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Computational methods for in situ structural studies with cryogenic electron tomography
Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10586593/ https://www.ncbi.nlm.nih.gov/pubmed/37868346 http://dx.doi.org/10.3389/fcimb.2023.1135013 |
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author | Zhao, Cuicui Lu, Da Zhao, Qian Ren, Chongjiao Zhang, Huangtao Zhai, Jiaqi Gou, Jiaxin Zhu, Shilin Zhang, Yaqi Gong, Xinqi |
author_facet | Zhao, Cuicui Lu, Da Zhao, Qian Ren, Chongjiao Zhang, Huangtao Zhai, Jiaqi Gou, Jiaxin Zhu, Shilin Zhang, Yaqi Gong, Xinqi |
author_sort | Zhao, Cuicui |
collection | PubMed |
description | Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and further build atomic models from a tilt series of two-dimensional projections. Low signal-to-noise ratio (SNR) and missing wedge are two major factors that make the reconstruction procedure challenging. Because only few near-atomic resolution structures have been reconstructed in cryo-ET, there is still much room to design new approaches to improve universal reconstruction resolutions. This review summarizes classical mathematical models and deep learning methods among general reconstruction steps. Moreover, we also discuss current limitations and prospects. This review can provide software and methods for each step of the entire procedure from tilt series by cryo-ET to 3D atomic structures. In addition, it can also help more experts in various fields comprehend a recent research trend in cryo-ET. Furthermore, we hope that more researchers can collaborate in developing computational methods and mathematical models for high-resolution three-dimensional structures from cryo-ET datasets. |
format | Online Article Text |
id | pubmed-10586593 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-105865932023-10-20 Computational methods for in situ structural studies with cryogenic electron tomography Zhao, Cuicui Lu, Da Zhao, Qian Ren, Chongjiao Zhang, Huangtao Zhai, Jiaqi Gou, Jiaxin Zhu, Shilin Zhang, Yaqi Gong, Xinqi Front Cell Infect Microbiol Cellular and Infection Microbiology Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and further build atomic models from a tilt series of two-dimensional projections. Low signal-to-noise ratio (SNR) and missing wedge are two major factors that make the reconstruction procedure challenging. Because only few near-atomic resolution structures have been reconstructed in cryo-ET, there is still much room to design new approaches to improve universal reconstruction resolutions. This review summarizes classical mathematical models and deep learning methods among general reconstruction steps. Moreover, we also discuss current limitations and prospects. This review can provide software and methods for each step of the entire procedure from tilt series by cryo-ET to 3D atomic structures. In addition, it can also help more experts in various fields comprehend a recent research trend in cryo-ET. Furthermore, we hope that more researchers can collaborate in developing computational methods and mathematical models for high-resolution three-dimensional structures from cryo-ET datasets. Frontiers Media S.A. 2023-10-04 /pmc/articles/PMC10586593/ /pubmed/37868346 http://dx.doi.org/10.3389/fcimb.2023.1135013 Text en Copyright © 2023 Zhao, Lu, Zhao, Ren, Zhang, Zhai, Gou, Zhu, Zhang and Gong https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cellular and Infection Microbiology Zhao, Cuicui Lu, Da Zhao, Qian Ren, Chongjiao Zhang, Huangtao Zhai, Jiaqi Gou, Jiaxin Zhu, Shilin Zhang, Yaqi Gong, Xinqi Computational methods for in situ structural studies with cryogenic electron tomography |
title | Computational methods for in situ structural studies with cryogenic electron tomography |
title_full | Computational methods for in situ structural studies with cryogenic electron tomography |
title_fullStr | Computational methods for in situ structural studies with cryogenic electron tomography |
title_full_unstemmed | Computational methods for in situ structural studies with cryogenic electron tomography |
title_short | Computational methods for in situ structural studies with cryogenic electron tomography |
title_sort | computational methods for in situ structural studies with cryogenic electron tomography |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10586593/ https://www.ncbi.nlm.nih.gov/pubmed/37868346 http://dx.doi.org/10.3389/fcimb.2023.1135013 |
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