Dormancy-associated synthesis of coproporphyrin III tetramethyl ester via a "revolver" methylation mechanism in mycobacteria

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.