ± 0.0419888
First Residue (nm): 4.9889800 ± 0.0502114
Last Residue (nm): 4.5686400 ± 0.0483881
Membrane (nm): 6.8303900 ± 0.0105201
Upper leaflet Head Group (nm): 8.7708900 ± 0.0125542
Lower leaflet Head Group (nm): 4.88945000 ± 0.00875701
Bilayer Thickness (nm): 3.8814400 ± 0.0153066
Peptide insertion (nm): 0.1043010 ± 0.0428923
Contacts
Peptide - Water: 32.682500 ± 0.815314
Peptide - Head groups: 9.042500 ± 0.281219
Peptide - Tail groups: 8.132500 ± 0.314615
Tilt (°): 83.02260 ± 1.59985
PepDF:
5(ns):  CVS
Displacement (nm): 0.8476390 ± 0.0345577
Precession(°): -0.708065 ± 3.287540
50(ns)  CVS
Displacement (nm): 2.569000 ± 0.139632
Precession(°): -13.3362 ± 7.2250
100(ns)  CVS
Displacement(nm): 3.807870 ± 0.179747
Precession(°): -26.7107 ± 10.3259
200(ns)  CVS
Displacement(nm): 5.722140 ± 0.295525
Precession(°): -54.5796 ± 14.4052

  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.