Real-time observation of native conformations and molecular behaviors of viral fusion proteins using high-speed atomic force microscopy (HS-AFM)
| Project/Area Number |
20K16262
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| Research Category |
Grant-in-Aid for Early-Career Scientists
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| Allocation Type | Multi-year Fund |
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| Review Section |
Basic Section 49060:Virology-related
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| Research Institution | Kanazawa University |
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Principal Investigator |
LIM KEE・SIANG 金沢大学, ナノ生命科学研究所, 特任助教 (60842987)
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| Project Period (FY) |
2020-04-01 – 2024-03-31
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| Project Status |
Granted (Fiscal Year 2022)
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| Budget Amount *help |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2023: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
Fiscal Year 2022: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
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| Keywords | SARS-CoV-2 spike protein / High-speed AFM / Neutralizing antibodies / COVID-19 / HS-AFM / Viral Fusion Protein / Viral fusion protein / fusogenic transition / exosome / Direct visualization / Virulence factors |
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| Outline of Research at the Start |
HS-AFM is an ideal tool for investigating properties of viral fusion proteins that include native conformation, binding activity with host factors, and structural dynamic during fusogenic transition. Furthermore, interaction between fusion proteins and exosomes will be also be recorded.
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| Outline of Annual Research Achievements |
The objectives of this project are: 1) to record the native conformation viral fusion proteins under physiological conditions using HS-AFM; 2) to visualize the rapid and transient intermediates during conformational changes triggered by acidic conditions using HS-AFM; 3) to elucidate the conformational dynamic of viral fusion proteins when interacting with exosomes or antibodies using HS-AFM. The PI has implemented HS-AFM to perform nanoscopic elucidation of SARS-CoV-2 spike (S) protein structural dynamics during its interaction with neutralizing antibodies (Objective 3). Certain neutralizing antibodies promote the transition of RBD from its close conformation to open confirmation to enhance RBD-ACE2 interaction. This effect is known as antibody-dependent enhancement effect (ADE). This study reveals that HS-AFM could be worked as an efficient nanoscopic assessment platform for S NAb testing. This study has been published in a well-reputed journal, Nano Letters. Furthermore, this study has also been presented in several domestic conferences. Envelope protein (E protein) of Dengue virus will be investigated in the near future.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
SARS-CoV-2 fusion protein, spike (S) protein, has been actively studied to fulfill three main objectives of this project. First and second objectives have been achieved and published in a high impact journal, Journal of Extracellular Vesicles (Lim et al, J Extracell Vesicles, 2021). Recently, the third objective regarding the interaction between S protein and a neutralizing antibody has been published in Nano Letters (Lim et al, Nano Lett, 2023). Altogether, these research achievements indicated that the project is running rather smoothly.
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| Strategy for Future Research Activity |
Envelope protein (E protein) of Dengue virus will be investigated in the near future. HS-AFM will be applied: 1) to record the native conformation of E protein under physiological conditions using HS-AFM; 2) to visualize the rapid and transient intermediates during conformational changes triggered by acidic conditions using HS-AFM; 3) to elucidate the conformational dynamic of viral fusion proteins when interacting with exosomes or antibodies using HS-AFM.
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Report
(3 results)
Research Products
(18 results)
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[Journal Article] Nanoscopic Assessment of Anti-SARS-CoV-2 Spike Neutralizing Antibody Using High-Speed AFM.2023
Author(s)
Keesiang Lim, Goro Nishide, Elma Sakinatus Sajidah, Tomoyoshi Yamano, Yujia Qiu, Takeshi Yoshida, Akiko Kobayashi, Masaharu Hazawa, Toshio Ando, Rikinari Hanayama, Richard W Wong
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Journal Title
Nano letters
Volume: 23
Issue: 2
Pages: 619-628
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Spatiotemporal tracking of small extracellular vesicle nanotopology in response to physicochemical stresses revealed by HS-AFM.2022
Author(s)
Elma Sakinatus Sajidah, Keesiang Lim, Tomoyoshi Yamano, Goro Nishide, Yujia Qiu, Takeshi Yoshida, Hanbo Wang, Akiko Kobayashi, Masaharu Hazawa, Firli R P Dewi, Rikinari Hanayama, Toshio Ando, Richard W Wong
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Journal Title
Journal of extracellular vesicles
Volume: 11
Issue: 11
Pages: 12275-12275
DOI
Related Report
Peer Reviewed / Open Access
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