Trajectory SP1324

Force field: martini_v3
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: 19207
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P451 AP03488
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LWENFKNAGKKFILNILDKIRCRVAGGCRT
Total charge (e): +5
Number of residues: 30
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 15
  Polar: 6
Electrostatic Dipolar Moment (e nm): 2.27
Longitudinal (e nm): 2.24
Transversal (e nm): 0.37
Hydrophobic Dipolar Moment (nm): 4.11
Longitudinal (nm): 3.89
Transversal (nm): 1.32
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): 0.65002200 ± 0.00126652
Upper leaflet (nm2): 0.65002200 ± 0.00126652
Lower leaflet (nm2): 0.65002200 ± 0.00126652
Average Z coordinate
Peptide (nm): 4.6149200 ± 0.0364087
First Residue (nm): 4.8292000 ± 0.0400345
Last Residue (nm): 4.2779200 ± 0.0585098
Membrane (nm): 6.8120000 ± 0.0132275
Upper leaflet Head Group (nm): 8.7498900 ± 0.0156048
Lower leaflet Head Group (nm): 4.8738900 ± 0.0109286
Bilayer Thickness (nm): 3.876000 ± 0.019051
Peptide insertion (nm): 0.2589700 ± 0.0380135
Contacts
Peptide - Water: 63.2375 ± 1.2726
Peptide - Head groups: 14.90750 ± 0.31735
Peptide - Tail groups: 12.645000 ± 0.327181
Tilt (°): 85.005100 ± 0.903491
PepDF:
5(ns):  CVS
Displacement (nm): 0.7208470 ± 0.0289978
Precession(°): 0.340795 ± 1.632820
50(ns)  CVS
Displacement (nm): 2.094790 ± 0.105027
Precession(°): 3.77569 ± 4.92327
100(ns)  CVS
Displacement(nm): 2.899870 ± 0.135521
Precession(°): 4.61225 ± 7.01980
200(ns)  CVS
Displacement(nm): 4.066230 ± 0.195242
Precession(°): -8.85567 ± 11.12720

  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.