RNA Dynamics using NMR spectroscopy and molecular dynamics simulations
Title: RNA Dynamics using NMR spectroscopy and molecular dynamics simulations
DNr: NAISS 2024/22-318
Project Type: NAISS Small Compute
Principal Investigator: Rubin Dasgupta <rubin.dasgupta@imbim.uu.se>
Affiliation: Uppsala universitet
Duration: 2024-03-01 – 2025-03-01
Classification: 10603


microRNAs (miRs) are short 22 nucleotides (nt) non-coding RNA molecules which are mis-regulated in ~ 75% of cancers. They associate with the argonaute protein to form an RNA-induced silencing complex (RISC) to downregulate protein expressions by targeting the 3’-untraslated-region of the messenger-RNA (mRNA). This target selection is mediated by a conserved seed region which is 7-8 nt however, emerging evidence shows that the remaining compensatory region is also crucial for the target identification. The mechanistic description and the biophysical characterisation of this compensatory region-based target identification is in its infancy. The researcher will model multiple miR-mRNA complexes to gain insight into the role of the compensatory region in target identification specifically miR-34a which is implicated in liver and breast cancers. The aim of the project will be to build NMR restrained models of multiple complexes, compare them, and characterise the target specific structure and dynamics of miR-34a using molecular dynamics simulations. This will provide a detailed conformational map of miR-34a for multiple target which can aid in its development as a cancer therapeutics. It has been previously shown that stabilising the transient conformation state of miR-34a which was specific for the mRNA encoding the protein, Sirtuin-1, lead to a 2-fold increase in the downregulation of Sirtuin-1 expression. Similar transient conformations will be identified here thereby providing a framework to modify miR-34a either by mutagenesis or chemically for therapeutic purpose. The researcher will employ the recently developed method of 2-dimensional replica exchange molecular dynamics (REMD) to solve the structure of multiple miR-34a-mRNA complexes using partial NMR data. Using long microsecond simulations at multiple temperatures, the conformational landscape and dynamics of these complexes will be probed and compared with the dynamics measured by NMR spectroscopy. This project will also provide a deeper understanding on the role of RNA-dynamics and the compensatory region of miR in regulating cellular biochemistry.