Computational Insights into BDM91531 Binding and Accessibility in AcrB Mutants

The datasets from the computational study explore the binding and accessibility of BDM91531 to the AcrB RND pump in E. coli across wild-type (WT) and five mutant variants (Q437E, K955E, F948A, D951A, E947A). The data are organized into three files: All_clusters_wt_Q437E_K955E_F948A_D951A_E947A_1_5.zip [BINDING] Contains five clusters (c0 to c4) from 50 ns molecular dynamics (MD) simulations (clustered from the last 25 ns) for WT and mutant AcrB variants. Variants were generated from the WT crystal structure via homology modeling, followed by minimization, equilibration, and a 50 ns production run using Amber24/pmemd.cuda. The top cluster for each variant was used for GBSA-based binding free energy calculations, as reported in the associated article. Accessibility_poses_at_the_cytoplasmic_gate.zip [ACCESSIBILITY/EARLY RECOGNITION] Contains top-scored poses from ensemble molecular docking using Glide, performed on the five MD-derived clusters for WT and mutant variants. Docking was conducted at the cytoplasmic gate of the transmembrane domain to assess ligand accessibility. Grid box parameters were tailored to the ligand’s conformational space. MD_simulation_of_wt_for_pi-pi_interaction_clusters_rep1_2_3.zip Includes 100 clusters from three replica simulations (100ns each) investigating pi-pi interactions between BDM91531 and F948 in the WT AcrB