Trajectory SP826

Force field: martini_v2.2
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: 19189
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P203 NC00258
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
KKEKDIMKKTI
Total charge (e): +3
Number of residues: 11
By amino acid:
  Basic: 5
  Acidic: 2
  Hydrophobic: 3
  Polar: 1
Electrostatic Dipolar Moment (e nm): 3.38
Longitudinal (e nm): 3.08
Transversal (e nm): 1.4
Hydrophobic Dipolar Moment (nm): 3.21
Longitudinal (nm): 3.18
Transversal (nm): 0.5
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: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC 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): 0.64327000 ± 0.00118146
Upper leaflet (nm2): 0.64327000 ± 0.00118146
Lower leaflet (nm2): 0.64327000 ± 0.00118146
Average Z coordinate
Peptide (nm): 4.8438700 ± 0.0401483
First Residue (nm): 4.5810200 ± 0.0491634
Last Residue (nm): 5.0534400 ± 0.0458332
Membrane (nm): 6.8283600 ± 0.0123415
Upper leaflet Head Group (nm): 8.787680 ± 0.014761
Lower leaflet Head Group (nm): 4.8681200 ± 0.0101275
Bilayer Thickness (nm): 3.9195600 ± 0.0179012
Peptide insertion (nm): 0.0242536 ± 0.0414059
Contacts
Peptide - Water: 23.565000 ± 0.831388
Peptide - Head groups: 9.195000 ± 0.268104
Peptide - Tail groups: 6.782500 ± 0.270806
Tilt (°): 104.70200 ± 2.16939
PepDF:
5(ns):  CVS
Displacement (nm): 0.762950 ± 0.031002
Precession(°): -1.21836 ± 3.41474
50(ns)  CVS
Displacement (nm): 2.285370 ± 0.115711
Precession(°): -12.1953 ± 10.7984
100(ns)  CVS
Displacement(nm): 3.124040 ± 0.167138
Precession(°): -23.8730 ± 14.8449
200(ns)  CVS
Displacement(nm): 4.224000 ± 0.275455
Precession(°): -44.2313 ± 19.6073

  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.