DOI: 10.5281/zenodo.7980949
title: Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules

description: (01-mutants_design.tar.gz) Mutants design:



Input structures of ecPGA from the PDB database (PDB IDs: 1GK9, 1GM7, and 1GM9), processed to resemble wild-type state, repaired by RepairPDB module of FoldX 4

Double-point mutants preparation, analysis and filtering:



text files including configuration for FoldX 4

inputs and outputs of CAVER 3.02 calculations on FoldX 4 PDB files of ecPGA double-point mutants

input configuration file and TransportTools library 0.9.4 calculations outputs generated based on the inputs produced in step 01 and 02 above

CSV files containing complete information about FoldX 4 stability prediction and geometrical properties from CAVER 3.02 and TransportTools library version 0.9.4 for ecPGA double-point mutants



Triple-point mutant preparation, analysis and filtering:



text files including configuration for FoldX 4

inputs and outputs of CAVER 3.02 calculations on FoldX 4 PDB files of ecPGA triple-point mutants

input configuration file and TransportTools library 0.9.4 calculations outputs generated based on the inputs produced in step 01 and 02 above

CSV files containing complete information about FoldX 4 stability prediction and geometrical properties from CAVER 3.02 and TransportTools library version 0.9.4 for ecPGA triple-point mutants




(02-docking.tar.gz) Preparation of protein-ligand complexes using molecular docking for wild-type ecPGA and 6 best designed triple-point mutants with 6 various bacterial signaling molecules:



PDB files of ligand, PDBQT files of the receptor and PDB files of the complexes selected from docking experiment:


Full names of presented protein variants:ecPGA_wt, wild-type Escherichia coli penicillin G acylaseLAF, Phe138αLeu & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_22LSF, Phe138αLeu & Met142αSer & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_98MAF, Phe138αMet & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_23MSF, Phe138αMet & Met142αSer & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_99VAF, Phe138αVal & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_30YAF, Phe138αTyr & Met142αAla & Ile177βPhe ecPGA variant internally referred as 1GK9_Repair_33Full names of presented AHLs:C06, N-hexanoyl-L-homoserine lactone;C06-3O, N-3-oxo-hexanoyl-L-homoserine lactone;C08, N-octanoyl-L-homoserine lactone;C08-3O, N-3-oxo-octanoyl-L-homoserine lactone;C10, N-decanoyl-L-homoserine lactone;C12-3O, N-3-oxo-dodecanoyl-L-homoserine lactone

(03-protein_ligand_MDs.tar.gz) Ligand-enzyme complexes molecular dynamics for wild-type ecPGA and 6 best designed triple-point mutants with 6 various bacterial signaling molecules:



Force field parameters in Amber format

Input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber

Amber input files *.in for minimization, equilibration and production runs

Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format

Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format

Output files generated during post-processing of production runs trajectories in a form of text files generated by cpptraj


(04-free_enzymes_MDs.tar.gz) Free enzymes molecular dynamics of 3 best triple-point ecPGA (VAF, YAF and MSF) mutants prioritized based on protein-ligand molecular dynamics simulations and experimental assays:



Force field parameters and input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber format

Amber input files *.in for minimization, equilibration and production runs

Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format

Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format

Post-processing analysis of generated trajectories:



Text files with distances, CSV files containing result of PCA and clustering, PNG files with clustered PCA results

Inputs and outputs of MDpocket analysis and visualization of the pocket frequency grid as an isomesh

CAVER input configuration files in text format, CAVER output data including parsed CSV and text files for visualization of entrance opening time evolution and cavity profiles inspection

cpptraj generated text files including RMSD, distances and chi1 angles measurements




All plots were generated using matplotlib or seaborn Python libraries. Figures containing structural representations were generated using PyMOL 2.0.1.

(05-ecPGA_VAF_YAF_MSF_penG_MDs.tar.gz) PenG-enzyme complexes molecular dynamics for wild-type ecPGA and 3 best designed triple-point mutants (VAF, YAF, MSF):



PenG force field parameters in Amber (GAFF) format

Input coordinates *.inpcrd, parameters *.parm7 and *.pdb files for each complex ready for simulation in Amber

Amber input files *.in for minimization, equilibration and production runs

Restart files for each stage of the minimization, equilibration and production runs in Amber *.rst format

Simulation output files for each stage of the minimization, equilibration and production runs in Amber *.mdout format and analysis output files generated during post-processing of production runs trajectories in a form of text files

Reactive Stabilization Score [RSS] statistics summarized in CSV files
description: This work was supported by the National Science Centre, Poland (Grant Number 2021/41/N/NZ2/01365), Institutional Research project RVO61388971 from the Institute of Microbiology of the CAS and by the Czech Foundation grant 21-17044S. B.S. is a recipient of a scholarship provided by POWER project POWR.03.02.00-00-I022/16. The computations were performed at the Poznan Supercomputing and Networking Center.