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:

  1. protein backbone RMSD evolution

  2. binding cavity dynamics analysis

  3. 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:

  1. protein backbone RMSD evolution

  2. near-attack-conformation (NAC) stabilization

  3. HSLs RMSD evolution

  4. MM/PBSA binding energy estimation

  5. 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