Lanthipeptide Folding Protocol Project

This project contains the protocol capture for "computational structure prediction of lanthipeptides with NMR data reeals underappreciated peptide flexibility."

Directory Structure

• af_pred/: Contains the AlphaFold predictions for four-helical lanthipeptides, as well as further analysis of these peptides. The peptides considered helical are 2KTO, 6VE9, 6VGT, and 8CWX.
• chem_shift_calc/: Calculation of backbone chemical shifts with sparta.
• input_pdb/: Stores input PDB files of lanthipeptides sourced from the Protein Data Bank (PDB).
• flex_ripp_scan/: Includes structure prediction and analysis of non-helical lanthipeptides. The non-helical peptides are 1AJ1, 6PQG, 6VHJ, 6VLJ, 7JU9, and 7JVF.
• NCAA/: Houses the parameterization of non-canonical amino acids (NCAA) used in the study. This includes paramaterization for Rosetta and parameter development with QM calculations.
• renamed_pdb/: Contains PDB files that have been processed and renamed according to the project's conventions.
• scripts/: A collection of Python scripts used for various analysis and processing tasks within the project.

Scripts

• get_pert_rmsd_ddg.py: Analyzes RMSD and ddG perturbations.
• lanthionine_rename.py: Renames residues in PDB files according to specific criteria so that they can be read in by Rosetta and lanthionine ring constraints properly applied.
• make_nmr_cst.py: Converts NMR restraints (tbl) to Rosetta a constraints file.
• make_ripp_structpred_xml.py: Creates XML files for structure prediction of RiPPs (ribosomally synthesized and post-translationally modified peptides).
• plot_folding_funnel.py: Plots folding funnel graphs for visualizing protein folding landscapes.

Example usage for renaming pdbs:

python ~/scripts/lanthionine_rename.py -i 7JVF.pdb -p renamed_pdb/
python ~/scripts/lanthionine_rename.py -i 6PQG.pdb -p renamed_pdb/ -f 6PQG_temp_named.pdb