Trajectory SP1341

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: 17408
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P459 AP03746
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
WKFGKKLERIGQNVFRAAEKVLPVATGYAQLPATL-
AGAKQG
Total charge (e): +5
Number of residues: 41
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 25
  Polar: 7
Electrostatic Dipolar Moment (e nm): 12.77
Longitudinal (e nm): 12.42
Transversal (e nm): 2.96
Hydrophobic Dipolar Moment (nm): 2.49
Longitudinal (nm): 0.28
Transversal (nm): 2.47
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: POPG:POPE (1:3) (Gram-negative bacteria)

POPE
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Total charge (e): 0

  See POPE lipid
  Download ITP File.
  Download PDB File.
POPG
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Total charge (e): -1

  See POPG 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): 0.61612600 ± 0.00104808
Upper leaflet (nm2): 0.61612600 ± 0.00104808
Lower leaflet (nm2): 0.61612600 ± 0.00104808
Average Z coordinate
Peptide (nm): 8.5861100 ± 0.0436542
First Residue (nm): 8.5440400 ± 0.0490637
Last Residue (nm): 9.0059500 ± 0.0665004
Membrane (nm): 6.3757800 ± 0.0110827
Upper leaflet Head Group (nm): 8.3811100 ± 0.0128276
Lower leaflet Head Group (nm): 4.36988000 ± 0.00946251
Bilayer Thickness (nm): 4.0112300 ± 0.0159401
Peptide insertion (nm): 0.2050020 ± 0.0454999
Contacts
Peptide - Water: 74.37000 ± 1.24064
Peptide - Head groups: 20.542500 ± 0.415368
Peptide - Tail groups: 19.222500 ± 0.381464
Tilt (°): 86.817800 ± 0.802991
PepDF:
5(ns):  CVS
Displacement (nm): 0.5991760 ± 0.0234164
Precession(°): 0.0460115 ± 0.8480130
50(ns)  CVS
Displacement (nm): 1.6753200 ± 0.0832625
Precession(°): 0.87893 ± 2.20639
100(ns)  CVS
Displacement(nm): 2.369030 ± 0.131934
Precession(°): 1.70664 ± 2.70243
200(ns)  CVS
Displacement(nm): 3.285350 ± 0.208866
Precession(°): 4.29886 ± 3.74148

  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.