Mechanism of Ligand Discrimination by the NMT1 Riboswitch

Riboswitches are conserved functional domains in mRNAthat almostexclusively exist in bacteria. They regulate the biosynthesis andtransport of amino acids and essential metabolites such as coenzymes,nucleobases, and their derivatives by specifically binding small molecules.Due to their ability to precisely discriminate between different cognatemolecules as well as their common existence in bacteria, riboswitcheshave become potential antibacterial drug targets that could deliverurgently needed antibiotics with novel mechanisms of action. In thiswork, we report the recognition mechanisms of four oxidization products(XAN, AZA, UAC, and HPA) generated during purine degradation by anRNA motif termed the NMT1 riboswitch. Specifically,we investigated the physical interactions between the riboswitch andthe oxidized metabolites by computing the changes in the free energyon mutating key nucleobases in the ligand binding pocket of the riboswitch.We discovered that the electrostatic interactions are central to liganddiscrimination by this riboswitch. The relative binding free energiesof the mutations further indicated that some of the mutations canalso strengthen the binding affinities of the ligands (AZA, UAC, andHPA). These mechanistic details are also potentially relevant in thedesign of novel compounds targeting riboswitches.

Automated summary

Riboswitches are conserved functional domains in bacteria that specifically bind small molecules to regulate biosynthesis and transport of amino acids and essential metabolites. They have potential as antibacterial drug targets and this study investigated the recognition mechanisms of oxidized metabolites by the NMT1 riboswitch. Electrostatic interactions were found to be central to ligand discrimination and some mutations could strengthen the binding affinities of the ligands. These findings are also relevant for designing novel compounds targeting riboswitches.