Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.

ABSTRACT: 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 struct

SUBMITTER: Posani E 

PROVIDER: S-EPMC12084557 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature