Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution

Ward, Shannon; Childs, Alex; Staley, Ceri; Waugh, Christopher; Watts, Julie A; Kotowska, Anna M; Bhosale, Rahul; Borkar, Aditi N

Abstract

The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural biology techniques in deciphering their complex structures and dynamic interactions. To address this limitation, we have benchmarked an integrated approach that combines cryogenic OrbiSIMS, a state-of-the-art solid-state mass spectrometry technique, with computational methods for modelling RNA structures at atomic resolution with enhanced precision. Furthermore, using 7SK RNP as a test case, we have successfully determined the full 3D structure of a native RNA in its apo, native and disease-remodelled states, which offers insights into the structural interactions and plasticity of the 7SK complex within these states. Overall, our study establishes cryo-OrbiSIMS as a valuable tool in the field of RNA structural biology as it enables the study of challenging, native RNA systems.

Citation

Ward, S., Childs, A., Staley, C., Waugh, C., Watts, J. A., Kotowska, A. M., Bhosale, R., & Borkar, A. N. (2024). Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution. Nature Communications, 15(1), Article 4367. https://doi.org/10.1038/s41467-024-48694-3

• Journal Article Type: Article
• Acceptance Date: May 5, 2024
• Online Publication Date: May 22, 2024
• Publication Date: May 22, 2024
• Deposit Date: May 28, 2024
• Publicly Available Date: May 28, 2024
• Journal: Nature Communications
• Electronic ISSN: 2041-1723
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 15
• Issue: 1
• Article Number: 4367
• DOI: https://doi.org/10.1038/s41467-024-48694-3
• Keywords: Ribonucleoproteins, RNA, Nucleic Acid Conformation, Models, Molecular, Mass Spectrometry, Molecular Dynamics Simulation
• Public URL: https://nottingham-repository.worktribe.com/output/35159618
• Publisher URL: https://www.nature.com/articles/s41467-024-48694-3
• PMID: 38777820
• Additional Information: Received: 18 September 2023; Accepted: 5 May 2024; First Online: 22 May 2024; : The authors declare no competing interests.