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

<ul> <li> <p>(File-01) Free enzymes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>binding cavity dynamics analysis</p> </li> <li> <p>principal component analysis of catalytic machinery (with states&#39; representatives in PDF format)</p> </li> </ol> </li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li> <p>(File-02) Ligand-enzyme complexes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>near-attack-conformation (NAC) stabilization</p> </li> <li> <p>HSLs RMSD evolution</p> </li> <li> <p>MM/PBSA binding energy estimation</p> </li> <li> <p>HSLs heavy atoms RMSF</p> </li> </ol> </li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li> <p>(File-03) Michaelis complex ensemble generation molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from ensemble generation production runs</p> </li> <li> <p>output files from ensemble generation production runs</p> </li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li> <p>(Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics:</p> <ul> <li> <p>input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>ensemble of input restart files generated in stage 3</p> </li> <li> <p>general input files for QM/MM steered MD simulations in AMBER</p> </li> <li> <p>output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations</p> </li> <li> <p>output files and output work from QM/MM steered MD simulations</p> </li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li> <p>(File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization:</p> <ul> <li> <p>reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured</p> </li> <li> <p>evolution of the reaction coordinate elements in the first and second step of acylation</p> </li> <li> <p>representative states of the reaction stages for visualization (in PDB format)</p> </li> <li> <p>different dynamics of the residues gating access to acyl-binding cavity at TS1</p> </li> <li> <p>different dynamics of the residues gating overall access to active site at TS2a</p> </li> <li> <p>different system-dependent bending of the HSLs at TS1 and TS2a</p> </li> </ul> </li> </ul> <p>&nbsp;</p>