Trajectory SP1255

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: 17399
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P416 AP02031
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: W

  Download all Compresed Files.


Sequence :
PFKKLEKVGRNIRDGIIKAGPAVAVIGQATSIARP-
TGK
Total charge (e): +6
Number of residues: 38
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 23
  Polar: 5
Electrostatic Dipolar Moment (e nm): 9.19
Longitudinal (e nm): 8.87
Transversal (e nm): 2.39
Hydrophobic Dipolar Moment (nm): 2.73
Longitudinal (nm): 1.53
Transversal (nm): 2.26
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): 0.61403200 ± 0.00103382
Upper leaflet (nm2): 0.61403200 ± 0.00103382
Lower leaflet (nm2): 0.61403200 ± 0.00103382
Average Z coordinate
Peptide (nm): 8.9448600 ± 0.0398968
First Residue (nm): 8.4521100 ± 0.0568973
Last Residue (nm): 9.3893800 ± 0.0664899
Membrane (nm): 6.3977800 ± 0.0104092
Upper leaflet Head Group (nm): 8.4065300 ± 0.0119651
Lower leaflet Head Group (nm): 4.38664000 ± 0.00887645
Bilayer Thickness (nm): 4.0198900 ± 0.0148981
Peptide insertion (nm): 0.5383310 ± 0.0416524
Contacts
Peptide - Water: 87.19000 ± 1.68605
Peptide - Head groups: 15.607500 ± 0.507189
Peptide - Tail groups: 11.210000 ± 0.485399
Tilt (°): 81.55800 ± 1.06636
PepDF:
5(ns):  CVS
Displacement (nm): 0.6470390 ± 0.0275213
Precession(°): -0.535324 ± 1.012990
50(ns)  CVS
Displacement (nm): 1.8741700 ± 0.0950563
Precession(°): -4.62341 ± 2.87739
100(ns)  CVS
Displacement(nm): 2.772080 ± 0.115981
Precession(°): -9.93573 ± 3.55820
200(ns)  CVS
Displacement(nm): 3.997290 ± 0.196104
Precession(°): -29.98870 ± 4.49241

  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.