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Article ; Online: Editorial overview: Cryogenic electron microscopy (cryoEM).

Rohou, Alexis / Zhang, Peijun

2024 Volume 84, Page(s) 102772

MeSH term(s)	Cryoelectron Microscopy ; Microscopy, Electron
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Editorial
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2023.102772
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Article ; Online: Learning from the heaviest ancient whale.

Zhang, Peijun / Goodman, Simon J

Innovation (Cambridge (Mass.))

2023 Volume 4, Issue 5, Page(s) 100501

Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2666-6758
ISSN (online)	2666-6758
DOI	10.1016/j.xinn.2023.100501
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Article ; Online: Recent structural advances in bacterial chemotaxis signalling.

Riechmann, Carlos / Zhang, Peijun

Current opinion in structural biology

2023 Volume 79, Page(s) 102565

Abstract: Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted ... ...

Abstract	Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
MeSH term(s)	Chemotaxis/physiology ; Bacterial Proteins/chemistry ; Histidine Kinase/chemistry ; Signal Transduction/physiology
Chemical Substances	Bacterial Proteins ; Histidine Kinase (EC 2.7.13.1)
Language	English
Publishing date	2023-03-01
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2023.102565
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Article ; Online: Cryo-electron tomography to study viral infection.

Graham, Miles / Zhang, Peijun

Biochemical Society transactions

2023 Volume 51, Issue 4, Page(s) 1701–1711

Abstract: Developments in cryo-electron microscopy (cryo-EM) have been interwoven with the study of viruses ever since its first applications to biological systems. Following the success of single particle cryo-EM in the last decade, cryo-electron tomography (cryo- ...

Abstract	Developments in cryo-electron microscopy (cryo-EM) have been interwoven with the study of viruses ever since its first applications to biological systems. Following the success of single particle cryo-EM in the last decade, cryo-electron tomography (cryo-ET) is now rapidly maturing as a technology and catalysing great advancement in structural virology as its application broadens. In this review, we provide an overview of the use of cryo-ET to study viral infection biology, discussing the key workflows and strategies used in the field. We highlight the vast body of studies performed on purified viruses and virus-like particles (VLPs), as well as discussing how cryo-ET can characterise host-virus interactions and membrane fusion events. We further discuss the importance of in situ cellular imaging in revealing previously unattainable details of infection and highlight the need for validation of high-resolution findings from purified ex situ systems. We give perspectives for future developments to achieve the full potential of cryo-ET to characterise the molecular processes of viral infection.
MeSH term(s)	Humans ; Electron Microscope Tomography/methods ; Cryoelectron Microscopy/methods ; Viruses ; Virus Diseases
Language	English
Publishing date	2023-08-10
Publishing country	England
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20230103
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Article ; Online: Advances in cryo-electron tomography and subtomogram averaging and classification.

Zhang, Peijun

Current opinion in structural biology

2019 Volume 58, Page(s) 249–258

Abstract: Cryo-electron tomography (cryoET) can provide 3D reconstructions, or tomograms, of pleomorphic objects such as organelles or cells in their close-to-native states. Subtomograms that contain repetitive structures can be further extracted and subjected to ... ...

Abstract	Cryo-electron tomography (cryoET) can provide 3D reconstructions, or tomograms, of pleomorphic objects such as organelles or cells in their close-to-native states. Subtomograms that contain repetitive structures can be further extracted and subjected to averaging and classification to improve resolution, and this process has become an emerging structural biology method referred to as cryoET subtomogram averaging and classification (cryoSTAC). Recent technical advances in cryoSTAC have had a profound impact on many fields in biology. Here, I review recent exciting work on several macromolecular assemblies demonstrating the power of cryoSTAC for in situ structure analysis and discuss challenges and future directions.
MeSH term(s)	Electron Microscope Tomography/methods ; Signal-To-Noise Ratio ; Workflow
Language	English
Publishing date	2019-07-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2019.05.021
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Article ; Online: Visualizing HIV-1 Capsid and Its Interactions with Antivirals and Host Factors.

Wilbourne, Morganne / Zhang, Peijun

Viruses

2021 Volume 13, Issue 2

Abstract: Understanding of the construction and function of the HIV capsid has advanced considerably in the last decade. This is due in large part to the development of more sophisticated structural techniques, particularly cryo-electron microscopy (cryoEM) and ... ...

