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Huang Y, Zhang Y, Ni T. Towards in situ high-resolution imaging of viruses and macromolecular complexes using cryo-electron tomography. J Struct Biol 2023; 215:108000. [PMID: 37467823 DOI: 10.1016/j.jsb.2023.108000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/15/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cryo-electron tomography and subtomogram averaging are rising and fast-evolving imaging techniques to study biological events, providing structural information at an unprecedented resolution while preserving spatial correlation in their native contexts. The latest technology and methodology development ranging from sample preparation to data collection and data processing, has enabled significant advancement in its applications to various biological systems. This review provides an overview of the current technology development enabling high-resolution structural study in situ, highlighting the use of a priori information of biological samples to assess the quality of subtomogram averaging pipeline. We exemplify the applications of this technique to understanding viruses and principles of macromolecule assembly using different biological systems, ranging from in vitro to in situ samples, which provide structural information at different resolutions and contexts.
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Affiliation(s)
- Yixin Huang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Yu Zhang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Tao Ni
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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Yu H, Li C, Wang X, Duan J, Yang N, Xie L, Yuan Y, Li S, Bi C, Yang B, Li Y. Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic. J Proteome Res 2020; 19:4242-4258. [PMID: 32957788 PMCID: PMC7640955 DOI: 10.1021/acs.jproteome.0c00372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Indexed: 12/12/2022]
Abstract
Viruses remain a major challenge in the fierce fight against diseases. There have been many pandemics caused by various viruses throughout the world over the years. Recently, the global outbreak of COVID-19 has had a catastrophic impact on human health and the world economy. Antiviral drug treatment has become another essential means to overcome pandemics in addition to vaccine development. How to quickly find effective drugs that can control the development of a pandemic is a hot issue that still needs to be resolved in medical research today. To accelerate the development of drugs, it is necessary to target the key target proteins in the development of the pandemic, screen active molecules, and develop reliable methods for the identification and characterization of target proteins based on the active ingredients of drugs. This article discusses key target proteins and their biological mechanisms in the progression of COVID-19 and other major epidemics. We propose a model based on these foundations, which includes identifying potential core targets, screening potential active molecules of core targets, and verifying active molecules. This article summarizes the related innovative technologies and methods. We hope to provide a reference for the screening of drugs related to pandemics and the development of new drugs.
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Affiliation(s)
| | | | | | - Jingyi Duan
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Na Yang
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Lijuan Xie
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Yu Yuan
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Shanze Li
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Chenghao Bi
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Bin Yang
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
| | - Yubo Li
- Tianjin University of Traditional
Chinese Medicine, No. 10, Poyang Lake Road, West Zone, Tuanbo New City, Jinghai District, Tianjin, 301617, China
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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