Trajectory SP1075

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: 45478
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P327 AP03763
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

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Sequence :
NKMAYNVGKAISRIMRRVR
Total charge (e): +6
Number of residues: 19
By amino acid:
  Basic: 6
  Acidic: 0
  Hydrophobic: 9
  Polar: 4
Electrostatic Dipolar Moment (e nm): 2.78
Longitudinal (e nm): 1.89
Transversal (e nm): 2.03
Hydrophobic Dipolar Moment (nm): 1.79
Longitudinal (nm): 0.41
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: 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): 0.64938300 ± 0.00110307
Upper leaflet (nm2): 0.64938300 ± 0.00110307
Lower leaflet (nm2): 0.64938300 ± 0.00110307
Average Z coordinate
Peptide (nm): 4.5467200 ± 0.0316221
First Residue (nm): 4.5762200 ± 0.0407543
Last Residue (nm): 4.5421900 ± 0.0368249
Membrane (nm): 6.5718300 ± 0.0111135
Upper leaflet Head Group (nm): 8.5393000 ± 0.0135424
Lower leaflet Head Group (nm): 4.60271000 ± 0.00898674
Bilayer Thickness (nm): 3.936590 ± 0.016253
Peptide insertion (nm): 0.0559856 ± 0.0328743
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 13.015000 ± 0.267813
Peptide - Tail groups: 10.157500 ± 0.260293
Tilt (°): 87.891300 ± 0.816601
PepDF:
5(ns):  CVS
Displacement (nm): 0.6300960 ± 0.0268826
Precession(°): 0.996864 ± 1.364540
50(ns)  CVS
Displacement (nm): 1.8287600 ± 0.0801952
Precession(°): 8.10379 ± 3.50508
100(ns)  CVS
Displacement(nm): 2.709760 ± 0.117911
Precession(°): 14.6804 ± 3.8676
200(ns)  CVS
Displacement(nm): 4.13105 ± 0.13877
Precession(°): 31.65010 ± 3.73633

  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.