Trajectory SP949

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: 45491
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P264 AP00955
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
IIRPIIQIIKQKIR
Total charge (e): +4
Number of residues: 14
By amino acid:
  Basic: 4
  Acidic: 0
  Hydrophobic: 8
  Polar: 2
Electrostatic Dipolar Moment (e nm): 2.14
Longitudinal (e nm): 1.99
Transversal (e nm): 0.78
Hydrophobic Dipolar Moment (nm): 4.53
Longitudinal (nm): 4.43
Transversal (nm): 0.94
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): 0.64937700 ± 0.00111414
Upper leaflet (nm2): 0.64937700 ± 0.00111414
Lower leaflet (nm2): 0.64937700 ± 0.00111414
Average Z coordinate
Peptide (nm): 8.40875 ± 0.03677
First Residue (nm): 8.1530300 ± 0.0439501
Last Residue (nm): 8.5150300 ± 0.0425766
Membrane (nm): 6.571560 ± 0.011162
Upper leaflet Head Group (nm): 8.5402600 ± 0.0130341
Lower leaflet Head Group (nm): 4.60354000 ± 0.00924778
Bilayer Thickness (nm): 3.9367100 ± 0.0159815
Peptide insertion (nm): -0.1315070 ± 0.0390118
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 10.710000 ± 0.239162
Peptide - Tail groups: 9.720000 ± 0.230096
Tilt (°): 85.2486 ± 1.1793
PepDF:
5(ns):  CVS
Displacement (nm): 0.6918050 ± 0.0284664
Precession(°): 0.271343 ± 1.708290
50(ns)  CVS
Displacement (nm): 2.035010 ± 0.093584
Precession(°): 6.73234 ± 5.58377
100(ns)  CVS
Displacement(nm): 2.541600 ± 0.126953
Precession(°): 16.7439 ± 8.4132
200(ns)  CVS
Displacement(nm): 3.218960 ± 0.203879
Precession(°): 44.9719 ± 10.5075

  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.