PeriProt

Periprot 1.0 is a sofware built to analyse Peripheral Membrane Proteins (PMPs) structure or Molecular Dynamics (MD) simulation data. Periprot can only analyse data from NAMD or CHARMM simulation (PSF format for the topology and dcd format for the trajectory).

The available analysis are:

• (1) Depth of Anchoring (MD)
• (2) Hydrophobic contact analysis (MD)
• (3) Cation-Pi interaction analysis (MD)
• (4) Hydrogen bond network analysis (MD)
• (5) Protein - Membrane Distances (MD)
• (6) Macrodipole (PDB structure)

Dependencies

Following packages are required:

• argparse (version >= 1.1)
• MDAnalysis (version == 0.20.1)
• Matplotlib (version >= 3.1.0)
• Numpy (version >= 1.19.1)
• Pandas (version >= 0.24.2)
• Scipy (version >= 1.5.2)

Usage

  -h, --help        show this help message and exit
  -top TOP          psf file only
  -traj TRAJ        trajectories (DCD format)
  -hydro            Hydrophobic contact analysis
  -hbond            hbond analysis
  -catpi            cation pi analysis
  -depth            depth of anchoring analysis
  -dist             Prot. - Memb distance
  -segmemb SEGMEMB  segid for membrane
  -segprot SEGPROT  segid for protein
  -first FIRST      first frame to read
  -last LAST        last frame to read
  -skip SKIP        first frame to read
  -out OUT          output name
  -pdb PDB          PDB file
  -mdipole          Macrodipole calculation

• top (string): topology file (PSF) file. This file is required for all analysis.

• traj (string): trajectory file, only DCD file is accepted.

• hydro (boolean): If this flag is present the hydrophobic contact interaction will be performed.

• hbond (boolean): If this flag is present the hbond interaction analysis will be performed.

• catpi (boolean): If this flag is present the cation-pi interaction analysis will be performed.

• depth (boolean): If this flag is present the depth of anchoring will be calculated.

• dist (boolean): If this flag is present the protein membrane distance will be calculated.

• first (integer): First frame to take into account. Default = 0

• last (integer): Last frame to take into account.

• skip (integer): Skip frames? Default = 1

• out (string): output name for results. Default = periprot

• pdb (string): PDB file of the system

• mdipole (boolean): If this flag is present the macrodipole of the protein will be calculated.

(1) Depth of anchoring

Periprot can be use to calculate the average depth of anchoring (DOA) of each residue in the bilayer. The DOA here represent the distance from the carbon alpha (CA) of the residue and the average phosphate plane. If the CA is below the phosphate plane the DOA will be negative.

usage: python PeriProt.py -top mydata.psf -traj mydata.dcd -pdb mydata.pdb -depth -out example

The output files:

• a csv file ("example_depth_of_anchoring.csv") containg the average DOA and the associated standard deviation for each residue
• A figure ("example_depth_of_anchoring.png") with the average DOA vs the residue number.
• A PDB file ("example_depth_of_anchoring.pdb"). If a PDB file is given on the command line, a new PDB file will be created with the average average DOA during the MD as the B-factor.

Example of output:

(2) Hydrophobic contact analysis

In Periprot, an hydrophobic contact are consider between to candidates atom (one from the protein and one from the bilayer) if there distance are less than 3 Å. The candidates atom can be picked automatically. The user can modified the list of candidiates in the folowing files: lib/hydrophobic_candidates_lipid.dat & hydrophobic_candidates_prot.dat

usage: python PeriProt.py -top mydata.psf -traj mydata.dcd -pdb mydata.pdb -hydro -out example

The output files:

• a csv file ("example_hydrophobic_contact_raw_data.csv") contating the raw data (all hydrophobic contact in all frame)
• a csv file ("example_average_hydrophobic_contact_per_frame.csv") containg the average number of hydrophobic contact per residues
• a PDB file ("example__average_hydrophobic_contact_per_frame.pdb"). If a PDB file is given on the command line, a new PDB file will be created with the average number of hydrophobic contact as the B-factor.

Example of output:

(3) Cation-Pi interaction analysis

The cation-pi interaction between tyrosines or tryptophane and the bilayer can be evaluated using Periprot. The cation-pi interaction is consider when the distances between each carbon of the aromatic cycle and the nitrogen atom of a PC lipid is less that 7 Å. Moreover, these distance should not differ by more than 1.5 Å.

/!\ Warning: the calculation will be done between PC lipid and the protein, other lipids (PS or PE) will be add later /!\

usage: python PeriProt.py -top mydata.psf -traj mydata.dcd -pdb mydata.pdb -catpi -out example

The output files:

• a csv file ("example_cation_pi_int.csv") contating the occupencies of the cation-pi interactions.
• a PDB file ("example_cation_pi_occupencies.pdb"). If a PDB file is given on the command line, a new PDB file will be created with the average number of hydrophobic contact as the B-factor.

Example of output:

(4) Hydrogen bond network analysis

With Periprot, the hydrogen bonds analysis is perform with MD analysis (mda.analysis.hbonds.HydrogenBondAnalysis). The raw date from this function is use to calculate the occupancy of each residue involve in a hbond.

/!\ Warning: The donor and acceptor atoms of hbonds in the membrane should be specify in the file: lib/hbond_acceptor_donnor_list_lipids.dat . The donor and acceptor atoms of hbonds for PC and PE lipid is already specified in the file. Other lipid will be add later /!\

usage: python PeriProt.py -top mydata.psf -traj mydata.dcd -pdb mydata.pdb -hbond -out example

The output files:

• a csv file ("exampl_hbonds_analysis_raw_data.csv") raw data from mda.analysis.hbonds.HydrogenBondAnalysis
• a csv file ("example_hbond_occupancies.csv") containg the occupancy per residue.
• a PDB file ("example_hbond_occupancies.pdb"). If a PDB file is given on the command line, a new PDB file will be created with the occupancies as the B-factor.

Example of output:

(5) Protein - Membrane Distance

The protein-Membrane distance can be calculated with Periprot. The user can be should between three different distances. When '-dist' the following dialogue will appears:

    Which distance ?:
    1: Prot (COM) - Memb (COM) distance
    2: Prot (COM) - Phosphate Plane (COM) distance
    3: Custom distance between two atoms (one in the prot. and one on the memb.)
    
    Selection:

1. distance between the protein center of mass and the membrane center of mass
2. distance between the protein center of mass and the phosphate plane center of mass
3. Custom distance between two atoms (one in the prot. and one on the memb.)

usage: python PeriProt.py -top mydata.psf -traj mydata.dcd -dist -out example

The output files:

• a csv file ("example__prot_memb_distance.csv") contating the prot./memb. distance.
• a figure ("example__prot_memb_distance.png"). Distance vs frame

Example of output:

(5) Macrodipole

Periprot can be use to calculate the macrodipole of a PMP: usage: python PeriProt.py -top mydata.psf -pdb mydata.pdb -mdipole -out example

The output files:

• a PDB file ("example_charge_info.pqr") contating the charge as the bfactor column
• a BILD file ("example_macrodipole_arrow.bild"). Information on the macrodipole. It can be visualized with chimera

Example of output:

Contact

If you have questions, feel free to contact me: mail: e.e.moutoussamy@gmail.com