Our group is interested in the molecular basis for site-specific aminoglycoside-RNA recognition both on natural and in vitro selected targets. Several groups have identified RNA folds following in vitro selection that target aminoglycoside antibiotics with affinities ranging from mM to nM. These RNA aptamer sequences are likely to undergo adaptive binding on complex formation to generate specific pockets for the bound aminoglycoside antibiotics.
Apramycin is unique among aminoglycoside antibiotics in containing a bicyclic core domain. It binds preferentially to eukaryotic decoding sites compared with prokaryotic counterparts and induces misreading of the genetic code during translation. The structure of the complex has been solved at 1.5 resolution, with the apramycin binding in the deep groove of the decoding site RNA, which forms a continuously stacked helix comprising novel non-canonical CA and GA pairs and a bulged adenine. Apramycin recognizes the RNA target by specific direct contacts and interactions mediated by a Mg cation and water molecules. We have also solved the free eukaryotic decoding site at 2.4 resolution, and observe that the RNA does not undergo a conformational transition on apramycin complex formation.
Hermann, T., Tereshko, V., Skripkin, E. & Patel, D. J. (2007). The structure of the apramycin-eukaryotic RNA decoding site complex. Blood Cells, Molecules, and Diseases 38, 193-198. [PubMed Abstract]
The aminocyclitol antibiotic streptomycin was the second antibiotic after penicillin to have a dramatic impact on medical practice and treatment. Streptomycin interacts with the central domain of 16S ribosomal RNA and also inhibits group I intron splicing. A modular streptomycin-binding RNA aptamer has been identified by in vitro selection in the Renee Schroeder laboratory. Streptomycin-RNA aptamer complex formation occurs with micromolar affinity and, strikingly, has an absolute requirement for divalent cations as an essential cofactor for the interaction. We describe a 2.9 Å x-ray structure of the complex between streptomycin and an in vitro selected RNA aptamer, solved using the anomalous diffraction properties of bound Ba cations. The RNA aptamer, which contains two asymmetric internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and non-canonical pairs and triples. The streptomycin streptose ring is encapsulated by stacked arrays of bases from both loops at the elbow of the L-shaped RNA architecture. Specificity is defined by direct hydrogen bonds between all streptose functional groups and base edges that line the inner walls of the cylindrical binding pocket. By contrast, the majority of the intermolecular interactions involve contacts to backbone phosphates in the published structure of streptomycin bound to 16S RNA.
Tereshko, V., Skripkin, E. & Patel, D. J. (2003). Encapsulating streptomycin within a small 40-mer RNA. Chem. Biol. 10, 175-187. [PubMed Abstract]