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Zhang X, Hong B, Wei P, Pei P, Xu H, Chen L, Tong Y, Chen J, Luo SZ, Fan H, He C. Pathogen-host adhesion between SARS-CoV-2 spike proteins from different variants and human ACE2 studied at single-molecule and single-cell levels. Emerg Microbes Infect 2022; 11:2658-2669. [PMID: 36153659 PMCID: PMC9639500 DOI: 10.1080/22221751.2022.2128887] [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: 06/19/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022]
Abstract
The binding of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein onto human angiotensin-converting enzyme 2 (ACE2) is considered as the first step for the virus to adhere onto the host cells during the infection. Here, we investigated the adhesion of spike proteins from different variants and ACE2 using single-molecule and single-cell force spectroscopy. We found that the unbinding force and binding probability of the spike protein from Delta variant to the ACE2 were the highest among the variants tested in our study at both single-molecule and single-cell levels. As the most popular variants, the Omicron variants have slightly higher unbinding force to the ACE2 than wild type. Molecular dynamics simulation showed that ACE2-RBD (Omicron BA.1) complex is destabilized by the E484A and Y505H mutations and stabilized by S477N and N501Y mutations, when compared with Delta variant. In addition, a neutralizing antibody, produced by immunization with wild type spike protein, could effectively inhibit the binding of spike proteins from wild type, Delta and Omicron variants (BA.1 and BA.5) onto ACE2. Our results provide new insight for the molecular mechanism of the adhesive interactions between spike protein and ACE2 and suggest that effective monoclonal antibody can be prepared using wild type spike protein against different variants.
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Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Bixia Hong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Peng Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Pengfei Pei
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Haifeng Xu
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Long Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Jialin Chen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, People’s Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, People’s Republic of China
| | - Shi-Zhong Luo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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Staufer O, Gantner G, Platzman I, Tanner K, Berger I, Spatz JP. Bottom-up assembly of viral replication cycles. Nat Commun 2022; 13:6530. [PMID: 36323671 PMCID: PMC9628313 DOI: 10.1038/s41467-022-33661-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Bottom-up synthetic biology provides new means to understand living matter by constructing minimal life-like systems. This principle can also be applied to study infectious diseases. Here we summarize approaches and ethical considerations for the bottom-up assembly of viral replication cycles.
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Affiliation(s)
- Oskar Staufer
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK.
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, OX3 7FY, UK.
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany.
| | - Gösta Gantner
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Theological Seminary, Heidelberg University, Kisselgasse 1, 69117, Heidelberg, Germany
| | - Ilia Platzman
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), University of Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
| | - Klaus Tanner
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Theological Seminary, Heidelberg University, Kisselgasse 1, 69117, Heidelberg, Germany
| | - Imre Berger
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- School of Biochemistry, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Bristol Synthetic Biology Centre BrisSynBio, University of Bristol, 4 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - Joachim P Spatz
- Max Planck-Bristol Center for Minimal Biology, University of Bristol, 1 Tankard's Close, Bristol, BS8 1TD, UK
- Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), University of Heidelberg, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany
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Carey TR, Kozminsky M, Hall J, Vargas-Zapata V, Geiger K, Coscoy L, Sohn LL. Detecting Intact Virus Using Exogenous Oligonucleotide Labels. Anal Chem 2022; 94:7619-7627. [PMID: 35584293 DOI: 10.1021/acs.analchem.2c00835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has revealed how an emerging pathogen can cause a sudden and dramatic increase in demand for viral testing. Testing pooled samples could meet this demand; however, the sensitivity of reverse transcription quantitative polymerase chain reaction (RT-qPCR), the gold standard, significantly decreases with an increasing number of samples pooled. Here, we introduce detection of intact virus by exogenous-nucleotide reaction (DIVER), a method that quantifies intact virus and is robust to sample dilution. As demonstrated using two models of severe acute respiratory syndrome coronavirus 2, DIVER first tags membraned particles with exogenous oligonucleotides, then captures the tagged particles on beads functionalized with a virus-specific capture agent (in this instance, angiotensin-converting enzyme 2), and finally quantifies the oligonucleotide tags using qPCR. Using spike-presenting liposomes and spike-pseudotyped lentivirus, we show that DIVER can detect 1 × 105 liposomes and 100 plaque-forming units of lentivirus and can successfully identify positive samples in pooling experiments. Overall, DIVER is well positioned for efficient sample pooling and clinical validation.
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Affiliation(s)
- Thomas R Carey
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States
| | - Molly Kozminsky
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California 94720, United States
| | - Jennifer Hall
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Valerie Vargas-Zapata
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Kristina Geiger
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Laurent Coscoy
- Department of Molecular and Cellular Biology, University of California, Berkeley, 3200 Weill Hall, Berkeley, California 94720, United States
| | - Lydia L Sohn
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, 306 Stanley Hall, Berkeley, California 94720, United States.,Department of Mechanical Engineering, University of California, Berkeley, 5118 Etcheverry Hall, Berkeley, California 94720, United States
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