Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

By Takanori Nakane, Dari Kimanius, Erik Lindahl, Sjors H. W. Scheres. bioRxiv, 2018

424 citations recorded by the source corpus.

Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particles in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes. Please note that this bioRxiv submission is ahead of the availability of the multi-body software in relion-3.0. We take great care in distributing stable software, but this does take time. We will announce the (beta-)release of relion-3.0 through the ccp-em mailing list (https://www.jiscmail.ac.uk/CCPEM) and on twitter (@SjorsScheres).

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

View Paper: https://www.semanticscholar.org/paper/254b36a3b250983c1d110e08ee4c6e51e26df0dd

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Citations in the corpus

3D Variability Analysis: Resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM (2020, methodology): “Local refinement methods (e.g., [12, 38] ) and multi-body refinement [26] methods allow high resolution refinement of some regions of flexible molecules, by assuming that the molecule is composed of a small number of rigid parts.”
New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “Secondly, multi-body refinement implements an automated and iterative approach for focused refinement with partial signal subtraction on multiple independently moving parts of a complex [Nakane et al., 2018].”
AI-based structure prediction empowers integrative structural analysis of human nuclear pores (2022, methodology): “To analyze the conformational flexibility, multibody refinement (77) was performed on the consensus map.”
Reconstructing continuous distributions of 3D protein structure from cryo-EM images (2019, background): “Traditional reconstruction algorithms address heterogeneity with discrete clustering approaches, however, protein conformations are continuous and may be poorly approximated with discrete clusters (Malhotra & Udgaonkar (2016); Nakane et al. (2018)).”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “The popular software RELION uses an alternate “Multi-Body Refinement” implementation, in which a multi-component complex can be manually segmented into multiple “bodies” (masked regions), which are then independently refined using a maximum likelihood approach.(63) The most significant molecular mov”