Abstract	Understanding of the construction and function of the HIV capsid has advanced considerably in the last decade. This is due in large part to the development of more sophisticated structural techniques, particularly cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). The capsid is known to be a pleomorphic fullerene cone comprised of capsid protein monomers arranged into 200-250 hexamers and 12 pentamers. The latter of these induce high curvature necessary to close the cone at both ends. CryoEM/cryoET, NMR, and X-ray crystallography have collectively described these interactions to atomic or near-atomic resolutions. Further, these techniques have helped to clarify the role the HIV capsid plays in several parts of the viral life cycle, from reverse transcription to nuclear entry and integration into the host chromosome. This includes visualizing the capsid bound to host factors. Multiple proteins have been shown to interact with the capsid. Cyclophilin A, nucleoporins, and CPSF6 promote viral infectivity, while MxB and Trim5α diminish the viral infectivity. Finally, structural insights into the intra- and intermolecular interactions that govern capsid function have enabled development of small molecules, peptides, and truncated proteins to disrupt or stabilize the capsid to inhibit HIV replication. The most promising of these, GS6207, is now in clinical trial.
MeSH term(s)	Animals ; Antiviral Agents/chemistry ; Antiviral Agents/metabolism ; Antiviral Agents/pharmacology ; Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/chemistry ; Capsid Proteins/metabolism ; HIV Infections/metabolism ; HIV Infections/virology ; HIV-1/chemistry ; HIV-1/drug effects ; HIV-1/metabolism ; HIV-1/physiology ; Host-Pathogen Interactions ; Humans ; Protein Binding ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Capsid Proteins
Language	English
Publishing date	2021-02-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13020246
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Article ; Online: Studying bacterial chemosensory array with CryoEM.

Qin, Zhuan / Zhang, Peijun

Biochemical Society transactions

2021 Volume 49, Issue 5, Page(s) 2081–2089

Abstract: Bacteria direct their movement in respond to gradients of nutrients and other stimuli in the environment through the chemosensory system. The behavior is mediated by chemosensory arrays that are made up of thousands of proteins to form an organized array ...

Abstract	Bacteria direct their movement in respond to gradients of nutrients and other stimuli in the environment through the chemosensory system. The behavior is mediated by chemosensory arrays that are made up of thousands of proteins to form an organized array near the cell pole. In this review, we briefly introduce the architecture and function of the chemosensory array and its core signaling unit. We describe the in vivo and in vitro systems that have been used for structural studies of chemosensory array by cryoEM, including reconstituted lipid nanodiscs, 2D lipid monolayer arrays, lysed bacterial ghosts, bacterial minicells and native bacteria cells. Lastly, we review recent advances in structural analysis of chemosensory arrays using state-of-the-art cryoEM and cryoET methodologies, focusing on the latest developments and insights with a perspective on current challenges and future directions.
MeSH term(s)	Chemotaxis/physiology ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Escherichia coli/enzymology ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Histidine Kinase/chemistry ; Histidine Kinase/metabolism ; Methyl-Accepting Chemotaxis Proteins/chemistry ; Methyl-Accepting Chemotaxis Proteins/metabolism ; Models, Molecular ; Protein Multimerization ; Signal Transduction/physiology
Chemical Substances	CheW protein, E coli ; Escherichia coli Proteins ; Methyl-Accepting Chemotaxis Proteins ; Histidine Kinase (EC 2.7.13.1) ; cheA protein, E coli (EC 2.7.13.3)
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20210080
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Article ; Online: A structural view of the SARS-CoV-2 virus and its assembly.

Hardenbrook, Nathan J / Zhang, Peijun

Current opinion in virology

2021 Volume 52, Page(s) 123–134

Abstract: The SARS-CoV-2 pandemic that struck in 2019 has left the world crippled with hundreds of millions of cases and millions of people dead. During this time, we have seen unprecedented support and collaboration amongst scientists to respond to this deadly ... ...

Abstract	The SARS-CoV-2 pandemic that struck in 2019 has left the world crippled with hundreds of millions of cases and millions of people dead. During this time, we have seen unprecedented support and collaboration amongst scientists to respond to this deadly disease. Advances in the field of structural biology, in particular cryoEM and cryo-electron tomography, have allowed unprecedented structural analysis of SARS-CoV-2. Here, we review the structural work on the SARS-CoV-2 virus and viral components, as well as its cellular assembly process, highlighting some important structural findings that have made significant impact on the protection from and treatment of emerging viral infections.
MeSH term(s)	COVID-19 ; Cryoelectron Microscopy ; Electron Microscope Tomography ; Humans ; Pandemics ; SARS-CoV-2
Language	English
Publishing date	2021-12-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2611378-8
ISSN	1879-6265 ; 1879-6257
ISSN (online)	1879-6265
ISSN	1879-6257
DOI	10.1016/j.coviro.2021.11.011
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Article ; Online: Triptolide promotes nerve repair after cerebral ischemia reperfusion injury by regulating the NogoA/NgR/ROCK pathway.

