Adinulos Week 11

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Annika G. Dinulos

Assignments

Journal Pages

Class Journal Pages

Purpose

To analyze the relevance of a scientific article and effectively deliver information in the form of a journal club to peers on 2019-nCoV. Analyze the structure of the novel coronavirus spike protein in the prefusion state and make comparisons to the SARS-CoV S.

Assignment

Key terms

  1. monoclonal antibodies: immunoglobulin derived from a single clone of antibody-producing cells (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  2. transient(ly): temporary, short-lived, disturbance or change (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  3. exclusion chromatography or permeation chromatography: form of chromatography in which a permeable stationary phase is used and in which separation components of the components of a mixture is based upon selective exclusion effects (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  4. trimer(ic): molecular complex having three components or subunits (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  5. stochastic: arrived at by skillful conjecture (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  6. furin: protein subtilisin with substrate specificity for consensus sequence arg X Lys/Arg arg at the cleavage site (Biology Online, 2020)
  7. hemagglutinin: substance that causes the agglutination of red blood cells (Biology Online, 2020)
  8. interferometry: method of gathering information about a medium by using an interferometer or similar technique (Biology Online, 2020)
  9. surface plasmon resonance: phenomenon that occurs when light is reflected off thin metal films, which may be used to measure the interaction of biomolecules on the surface (Oxford Dictionary of Biochemistry and Molecular Biology, 2008)
  10. protomer: any of the subunits constituting a larger structure, such as any of the polypeptide chains in an oligomeric protein (Biology Online, 2020)

Outline

Importance

This work is significant because the 2019 novel coronavirus is rapidly infecting humans and caused a global pandemic. It offers information on the spike protein of the novel coronavirus which would be helpful in designing vaccines.

Limitations in previous studies

Previous research on the spike protein in the prefusion conformation has not been done for 2019-nCoV, only SARS-CoV, the virus that infected others in 2004.

Overcome limitations

The researchers specifically analyzed the spike protein for 2019-nCoV in the prefusion conformation. The gene encoding resides were derived from GenBank. The researchers also specifically looked at the previous SARS-CoV antibodies in to determine differences within 2019-nCoV.

Main result

The researchers were able to obtain a cryo-electron microscopy structure of the S trimer. The researchers also found that compared to the SARS-CoV the spike protein binds ACE2 with a higher affinity, and that SARS specific antibodies do not show much cross-reactivity to the 2019 coronavirus spike protein.

Methods

The researchers expressed the prefusion S ectodomain and purified it using different proline substitutions and different residues. They performed a cryo-electron microscopy and processed the data using Warp. Surface plasmon resonance was done by injecting serial dilutions of ACE2 ranging concentrations to visualize the spike. The researchers also performed a negative stain electron microscopy and a biolayer interferometry.

Results of Images

  • Figure 1
    • Schematic of the spike protein primary structure in the prefusion conformation that is colored by domain. 1B is a 90-degree flip to show the trimer in a RBD in an up conformation from the side and top view.
  • Figure 2
    • Compares the structure of the SARS-CoV spike protein and the 2019-nCoV spike protein.
      • (A) displayes the protomor of the 2019-nCoV spike protein in the down conformation (left), up conformation (middle) and the SARS-CoV spike protein in the up conformation (right).
      • (B) displays the receptor binding domain of 2019-nCoV in green and the receptor-binding domain of the SARS-CoV receptor binding domain in white. The 2019-nCoV n-terminal domain is depicted in blue. The 2019-nCoV is closer to the center trimer cmpared to the SARS-CoV RBD.
      • (C) depicts that structurally, there are homologies between the RBDs, NTDs, SD 1 and SD 2 of the two viruses.
  • Figure 3
    • (A) Image of the surface plasmon resonance sensorgram results. The black line shows the data, the red line is the result of a 1:1 binding model. There is high affinity for the 2019-nCoV spike protein to bind to the ACE2. **(B) Shows the negative-stain electron microscopy averages of the novel coronavirus S bound to the ACE2. The complex is similar to the binding of SARS-CoV S to ACE2.
  • Figure 4:
    • (A) Depicts the receptor binding domain of the SARS-CoV, the red parts indicate places of differences in the 2019-nCoV RBD. The binding site is indicated in black dashed lines.
    • (B) shows the biolayer interferometry sensorgram of the binding of ACE2 by the RBD-SD1 fragment. The black line is the binding data while the red line indicated the 1:1 binding model data.
    • (C) shows three different monoclonal antibodies of SARS-CoV and their cross-reactivity to the 2019-nCoV RBD. No binding is shown for the SARS mAbs.

Comparisons of Results

Previous studies that examine SARS-CoV spike protein and receptor binding sites indicate that the novel coronavirus may have structural similarities to the SARS coronavirus but do not bind the same. The novel coronavirus binds with a higher affinity to the ACE2, and its' RBD does not bind to the same antibodies as the SARS-CoV.

Important implications

It is important to analyze differences between the coronaviruses to accurately develop vaccines and treatment for the epidemic.

Future directions

Researchers should then look to isolate 2019-nCoV spike proteins as probes and isolate the antibodies that bind to the ACE2 site.

Critical Evaluation/Major Flaws

The paper was slightly difficult to read, and I would imagine be very difficult to read for the general public. More information could have been given in the introduction to explain about the significance of the ACE2 site.

Link to Presentation

Box Link

Conclusion

The article explained the differences between the SARS-CoV and the 2019 novel coronavirus spike protein and RBD binding. 2019-nCoV binds to the ACE2 with higher affinity. Structural information of the spike protein will allow for the visualization of mutations which is important for future directions for a vaccine.

Acknowledgments

  • I worked with my partners Jenny and Sahil on our journal club presentation. We communicated over text for about two days.
  • I copied and modified the procedures on the Week 11 page to generate this lab notebook entry.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Adinulos (talk) 12:05, 15 April 2020 (PDT)

References

Biology-Online. (2020). Furin. Retrieved April 15, 2020 from https://www.biology-online.org/dictionary/Furin

Biology-Online. (2020). Hemagglutinin. Retrieved April 15, 2020 from https://www.biology-online.org/dictionary/Hemagglutinin

Biology-Online. (2020). Interferometry. Retrieved April 15, 2020 from https://www.biology-online.org/dictionary/Interferometry

Biology-Online. (2020). Protomer. Retrieved April 15, 2020 from https://www.biology-online.org/dictionary/Protomer

OpenWetWare. (2020). BIOL368/S20:Week 11. Retrieved April 15, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_11

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). monoclonal antibody. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-12867?rskey=dPWR0h&result=1

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). Permeation chromatography. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-15054?rskey=dyNlAZ&result=7

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). Stochastic. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-18788?rskey=D5i7PX&result=1

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). Trimer. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-19978?rskey=4FeX4H&result=1

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). Transient. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-19856?rskey=k9zxRo&result=4

Oxford Dictionary of Biochemistry and Molecular Biology. (2008). Surface Plasmon Resonance. Retrieved from https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-19015?rskey=y2tOt9&result=1

Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., ... & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260-1263. DOI: 10.1126/science.abb2507

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