Solution-Binding and Molecular Docking Approaches Combine to Provide an Expanded View of Multidrug Recognition in the MDR Gene Regulator BmrR

Abstract

Solution-binding and molecular docking have been combined with a diverse collection of chemical probes to further elucidate multidrug (MD) recognition in BmrR. Whereas previous efforts have focused on structural elucidations of MD binding, the present study examines features imparted by structure, including the recognition properties of the ligand-pocket, ligand structural requirements, and key factors that define and influence binding. Whereas MD-pockets are generally believed to be featureless and very hydrophobic, log KD-clog P correlations observed for BmrR and other polyspecific proteins suggest polar contributions are required for broad-spectrum recognition of amphipathic ligands. We show that molecular docking simulations recapitulate key features of MD recognition and have been employed to further inform contributions from structure. In addition to elaborating our understanding of the structures and functional roles of pocket elements that dictate broad-spectrum binding, molecular docking has implication additional features that likely play major roles, including ligand dynamics and multiple ligand-binding modes.

Unconventional Coupling between Ligand Recognition and Allosteric Control in the Multidrug Resistance Gene Regulator, BmrR

“…The corresponding ligand DG BIND values were determined separately in solutionb indinge xperiments (seeT able S1). [13] Data pointsf or cationic ligandsa re depicted as blue circles;t hose for zwitterions and charge neutral ligands are orange. This schemea pplies to panel D. C) Metal selectivity and sensitivity in CueR.…”

Solution Binding and Structural Analyses Reveal Potential Multidrug Resistance Functions for SAV2435 and CTR107 and Other GyrI-like Proteins

“…MD recognition is central to efflux-related mechanisms that offer broad cellular protection against toxic chemical agents. ,− Current models describing MD recognition by MDR proteins draw from investigations of interactions of ligands with efflux pumps and regulator proteins. − In these studies, structural and other biochemical approaches were combined with diverse sets of chemical probes to identify putative MD-binding pockets as well as structural features within those pockets that confer polyspecific binding. , Thus, these studies provide a framework for distinguishing proteins with promiscuous binding specificity from their highly selective counterparts. Global domain architecture and local features are both functional components of ligand recognition, the latter of which appear to be shared more among MDR proteins than among the former .…”

Charge is Major Determinant of Activation of the Ligand‐Responsive Multidrug Resistance Gene Regulator, BmrR

“…We have previously noted the significance of charge in ligand recognitionb yB mrR ( Figure 5A). [8] The results presented here suggest ad eeper importanceo fchargei na llosteric control ( Figure 5B). This is supported by closer examination of analogue series displaying similar structures but differing in charge due to the pK a values of their basic centers ( Figure S1 in the SupportingI nformation).…”

“…We have previously noted the significance of charge in ligand recognition by BmrR (Figure A) . The results presented here suggest a deeper importance of charge in allosteric control (Figure B).…”

“…The measurementsu tilize single-shota ssays, which derive from run-off transcription performed at ligand concentrations presumed to be saturating in each case based on our knowledge of binding. [8] Similar approaches have been used to investigate transcriptional activationb yanumber of metal-binding MerR-related regulators, including MerR, [9] CueR [10] and ZntR. [11] Ligand-dependent transcription was reconstituted Figure 1.…”