Trajectory SP1174

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: 39854
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P376 NC03613
Lipids: POPE, POPG
Heteromolecules:
Ions: NA
Water model: PW

  Download all Compresed Files.


Sequence :
ECTRSGGACNSHDQCCANFCRKATSTCM
Total charge (e): +1
Number of residues: 28
By amino acid:
  Basic: 6
  Acidic: 2
  Hydrophobic: 7
  Polar: 15
Electrostatic Dipolar Moment (e nm): 2.67
Longitudinal (e nm): 2.08
Transversal (e nm): 1.67
Hydrophobic Dipolar Moment (nm): 6.43
Longitudinal (nm): 6.19
Transversal (nm): 1.74
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)
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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): 0.634252000 ± 0.000954403
Upper leaflet (nm2): 0.634252000 ± 0.000954403
Lower leaflet (nm2): 0.634252000 ± 0.000954403
Average Z coordinate
Peptide (nm): 7.20953 ± 1.51467
First Residue (nm): 6.96928 ± 1.33349
Last Residue (nm): 7.40806 ± 1.77111
Membrane (nm): 6.06802000 ± 0.00877722
Upper leaflet Head Group (nm): 8.0659600 ± 0.0107363
Lower leaflet Head Group (nm): 4.07007000 ± 0.00664913
Bilayer Thickness (nm): 3.9958900 ± 0.0126285
Peptide insertion (nm): -0.85643 ± 1.51471
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 1.42750 ± 1.39736
Peptide - Tail groups: 0.287500 ± 0.466324
Tilt (°): 78.19660 ± 8.57504
PepDF:
5(ns):  CVS
Displacement (nm): 1.4276600 ± 0.0725788
Precession(°): 4.68546 ± 8.04888
50(ns)  CVS
Displacement (nm): 4.395170 ± 0.223583
Precession(°): 55.1544 ± 27.7169
100(ns)  CVS
Displacement(nm): 5.678470 ± 0.268722
Precession(°): 111.8170 ± 39.3945
200(ns)  CVS
Displacement(nm): 7.054820 ± 0.411906
Precession(°): 285.4300 ± 43.6939

  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.