Protein-Membrane MD Analysis

Analyse a protein-membrane MD trajectory from MDDB: leaflets, lipid z-positions, order parameters, area per lipid, density profile, channel pore radius and lipid flip-flop.

by Temple Compute

Run Protein-Membrane MD Analysis on Horus

W-26 · Protein-Membrane MD Analysis

Analyse a protein-membrane MD trajectory from MDDB: leaflets, lipid z-positions, order parameters, area per lipid, density profile, channel pore radius and lipid flip-flop.

Domain: BioExcel Building Blocks

Overview

Analyses a protein-membrane MD trajectory downloaded from MDDB (default A023K: a GABA-gated chloride channel in a DPPC bilayer). The trajectory is fitted so the membrane lies in the xy-plane, leaflets are identified with FATSLiM and Lipyphilic, and the workflow computes lipid z-positions, order parameters, area per lipid, density profile, channel pore radius and lipid flip-flop. The workflow has 12 tasks.

Pipeline

download_trajectory                     Structure, trajectory and tpr from MDDB
fit_membrane -> fit_protein             Fit to membrane normal (rot+trans), then to protein (xy translation)
identify_leaflets_fatslim -> assign_leaflets    Leaflet identification and per-frame assignment
compute_zpositions, compute_zpositions_around   Lipid z-positions, whole membrane and around the protein
compute_order_parameters                Deuterium order parameters of acyl tails
compute_area_per_lipid                  Area per lipid, 2D Voronoi
compute_density_profile                 Density profile along z
compute_pore_dimensions                 Channel pore-radius profile (HOLE)
compute_flip_flop                       Lipid flip-flop events

Inputs / Outputs

The entry must be a single-lipid bilayer whose lipid residue name is lipid_resname; the lipid headgroups are selected as its phosphorus atoms. Outputs (results/):

structure.pdb, trajectory.xtc, topology.tpr: downloaded structure, trajectory, topology
membrane_fit.xtc, protein_fit.xtc: membrane-fitted and protein-fitted trajectories
leaflets.ndx, leaflets_data.csv: leaflet groups and per-frame assignment
zpositions.csv, zpositions_around.csv, order.csv, apl.csv, density.dat
hole.vmd, hole_profile.csv: pore-radius profile
flip_flop.csv: flip-flop events

Parameters

| id | Default | Meaning | |---|---|---| | mddb_project | A023K | MDDB accession of a protein in a lipid bilayer. | | lipid_resname | DPPC | Lipid residue name (1-4 characters). Its phosphorus atoms (element P) are the headgroup selection for leaflets, z-positions, area per lipid and flip-flop; the membrane fit uses the GROMACS index group of the same name. The density profile uses the first 3 characters, because cpptraj reads 3-character PDB residue names. | | frame_stride | 1000 | Keep every Nth frame when downloading (1-10000). | | pore_frame_step | 20 | Analyse the pore radius every Nth downloaded frame (1-1000). |