DOI: 10.5061/dryad.ck3dh
title: Data from: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

description: The CTX-M family of beta lactamases mediate broad-spectrum antibiotic
 resistance and present in the majority of drug-resistant gram-negative
 bacteria infections worldwide. Allosteric mutations that increase
 catalytic rates of these drug resistance enzymes have been identified in
 clinical isolates but are challenging to predict prospectively. We have
 used molecular dynamics simulations to predict allosteric mutants
 increasing CTX-M9 drug resistance, experimentally testing top mutants
 using multiple antibiotics. Purified enzymes show an increase in catalytic
 rate and efficiency, while mutant crystal structures show no detectable
 changes from wild-type CTX-M9. We hypothesize that increased drug
 resistance results from changes in the conformational ensemble of an acyl
 intermediate in hydrolysis. Machine-learning analyses on top-scoring
 mutants identify changes to the binding-pocket conformational ensemble by
 which these allosteric mutations transmit their effect. These findings
 show how molecular simulation can predict how allosteric mutations alter
 active-site conformational equilibria to increase catalytic rates and thus
 resistance against common clinically used antibiotics.
description: CTX-M9:meropenem
 acylenzyme run input fileGromacs TPR for
 wild-type CTX-M9 in complex with meropenemctx_acyl.tprBinding pocket trajectories for CTX-M9Gromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.ctx_pocket_trajs.tgzBinding pocket trajectories for CTX-M9 L48AGromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.l48a_pocket_trajs.tgzBinding pocket trajectories for CTX-M9 T165WGromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.t165w_pocket_trajs.tgzBinding pocket trajectories for CTX-M9 S281AGromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.s281a_pocket_trajs.tgzCTX-M9 L48A:meropenem acylenzyme run input fileGromacs TPR for CTX-M9 L48A in complex with meropenemctx_l48a.tprCTX-M9 T165W:meropenem acylenzyme run input fileGromacs TPR for CTX-M9 T165W in complex with meropenemctx_t165w.tprCTX-M9 S281A:meropenem acylenzyme run input fileGromacs TPR for CTX-M9 S281A in complex with meropenemctx_s281a.tprPDB file for solvated CTX-M9:meropenem adductPDB file corresponding to simulation start state for CTX-M9:meropenemctx_acyl.pdbPDB file for solvated CTX-M9 L48A:meropenem adductPDB file corresponding to simulation start state for L48A:meropenem acylenzyme.ctx_l48a.pdbPDB file for solvated CTX-M9 T165W:meropenem adductPDB file corresponding to simulation start state for CTX-M9 T165W meropenem acylenzymectx_t165w.pdbPDB file for solvated CTX-M9 S281A:meropenem adductPDB file corresponding to simulation start state for CTX-M9 S281A meropenem acylenzymectx_s281a.pdbResidue definitions for meropenem and cefotaxime acylenzymesModified GROMACS aminoacids.rtp file for AMBER99SB-ILDN force field containing residue definitions for serine-meropenem adducts and serine-cefotaxime adducts.aminoacids.rtpatom type fileaminoacids.atp in GROMACS format for modified AMBER99SB-ILDN parameters to describe acylenzymes.atomtypes.atpffnonbonded.itpNonbonded parameter file ffnonbonded.itp for modified AMBER99SB-ILDN to define acylenzymes.