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RNAs are critical regulators of gene expression, and their functions are often mediated by complex secondary and tertiary structures. Structured regions in RNA can selectively interact with small molecules—via well-defined ligand-binding pockets—to modulate the regulatory repertoire of an RNA. The broad potential to modulate biological function intentionally via RNA–ligand interactions remains unrealized, however, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good physicochemical properties (often termed drug-like). Here, we devisefpocketR, a computational strategy that accurately detects pockets capable of binding drug-like ligands in RNA structures. Remarkably few, roughly 50, of such pockets have ever been visualized. We experimentally confirmed the ligandability of novel pockets detected withfpocketRusing a fragment-based approach introduced here, Frag-MaP, that detects ligand-binding sites in cells. Analysis of pockets detected byfpocketRand validated by Frag-MaP reveals dozens of sites able to bind drug-like ligands, supports a model for RNA secondary structural motifs able to bind quality ligands, and creates a broad framework for understanding the RNA ligand-ome. 

Menaquinones are lipoquinones that consist of a headgroup (naphthoquinone, menadione) and an isoprenyl sidechain. They function as electron transporters in prokaryotes such as Mycobacterium tuberculosis. For these studies, we used Langmuir monolayers and microemulsions to investigate how the menaquinone headgroup (menadione) and the menahydroquinone headgroup (menadiol) interact with model membrane interfaces to determine if differences are observed in the location of these headgroups in a membrane. It has been suggested that the differences in the locations are mainly caused by the isoprenyl sidechain rather than the headgroup quinone-to-quinol reduction during electron transport. This study presents evidence that suggests the influence of the headgroup drives the movement of the oxidized quinone and the reduced hydroquinone to different locations within the interface. Utilizing the model membranes of microemulsions and Langmuir monolayers, it is determined whether or not there is a difference in the location of menadione and menadiol within the interface. Based on our findings, we conclude that the menadione and menadiol may reside in different locations within model membranes. It follows that if menaquinone moves within the cell membrane upon menaquinol formation, it is due at least in part, to the differences in the properties of headgroup interactions with the membrane in addition to the isoprenyl sidechain.