Trajectory SP408

Force field: martini_v2.2P
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: 24407
Time step (fs) : 25
Software: GROMACS 2020
Supercomputer: Finisterrae II CESGA
Peptides: P68 DRAMP01610
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
GLFDIVKKVVGAIGSL
Total charge (e): +1
Number of residues: 16
By amino acid:
  Basic: 2
  Acidic: 1
  Hydrophobic: 12
  Polar: 1
Electrostatic Dipolar Moment (e nm): 2.55
Longitudinal (e nm): 2.53
Transversal (e nm): 0.34
Hydrophobic Dipolar Moment (nm): 5.76
Longitudinal (nm): 2.98
Transversal (nm): 4.93
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.64869 ± 0.00059
Upper leaflet (nm2): 0.64869 ± 0.00059
Lower leaflet (nm2): 0.64869 ± 0.00059
Average Z coordinate
Peptide (nm): 5.865 ± 0.021
First Residue (nm): 5.950 ± 0.025
Last Residue (nm): 5.846 ± 0.027
Membrane (nm): 4.1195 ± 0.0036
Upper leaflet Head Group (nm): 6.0994 ± 0.0048
Lower leaflet Head Group (nm): 2.1417 ± 0.0025
Bilayer Thickness (nm): 3.9577 ± 0.0054
Peptide insertion (nm): -0.234 ± 0.022
Contacts
Peptide - Water: 22.23 ± 0.36
Peptide - Head groups: 9.87 ± 0.16
Peptide - Tail groups: 10.29 ± 0.15
Tilt (°): 90.45 ± 0.82
PepDF:
5(ns):  CVS
Displacement (nm): 0.524 ± 0.026
Precession(°): -0.3 ± 2.9
50(ns)  CVS
Displacement (nm): 1.38 ± 0.19
Precession(°): -2.0 ± 21.0
100(ns)  CVS
Displacement(nm): 1.95 ± 0.35
Precession(°): -3.0 ± 32.0
200(ns)  CVS
Displacement(nm): 2.6 ± 1.0
Precession(°): -6.0 ± 52.0

  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.