title: 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.
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 N. Wolfe Street, Baltimore, Maryland 21205, United States.
authors.forename: Drew
authors.initials: D
authors.lastname: Gunio
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 N. Wolfe Street, Baltimore, Maryland 21205, United States.
authors.forename: John
authors.initials: J
authors.lastname: Froehlig
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 N. Wolfe Street, Baltimore, Maryland 21205, United States.
authors.forename: Katerina
authors.initials: K
authors.lastname: Pappas
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 N. Wolfe Street, Baltimore, Maryland 21205, United States.
authors.forename: Uneeke
authors.initials: U
authors.lastname: Ferguson
authors.affiliation: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 N. Wolfe Street, Baltimore, Maryland 21205, United States.
authors.forename: Herschel
authors.initials: H
authors.lastname: Wade
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D062105:Molecular Docking Simulation; D015335:Molecular Probes; D012996:Solutions; D015534:Trans-Activators / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; C098722:BmrR protein, bacteria; D008024:Ligands; D015335:Molecular Probes; D012996:Solutions; D015534:Trans-Activators