Multidrug resistance (MDR) refers to the acquired ability of cells to tolerate a broad range of toxic compounds. One mechanism cells employ is to increase the level of expression of efflux pumps for the expulsion of xenobiotics. A key feature uniting efflux-related mechanisms is multidrug (MD) recognition, either by efflux pumps themselves or by their transcriptional regulators. However, models describing MD binding by MDR effectors are incomplete, underscoring the importance of studies focused on the recognition elements and key motifs that dictate polyspecific binding. One such motif is the GyrI-like domain, which is found in several MDR proteins and is postulated to have been adapted for small-molecule binding and signaling. Here we report the solution binding properties and crystal structures of two proteins containing GyrI-like domains, SAV2435 and CTR107, bound to various ligands. Furthermore, we provide a comparison with deposited crystal structures of GyrI-like proteins, revealing key features of GyrI-like domains that not only support polyspecific binding but also are conserved among GyrI-like domains. Together, our studies suggest that GyrI-like domains perform evolutionarily conserved functions connected to multidrug binding and highlight the utility of these types of studies for elucidating mechanisms of MDR.

No 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.

Small ankyrin-1 (sAnk1, Ank1.5) is a splice variant of the ANK1 gene that binds to the large modular protein, obscurin A, with nanomolar affinity, a reaction that may help to organize the sarcoplasmic reticulum in striated muscle. A subset of lysine and arginine residues in the 2 ankyrin repeats of sAnk1 interact specifically with 4 glutamate residues in a stretch of 30 amino acids of obscurin to mediate binding. Homology modeling and molecular dynamics simulations have revealed a ''hot spot'' of 4 hydrophobic residues exposed on the surface of the ankyrin repeat domain of sAnk1. We used site-directed mutagenesis of bacterially expressed fusion proteins, followed by blot overlays and surface plasmon resonance assays, to study the contribution of these 4 residues, V70, F71, I102 and I103, to binding to the 30-mer of obscurin. Alanine mutations of each of these four residues inhibited binding to residues 6316-6345 of obscurin (Obsc 6316-6345 ). In contrast, V70A and I102A mutations had no effect on binding to a second sAnk1 binding site on obscurin, located within residues 6231-6260 (Obsc 6231-6260 ). Using the same methods, we mutated the 5 hydrophobic residues present in Obsc 6316-6345 to alanine and identified V6328, I6332, and V6334 as critical for proper binding. Our results suggest that hydrophobic interactions as well as electrostatic interactions are important for the binding of sAnk1 to Obsc 6316-6345 , consistent with studies of the complexes formed by other ankyrin repeat proteins with their ligands. Hydrophobic interactions are likely to contribute to the difference in affinity of sAnk1 for Obsc 6316-6345 and Obsc 6231-6260 , and for the dominant role played by the more C-terminal sequence in binding. Supported by grant R01-AR056330 from the NIH to RJB and training grants T32 GM08181 (to RJB) and T32 AR07592 (to M. Schneider).