Journal Article

A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST

Li, Dongyu, Song, Kai, Bao, Keyan, Li, Yan, Zhang, Haonan, Wang, Lin, Zhu, Ping, Liu, Yanan

2023

Overview

Cryo-electron tomography (cryo-ET) is widely used to explore the 3D density of biomacromolecules. However, the heavy noise and missing wedge effect prevent directly visualizing and analyzing the 3D reconstructions. Here, we introduced REST, a deep learning strategy-based method to establish the relationship between low-quality and high-quality density and transfer the knowledge to restore signals in cryo-ET. Test results on the simulated and real cryo-ET datasets show that REST performs well in denoising and compensating the missing wedge information. The application in dynamic nucleosomes, presenting either in the form of individual particles or in the context of cryo-FIB nuclei section, indicates that REST has the capability to reveal different conformations of target macromolecules without subtomogram averaging. Moreover, REST noticeably improves the reliability of particle picking. These advantages enable REST to be a powerful tool for the straightforward interpretation of target macromolecules by visual inspection of the density and of a broad range of other applications in cryo-ET, such as segmentation, particle picking, and subtomogram averaging. Heavy noise and missing wedge effect hamper the efficient visualization and analysis in cryo-ET. Here, authors present a deep learning-based method for directly visualizing and revealing the dynamic states of target molecules.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/28 / 631/114/794 / 631/1647/2258/1258/1260 / 631/535/1258/1260 / Cryoelectron Microscopy - methods / Deep learning / Density / Electron Microscope Tomography - methods / Humanities and Social Sciences / Image Processing, Computer-Assisted - methods / Inspection / Knowledge management / Macromolecular Substances / Macromolecules / multidisciplinary / Nucleosomes / Reproducibility of Results / Science / Science (multidisciplinary)