2025/05/16 by Elisa Posani, Pavel Janoš, Daniel B. Haack +4 · 1 voice · 8 citations
Biochemistry, Genetics and Molecular Biology · #Advanced Electron Microscopy Techniques and Applications #Atom (system on chip) #Biology #Computational biology #Computer science #Gene #Genetics #Parallel computing #Physics #RNA #RNA and protein synthesis mechanisms #RNA modifications and cancer #Statistical physics
paper · pdf · doi:10.1038/s41467-025-59769-0
published in Nature Communications 16(1), 4549 (Nature Portfolio)
openalex publication_date 2025/05/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/23
The advent of single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution imaging of large macromolecules, enhancing functional insights. However, current cryo-EM refinement tools condense all single-particle images into a single structure, which can misrepresent highly flexible molecules like RNAs. Here, we combine molecular dynamics simulations with cryo-EM density maps to better account for the structural dynamics of a complex and biologically relevant RNA macromolecule. Namely, using metainference, a Bayesian method, we reconstruct an ensemble of structures of the group II intron ribozyme, which better matches experimental data, and we reveal inaccuracies of single-structure approaches in modeling flexible regions. An analysis of all RNA-containing structures deposited in the Protein Data Bank reveals that this issue affects most cryo-EM structures in the 2.5–4 Å range. Thus, RNA structures determined by cryo-EM require careful handling, and our method may be broadly applicable to other RNA systems. Cryo-EM often misrepresents flexible RNA molecules by averaging their conformations. Here, the authors combine cryo-EM data with all-atom simulations to refine a dynamic ensemble of complex RNA macromolecules, revealing the limits of single-structure models in flexible regions.