Friday, April 4, 2025
4/4/2025
Thermodynamically Calibrated RNA Simulations to Decode Mechanisms of RNA MolecularRecognition - ABSTRACT This MIRA proposal details the continued development of improved, thermodynamically accurate computer models for simulating RNA structures, folding pathways, and molecular recognition at atomistic resolution. These models differ from existing models for RNA in that they are calibrated to reproduce solution thermodynamic data on the physical behavior of nucleotides and nucleosides, an approach that is readily extended to include the effects of unnatural RNAs and RNA-ligand interactions. This technology is particularly important as many biomedically important RNAs are not amenable to traditional structural biology techniques, which makes it difficult to establish basic structure-function relationships that must be understood before potential therapeutic interventions could be designed. This proposal builds on several recent successes including using SHAPE restrained simulations to explore the folding pathway of a co-transcriptionally folded RNA, reveal the switching mechanism of riboswitches, and predict the structure of a novel RNA aptamers that only fold upon binding their ligands. Building on these recent results, a comprehensive research program is proposed in three major parts. First, we will de-novo fold an entire 76 nt tRNA molecule, including all native modification and divalent ions. This will be made possible due to our extensive experience in simulating modified nucleotides, recent progress in simulating Mg-RNA interactions and our multi-simulation restrained folding technology. Secondly, we will expand our ability to simulate induced-fit binding of a range of small molecule ligands to their RNA aptamers, enabling us to predict where modifications can be introduced to improve target specificity. Finally, we will develop improved ways to simulate protein-RNA complexes, using the modular PPR proteins as a calibration, and miRNA/mRNA complexes annealed within the hAGO2 protein as a model system.
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