Title:	Structural biology of ribosomes
DNr:	NAISS 2024/5-281
Project Type:	NAISS Medium Compute
Principal Investigator:	Katja Petzold <katja.petzold@imbim.uu.se>
Affiliation:	Karolinska Institutet
Duration:	2024-06-01 – 2025-06-01
Classification:	10603
Keywords:

Abstract

The ribosome is a large RNA-protein complex that synthesizes proteins in all living organisms. It undergoes global conformational rearrangements during translation, where its two subunits move relative each other, motions that are well characterized. However, local dynamics of RNA have not been studied in the same detail. The RNA helix 44 (h44) is located at the interface of the two subunits, containing intersubunit bridges that get rearranged during protein synthesis(1) and is therefore our research interest. Biomolecules exist in an ensemble of conformations, an equilibrium that can be altered due to molecular interactions(2). We study the higher energy conformational states, termed excited states (ES), interchanging on a micro-to-millisecond time-scale with the most populated state, the ground state (GS), through base-pair rearrangements. These excited states can be elucidated using R1ρ relaxation dispersion NMR(3). Next, trapping the excited states by mutations will give us information on the effect on the dynamics of the small construct by NMR, and on the overall structure of the entire ribosome using cryo-EM studies. Time on the cluster would be used to process the data from cryo-EM data collection. We investigate what effect the local RNA dynamics and excited states have on the global structure and motions of the ribosome. Characterizing the dynamic behaviour of h44 in human and bacterial ribosomal RNA will help increase our understanding of the ribosome function during protein synthesis. The differences and similarities between species can further be exploited for designing new and more specific drug interactions for antibiotics. 1. Yusupova G, Yusupov M. Crystal structure of eukaryotic ribosome and its complexes with inhibitors. Phil. Trans. R. Soc. B 372: 20160184 (2017) 2. Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019) 3. Marušič M., Schlagnitweit J., Petzold K. RNA Dynamics by NMR Spectroscopy. ChemBioChem, 20, 2685 (2019)