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251 results on '"Chen, Dong-Hua"'

4. Accurate model annotation of a near-atomic resolution cryo-EM map

Author

Hryc, Corey F, Chen, Dong-Hua, Afonine, Pavel V, Jakana, Joanita, Wang, Zhao, Haase-Pettingell, Cameron, Jiang, Wen, Adams, Paul D, King, Jonathan A, Schmid, Michael F, and Chiu, Wah

Subjects
Biochemistry and Cell Biology, Physical Sciences, Biological Sciences, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Bacteriophage P22, Binding Sites, Capsid Proteins, Cryoelectron Microscopy, Macromolecular Substances, Models, Molecular, Molecular Conformation, Protein Binding, Protein Conformation, Reproducibility of Results, cryo-EM, P22, model, structure, annotation
Abstract

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

Published
2017

9. eIF5B gates the transition from translation initiation to elongation

Author

Wang, Jinfan, Johnson, Alex G., Lapointe, Christopher P., Choi, Junhong, Prabhakar, Arjun, Chen, Dong-Hua, and Petrov, Alexey N.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Translation initiation determines both the quantity and identity of the protein that is encoded in an mRNA by establishing the reading frame for protein synthesis. In eukaryotic cells, numerous translation initiation factors prepare ribosomes for polypeptide synthesis; however, the underlying dynamics of this process remain unclear.sup.1,2. A central question is how eukaryotic ribosomes transition from translation initiation to elongation. Here we use in vitro single-molecule fluorescence microscopy approaches in a purified yeast Saccharomyces cerevisiae translation system to monitor directly, in real time, the pathways of late translation initiation and the transition to elongation. This transition was slower in our eukaryotic system than that reported for Escherichia coli.sup.3-5. The slow entry to elongation was defined by a long residence time of eukaryotic initiation factor 5B (eIF5B) on the 80S ribosome after the joining of individual ribosomal subunits--a process that is catalysed by this universally conserved initiation factor. Inhibition of the GTPase activity of eIF5B after the joining of ribosomal subunits prevented the dissociation of eIF5B from the 80S complex, thereby preventing elongation. Our findings illustrate how the dissociation of eIF5B serves as a kinetic checkpoint for the transition from initiation to elongation, and how its release may be governed by a change in the conformation of the ribosome complex that triggers GTP hydrolysis. Single-molecule dynamics reveal that the GTPase activity of eukaryotic initiation factor eIF5B serves as a kinetic checkpoint for the transition from translation initiation to elongation., Author(s): Jinfan Wang [sup.1] , Alex G. Johnson [sup.1] [sup.2] , Christopher P. Lapointe [sup.1] , Junhong Choi [sup.1] [sup.3] , Arjun Prabhakar [sup.1] [sup.4] , Dong-Hua Chen [sup.1] , [...]

Published
2019
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27. A nitrobenzoxadiazole-based near-infrared fluorescent probe for the specific imaging of H2S in inflammatory and tumor mice.

Author

Wang, Wen-Xin, Wang, Zhi-Qing, Tan, Zhi-Ke, Mao, Guo-Jiang, Chen, Dong-Hua, and Li, Chun-Yan

Subjects
FLUORESCENT probes, MICE, STOKES shift, BIOLOGICAL systems, HYDROGEN sulfide, CELL imaging
Abstract

As a common gaseous signaling molecule, hydrogen sulfide (H2S) plays a vital role in physiology and pathology. The development of fluorescent probes for detecting H2S has attracted widespread attention. However, most of the reported fluorescent probes with nitrobenzoxadiazole (NBD) as the recognition group have been widely used to simultaneously detect biothiols and H2S, instead of specifically detecting H2S. Herein, a novel NBD-based near-infrared (NIR) fluorescent probe named CX-N for the detection of H2S is synthesized. The selectivity of CX-N for H2S is significantly higher than that for biothiols and other potential interferences. After reacting with H2S, CX-N shows a significant increase in NIR fluorescence (75-fold), large Stokes shift (155 nm) and fast response (4 min). And the possible response mechanism of CX-N to H2S is given and confirmed by HPLC and HRMS. Based on the low cytotoxicity of CX-N, it has been used for H2S imaging in live cells and zebrafish. More importantly, CX-N has also been successfully applied for the real-time imaging of H2S in inflammatory and tumor mice based on its NIR emission, which provides a reliable platform for the specific recognition of H2S in complex biological systems. [ABSTRACT FROM AUTHOR]

Published
2022
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28. Mediator structure and conformation change

Author

Zhang, Heqiao, primary, Chen, Dong-Hua, additional, Mattoo, Rayees U.H., additional, Bushnell, David A., additional, Wang, Yannan, additional, Yuan, Chao, additional, Wang, Lin, additional, Wang, Chunnian, additional, Davis, Ralph E., additional, Nie, Yan, additional, and Kornberg, Roger D., additional

Published
2021
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40. Unraveling the origin of chirality from plasmonic nanoparticle-protein complexes

Author

Zhang, Qingfeng, primary, Hernandez, Taylor, additional, Smith, Kyle W., additional, Hosseini Jebeli, Seyyed Ali, additional, Dai, Alan X., additional, Warning, Lauren, additional, Baiyasi, Rashad, additional, McCarthy, Lauren A., additional, Guo, Hua, additional, Chen, Dong-Hua, additional, Dionne, Jennifer A., additional, Landes, Christy F., additional, and Link, Stephan, additional

Published
2019
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