Trajectory SP1236

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: 19218
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P407 AP01018
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
AFQTFKPDWNKIRYDAMKMQTSLGQMKKRFNL
Total charge (e): +5
Number of residues: 32
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 14
  Polar: 9
Electrostatic Dipolar Moment (e nm): 2.54
Longitudinal (e nm): 1.97
Transversal (e nm): 1.6
Hydrophobic Dipolar Moment (nm): 4.37
Longitudinal (nm): 4.03
Transversal (nm): 1.7
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): 0.64834300 ± 0.00122391
Upper leaflet (nm2): 0.64834300 ± 0.00122391
Lower leaflet (nm2): 0.64834300 ± 0.00122391
Average Z coordinate
Peptide (nm): 9.8311500 ± 0.0838121
First Residue (nm): 8.786630 ± 0.051574
Last Residue (nm): 10.962000 ± 0.185375
Membrane (nm): 6.8318100 ± 0.0130679
Upper leaflet Head Group (nm): 8.7744400 ± 0.0153474
Lower leaflet Head Group (nm): 4.8891300 ± 0.0106085
Bilayer Thickness (nm): 3.8853200 ± 0.0186569
Peptide insertion (nm): 1.0567000 ± 0.0852057
Contacts
Peptide - Water: 103.66000 ± 1.58587
Peptide - Head groups: 9.200000 ± 0.606282
Peptide - Tail groups: 5.9000 ± 0.3426
Tilt (°): 61.9470 ± 2.7214
PepDF:
5(ns):  CVS
Displacement (nm): 0.9017330 ± 0.0383713
Precession(°): 2.26702 ± 2.35975
50(ns)  CVS
Displacement (nm): 2.91112 ± 0.14886
Precession(°): 21.80620 ± 8.71018
100(ns)  CVS
Displacement(nm): 3.755890 ± 0.187364
Precession(°): 42.6624 ± 12.4186
200(ns)  CVS
Displacement(nm): 3.65620 ± 0.20971
Precession(°): 101.2240 ± 20.9944

  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.