Data supporting: Membrane Selectivity Mechanisms of Antimicrobial Peptide Snakin-Z against Prokaryotic and Eukaryotic Membranes
Creators: name: Kumar, Nandan
name: Li, Yonghui
Publisher: name: Zenodo
Year: 2024

description: This repository contains the code used to generate the results presented in the paper titled "Membrane Selectivity Mechanisms of Antimicrobial Peptide Snakin-Z against Prokaryotic and Eukaryotic Membranes."

Folder Structure

The uploaded folder, Zenodo_Membran-peptide_MD_Data contains nine subfolders: 

Zenodo_Peptide - MD Data of PeptideZenodo_BSM - MD data of pure Bacillus subtilis membraneZenodo_BSMP - MD data of Bacillus subtilis membrane-peptide complexZenodo_CAM - MD data of pure Candida albicans membraneZenodo_CAMP - MD data of BCandida albicans membrane-peptide complexZenodo_ECM - MD data of pure Escherichia coli membraneZenodo_ECMP - MD data of Escherichia coli membrane-peptide complexZenodo_RBC - MD data of pure red blood cells membraneZenodo_RBCP - MD data of red blood cells membrane-peptide complex

 

Gromacs Simulation Files:

membrane.gro, membrane.top: These files define the structure (coordinates and topology) of the simulated membrane in its initial state.membrane_with_peptide.gro: This file represents the initial configuration of the membrane with the peptide, ready for simulation.peptide.gro, peptide.top: These files define the structure of the peptide molecule you simulated in its initial state.peptide_newBox.gro (optional): This file could be a configuration file for the peptide placed in a new simulation box with different dimensions. It might not be used in all simulations.

Minimization and Equilibration Steps (Gromacs):

step6.0_minimization.gro, step6.0_minimization.mdp: These files define the initial configuration and parameters for the energy minimization step (step 6.0) in your simulation protocol.step6.1_equilibration.gro, step6.1_equilibration.mdp - step6.6_equilibration.gro, step6.6_equilibration.mdp: Similar to minimization files, these define configurations and parameters for multiple equilibration steps (steps 6.1 to 6.6) before the production simulation run.

Production Simulation Run (Gromacs):

step7_production.gro, step7_production.mdp: These files define the initial configuration and parameters for the main production simulation run (step 7).

Force Field Files (CHARMM):

CLA.itp, forcefield.itp, POPE.itp, POPG.itp, POT.itp, PVCL2.itp, TIP3.itp: These files contain definitions for the force field used in your simulation. They describe the interactions between atoms based on specific parameters for different atom types (e.g., water, lipids).

Analysis Scripts

In addition to the simulation files, various scripts were used for data analysis:



contact.py: Counts contacts between membrane & peptide (uses MDAnalysis).

contact_area.py: Estimates contact area between membrane & peptide (uses SASA data).

contact_area_mean-sd.py: Calculates average & standard deviation of contact area.

distance_residues.py: Analyzes average distances between peptide residues & membrane center.

distance_test.py (Optional): Analyzes internal membrane distances (might differ from distance_residues.py).


For pure peptide MD simulations, Principal Component Analysis (PCA) was followed by free energy landscape generation. Scripts used for this analysis are listed below:





identify_min_points.py: Finds top 3 minimum points & their values in a free energy landscape data file.




plot_2d_free_energy.py: Creates a 2D color-coded contour plot of a free energy landscape.




plot_3d_free_energy.py: Creates a 3D color-coded surface plot of a free energy landscape.




Xpm2txt.py: Converts a Gromacs XPM image file into a three-column text file for data extraction.




sham.pl (Perl script): Combines two data files into a single format for free energy landscape analysis with g_sham of gromacs.