LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

• Published in: Scientific reports 2020-06, Vol.10 (1), p.10489-10489, Article 10489
• Main Authors: Zhai, Xiaobo, Lei, Dongsheng, Zhang, Meng, Liu, Jianfang, Wu, Hao, Yu, Yadong, Zhang, Lei, Ren, Gang
• Format: Article
• Language: English
• Subjects: 631/1647/2258; 631/1647/245; 631/1647/794; 631/535/1258/1260; 631/57/2272/2273; 631/57/2272/951; Algorithms; Atoms & subatomic particles; Chemical activity; Chemical reactions; Cryoelectron Microscopy - methods; cryoelectron tomography; Electron Microscope Tomography - methods; Humanities and Social Sciences; Image processing; Image Processing, Computer-Assisted - methods; imaging; Imaging, Three-Dimensional - methods; Lipoproteins; Macromolecular Substances - chemistry; Macromolecules; MATHEMATICS AND COMPUTING; Molecular Conformation; multidisciplinary; Negative Staining - methods; NMR; Nuclear magnetic resonance; Proteins; Radiation; Science; Science (multidisciplinary); software; structure determination; thermodynamics; Tomography; Tomography, X-Ray Computed - methods; Vibrations
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-66793-1

A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e ., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.