DOI: 10.5281/zenodo.17359970
title: Dormancy-associated synthesis of coproporphyrin III tetramethyl ester via a "revolver" methylation mechanism in mycobacteria

description: Data for Publication "Dormancy-associated synthesis of coproporphyrin III tetramethyl ester via a “revolver” methylation mechanism in mycobacteria".

Molecular dynamics-related files.

Molecular dynamics simulations of catalytic cycle of MSMEG_0614:

MSMEG_0614 in water – the apo-state;

Complex prior to methylation – ligands-bound state (SAM, CP-III/CP-I) prior to first methylation reaction;

Complex after methylation – ligands-bound state (SAH, MMC) after the first step of methylation; and ligands-bound state (SAH, TMC) after the fourth step of methylation;

Mutants prior to methylation – predicted in silico mutants Y184F and S235A in complex with SAM and CP-III.

Starting structures in .pdb format (without water molecules), along with trajectories (dt=500 ps) and topologies with all the simulation parameters in .xtc and .tpr formats (GROMACS), respectively:




System
Starting structure
Trajectory
Topology


MSMEG_0614 in water 
apo.pdb
apo.xtc
apo.tpr


Complex prior to methylation 
cpIII_prot.pdb
cpIII_prot.xtc
cpIII_prot.tpr


 
cpI_prot.pdb
cpI_prot.xtc
cpI_prot.tpr


Complex after methylation
MMC_prot.pdb
MMC_prot.xtc
MMC_prot.tpr


 
TMC_prot.pdb
TMC_prot.xtc
TMC_prot.tpr


Mutants prior to methylation
Y184F_cp.pdb
Y184F_cp.xtc
Y184F_cp.tpr


 
S235A_cp.pdb
S235A_cp.xtc
S235A_cp.tpr




The molecular topologies are given in .itp format (CHARMM36 force field for GROMACS) as well as additional atom type and bonded parameters (extra.itp).

3d_density.pse – PyMOL Session: 3D visualization of MD-derived densities of CP derivatives (fig. Proposed mechanism of MSMEG_0614 catalysis. C.)

Molecular dynamics simulations of CP/TMC in lipid bilayer:

Starting structures in .pdb format (water molecules removed), along with the number of molecules, trajectories (dt=500 ps) and topologies with all the simulation parameters in .xtc and .tpr formats (GROMACS), respectively:






Porphyrins in lipid-water systems 

Starting structure
Trajectory
Topology


Number of molecules*



Single CPIII
CPIII_single.pdb
CPIII_single.xtc
CPIII_single.tpr
1:96:32


CPIII dimer
CPIII_dimer.pdb
CPIII_dimer.xtc
CPIII_dimer.tpr
2:96:32


Single TMC
TMC_single.pdb
TMC_single.xtc
TMC_single.tpr
1:96:32


TMC dimer
TMC_dimer.pdb
TMC_dimer.xtc
TMC_dimer.tpr
2:96:32


TMC in medium concentration
TMC_med.pdb
TMC_med.xtc
TMC_med.tpr
20:120:60


TMC in high concentration
TMC_high.pdb
TMC_high.xtc
TMC_high.tpr
50:100:50




* Number of molecules in simulation boxes, colon separated. Columns represent CPIII or TMC, POPE and POPG molecules respectively.                         

QM/MM-related files.

reagCP3 – model system corresponding to reactants with coproporphyrin III;

reagCP3triME – model system corresponding to reactants with coproporphyrin III trimethyl ester;

 

*str files contain topology and additional parameters for CGenFF to build  for S-adenosyl methionine, coproporphyrin III and coproporphyrin III trimethyl ester;

par_all36_cgenff.prm – CGenFF parameter file version with all required parameters.