CAREER: Predicting high-resolution RNA tertiary structures using an experimentally callibrated force-field for RNA folding

Suny At Albany, Albany NY

Investigators

Abstract

CAREER: Predicting high-resolution RNA tertiary structures using an experimentally calibrated force-field for RNA folding Ribonucleic acid (RNA) is a versatile molecule that plays many important roles inside cells. Small microRNAs can bind to and recognize messenger RNA and control their translation into protein, while giant ribonucleoprotein complexes can splice genes with perfect precision. Despite RNA's important role in modern cellular biology, current methods for predicting RNA's 3D structure are inadequate and have hampered our ability to discern the underling molecular basis of RNA function. This project entails the development of improved computer models for simulating RNA folding, in 3D atomic resolution. In this project, a new approach to calibrate the forces for RNA folding is developed, in which experimental properties of building blocks of RNA (nucleosides and nucleotides) in their natural environment are used to calibrate the model. The improved simulations will be applied to tackle two vexing problems in RNA structural biology. The first is determining how 3D structure plays a role in microRNA targeting, in which hundreds of distinct messenger RNAs can be targeted by a single microRNA. The second challenge is in the interpretation of RNA chemical probing experiments, which can be highly ambiguous to interpret for RNAs whose 3D structure is unknown. Along with this research program, an education program will be implemented to expose those students coming from disadvantaged backgrounds to STEM fields. To do this, freshman chemistry majors will live, eat, and attend a weekly seminar series together in order to expose these students as early as possible to real scientific careers (through invited speakers) and encourage early participation in undergraduate research. In order for molecular dynamics (MD) simulations to accurately predict RNA tertiary structure the atomistic "force-field" must capture the complex behavior of single-stranded regions such as loops, bulges, and helical junctions. A thermodynamic cycle is devised for calibrating the strength of base-base interactions against experimentally determined free energies. Through this process, the solvation-dependent balance between base-stacking and base-pairing can be finely tuned for each nucleobase. Finally, a protocol is developed to determine RNA tertiary structures using MD simulations using secondary structure profiles as constraints. The salmonella four-U RNA thermometer will be used as a model-system where base-pair specific melting profiles can be directly compared with NMR. The model will then be used to investigate the structural basis of the microRNA "code", by testing the hypothesis that bulge dynamics dictates microRNA recognition of mRNA targets by using miR-34a, a highly promiscuous microRNA.