Common Dynamic Determinants Govern Quorum Quenching Activity in N-terminal Serine Hydrolases

(File-01) Free enzymes molecular dynamics:

input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes

general input files for MD simulations in AMBER

output restart files from minimization, equilibration and production runs

output files from minimization, equilibration and production runs

raw data for analysis and visualization:

protein backbone RMSD evolution

binding cavity dynamics analysis

principal component analysis of catalytic machinery (with states' representatives in PDF format)

(File-02) Ligand-enzyme complexes molecular dynamics:

input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules

general input files for MD simulations in AMBER

output restart files from minimization, equilibration and production runs

output files from minimization, equilibration and production runs

raw data for analysis and visualization:

protein backbone RMSD evolution

near-attack-conformation (NAC) stabilization

HSLs RMSD evolution

MM/PBSA binding energy estimation

HSLs heavy atoms RMSF

(File-03) Michaelis complex ensemble generation molecular dynamics:

input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules

general input files for MD simulations in AMBER

output restart files from ensemble generation production runs

output files from ensemble generation production runs

(Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics:

input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules

ensemble of input restart files generated in stage 3

general input files for QM/MM steered MD simulations in AMBER

output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations

output files and output work from QM/MM steered MD simulations

(File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization:

reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured

evolution of the reaction coordinate elements in the first and second step of acylation

representative states of the reaction stages for visualization (in PDB format)

different dynamics of the residues gating access to acyl-binding cavity at TS1

different dynamics of the residues gating overall access to active site at TS2a

different system-dependent bending of the HSLs at TS1 and TS2a