Trajectory SP738

Force field: martini_v2.2
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: 19192
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P159 AP02895
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
MATPHVAGAAALILSKHPTWTNAQVRDRLESTATY-
LGNSFYYGK
Total charge (e): +2
Number of residues: 44
By amino acid:
  Basic: 10
  Acidic: 2
  Hydrophobic: 22
  Polar: 14
Electrostatic Dipolar Moment (e nm): 6.56
Longitudinal (e nm): 6.52
Transversal (e nm): 0.71
Hydrophobic Dipolar Moment (nm): 10.81
Longitudinal (nm): 10.8
Transversal (nm): 0.24
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): 0.64633600 ± 0.00103733
Upper leaflet (nm2): 0.64633600 ± 0.00103733
Lower leaflet (nm2): 0.64633600 ± 0.00103733
Average Z coordinate
Peptide (nm): 8.6883300 ± 0.0335207
First Residue (nm): 8.5749100 ± 0.0483033
Last Residue (nm): 8.8623400 ± 0.0490098
Membrane (nm): 6.7827500 ± 0.0107288
Upper leaflet Head Group (nm): 8.738750 ± 0.012935
Lower leaflet Head Group (nm): 4.830750 ± 0.008501
Bilayer Thickness (nm): 3.9080000 ± 0.0154784
Peptide insertion (nm): -0.0504194 ± 0.0359298
Contacts
Peptide - Water: 54.00000 ± 1.00419
Peptide - Head groups: 24.385000 ± 0.433243
Peptide - Tail groups: 21.730000 ± 0.319396
Tilt (°): 88.37460 ± 1.28765
PepDF:
5(ns):  CVS
Displacement (nm): 0.6218740 ± 0.0254906
Precession(°): 0.101292 ± 0.339217
50(ns)  CVS
Displacement (nm): 1.949740 ± 0.090162
Precession(°): 1.24689 ± 1.09196
100(ns)  CVS
Displacement(nm): 2.680390 ± 0.140748
Precession(°): 2.36559 ± 1.59795
200(ns)  CVS
Displacement(nm): 3.968460 ± 0.211149
Precession(°): 4.64240 ± 2.17657

  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.