Trajectory SP444

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: 24034
Time step (fs) : 25
Software: GROMACS 2020
Supercomputer: Finisterrae II CESGA
Peptides: P74 DRAMP02330
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

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Sequence :
FFHHIFRGIVHVGKTIHRLVTG
Total charge (e): +3
Number of residues: 22
By amino acid:
  Basic: 7
  Acidic: 0
  Hydrophobic: 13
  Polar: 2
Electrostatic Dipolar Moment (e nm): 3.51
Longitudinal (e nm): 3.13
Transversal (e nm): 1.59
Hydrophobic Dipolar Moment (nm): 8.46
Longitudinal (nm): 4.48
Transversal (nm): 7.18
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): 0.64917 ± 0.00067
Upper leaflet (nm2): 0.64917 ± 0.00067
Lower leaflet (nm2): 0.64917 ± 0.00067
Average Z coordinate
Peptide (nm): 2.301 ± 0.020
First Residue (nm): 2.437 ± 0.025
Last Residue (nm): 2.058 ± 0.030
Membrane (nm): 4.0757 ± 0.0041
Upper leaflet Head Group (nm): 6.0533 ± 0.0055
Lower leaflet Head Group (nm): 2.0955 ± 0.0028
Bilayer Thickness (nm): 3.9578 ± 0.0062
Peptide insertion (nm): -0.206 ± 0.020
Contacts
Peptide - Water: 35.26 ± 0.51
Peptide - Head groups: 13.88 ± 0.20
Peptide - Tail groups: 13.99 ± 0.17
Tilt (°): 92.99 ± 0.69
PepDF:
5(ns):  CVS
Displacement (nm): 0.484 ± 0.021
Precession(°): 0.0 ± 2.0
50(ns)  CVS
Displacement (nm): 1.51 ± 0.21
Precession(°): 0.0 ± 12.0
100(ns)  CVS
Displacement(nm): 2.17 ± 0.35
Precession(°): -2.0 ± 18.0
200(ns)  CVS
Displacement(nm): 3.35 ± 0.48
Precession(°): 0.0 ± 11.0

  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.