Zhang, Huiyu / Guo, Minfang / Zhang, Peijun / Mu, Bingtao / Bai, Zhenjun / Li, Liang / Yu, Jingwen

Folia neuropathologica

2024

Abstract: Activation of the NogoA/NgR/ROCK pathway limits nerve repair after brain ischemia-reperfusion (I/R) injury. Triptolide displays anti-inflammatory, anti-oxidant, and immunosuppressive effects and is derived from the traditional Chinese medicine ... ...

Abstract	Activation of the NogoA/NgR/ROCK pathway limits nerve repair after brain ischemia-reperfusion (I/R) injury. Triptolide displays anti-inflammatory, anti-oxidant, and immunosuppressive effects and is derived from the traditional Chinese medicine Tripterygium wilfordii Hook F. This agent can also penetrate the blood-brain barrier, where it has a neuroprotective effect and ameliorates cerebral I/R injury via an as yet unknown mechanism(s). Here, an animal model of middle cerebral artery occlusion and reperfusion (MCAO/R) was employed to assess triptolide's therapeutic impact on brain I/R injury and the possible mechanism of action. The results indicate that triptolide treatment can decrease cerebral infarction and nerve injury after cerebral I/R injury. Importantly, in vivo and in vitro experiments revealed that treatment with triptolide decreased NogoA, NgR, p75NTR and ROCK2 expression, and upregulated the expression of GAP43 and PSD-95, thus suggesting improved synaptic function. These results indicate that triptolide can promote nerve repair following brain I/R injury by inhibiting NogoA/NgR/ROCK signalling.
Language	English
Publishing date	2024-01-04
Publishing country	Poland
Document type	Journal Article
ZDB-ID	1310363-5
ISSN	1509-572X ; 0028-3894 ; 1641-4640
ISSN (online)	1509-572X
ISSN	0028-3894 ; 1641-4640
DOI	10.5114/fn.2023.133065
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Article ; Online: Geographic and tissue-specific variations of the trace elements and trophic niches of three offshore cetaceans in Chinese waters.

Zhai, Yuhuan / Li, Pingjing / Zhang, Qinglin / Zhang, Peijun / Li, Songhai

Journal of hazardous materials

2023 Volume 465, Page(s) 133380

Abstract: Systematical investigation on trace elements' (TEs) distribution and trophic niches of cetaceans are essential to understand marine mammal ecology and environmental toxicology. Here, the concentrations of 10 TEs and isotopic values in six tissues of ... ...

Abstract	Systematical investigation on trace elements' (TEs) distribution and trophic niches of cetaceans are essential to understand marine mammal ecology and environmental toxicology. Here, the concentrations of 10 TEs and isotopic values in six tissues of stranded Stenella attenuata (SA) and Kogia breviceps (KB) from the northern South China Sea (SCS) and Peponocephala electra (PE) from the East China Sea (ECS) were investigated. The TEs levels of the studied cetaceans were characterized by geo- and tissue-specific distributions. For SA and KB, most TEs levels were in the normal ranges, with low toxicological risk. For PE, several toxic TEs accumulated above the thresholds up to 892.80 μg/g of Hg and 335.24 μg/g of Cd, indicating that land-based anthropogenic pollution may be an ongoing threat to top predators in the ECS. The liver, spleen, and kidney are the main organs that accumulate toxic TEs, and there are strong positive, such as Se-Hg, correlations in several tissues. In particular, for PE with severe Hg and Cd exposure, tissue-specific distribution and correlations were more obvious. The results of stable carbon and nitrogen isotopes showed partly overlapped trophic niches of the three cetaceans, with similar calculated trophic levels in a narrow range of 4.29-4.43.
MeSH term(s)	Animals ; Trace Elements/analysis ; Cadmium ; Cetacea ; Mercury/analysis ; Nitrogen Isotopes/analysis ; Environmental Monitoring
Chemical Substances	Trace Elements ; Cadmium (00BH33GNGH) ; Mercury (FXS1BY2PGL) ; Nitrogen Isotopes
Language	English
Publishing date	2023-12-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2023.133380
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