Jmenzago Week 11

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Purpose

The purpose of this assignment is to read and critique a paper about the structure-function relationship of SARS-CoV-2 to prepare for research projects on the structure-function relationship of of the virus.

Definitions

  1. virion - A single virus particle, complete with coat (Biology Online, 2020)
  2. homodimerization - The process of joining two identical subunits to form a single compound (Biology Online, 2020)
  3. trimeric - A polymer comprising three monomer units (Lexico, 2020)
  4. monodisperse - (of a colloid) containing particles of uniform size (Biology Online, 2020)
  5. protomer - Any of the subunits constituting a larger structure, such as any of the polypeptide chains in an oligomeric protein (Biology Online, 2020)
  6. pellagra - A deficiency disease caused by a lack of nicotinic acid or its precursor tryptophan in the diet. It is characterized by dermatitis, diarrhoea, and mental disturbance, and is often linked to over-dependence on maize as a staple food (Lexico, 2020)
  7. ataxia - Failure of muscular coordination, irregularity of muscular action (Biology Online, 2020)
  8. moieties - Each of two parts into which a thing is or can be divided (Lexico, 2020)
  9. ternary - Containing, or consisting of, three different parts, as elements, atoms, groups, or radicals, which are regarded as having different functions or relations in the molecule; thus, sodic hydroxide, NaOH, is a ternary compound (Biology Online, 2020)
  10. enteric - Pertaining to the inside of, or by way of, or originating from, the intestines; intestinal (Biology Online, 2020)

Article Outline

General Information

  • The interaction between the spike glycoprotein (S protein) and angiotensin-converting enzyme 2 (ACE2) mediates receptor recognition and membrane fusion, exploiting it for viral infection
    • The receptor binding domain (RBD) of S1 binds to the peptidase domain (PD) of ACE2
    • after S1 binds to ACE2, S2 proceeds with membrane fusion
  • Analysis of the structure of ACE2-PD with and without RBD or S protein of SARS-CoV-2 helped reveal some information about the interaction between the two
    • Sequencing the entire structure of ACE2 could provide more information about the structure function relationship between the enzyme and SARS-CoV-2
      • Currently, the only structural information for ACE2 comes from the PD domain
      • Sequencing the full-length protein has been difficult because of its transmembrane helix structure
  • This study aims to provide the structure of the full-length human ACE2 to help better understand the structure function relationship between the enzyme and virus
    • ACE2 acts as a chaperone for for membrane trafficking of B0AT1
      • the trafficking mechanism of ACE2-B0AT1 is similar to that of LAT1-4F2hc, in which 4F2hc interacts with both the extracellular and intercellular domains
      • The full length structure of ACE2 should be revealed in the presence of B0AT1

Methods

  • Full-length ACE2 and B0AT1 were coexpressed in human embryonic kidney 293F cells and purified
    • Purified through tandem affinity resin and size exclusion chromatography
    • Both tagged with Strep and FLAG on their N-termini
  • mixed 0.2 mg of RBD-mFc from SARS-CoV-2 with purified ACE2-B0AT1 complex
    • mFc - mouse Fc tag
    • mixed at stoichiometric ratio of ~1.1:1
  • RBD-ACE2-B0AT1 mixture imaged using cryo-electron microscopy (cryo-EM)

Results

Results from Tables and Figures

  • Figure 1
    • 1A shows size exclusion chromatography purification profile of full-length human ACE2-B0AT1 complex
      • The single monodisperse peak indicates high homogeneity
    • 1B, 1C, and 1D show a 3D model of the ACE2-B0AT1 complex
      • Blue - CLD
      • Cyan - PD
      • Grey and Pink - B0AT1 protomers
      • 1B and 1C show the closed conformation of the complex
        • The PDs are in contact with each other
      • 1D shows the open conformation of the complex
        • There is no interaction between the PDs
  • Figure 2
    • 2A highlights regions in which dimerization occurs
      • Dimerization is primarily mediated by the neck, but also by the PDs
    • 2B shows the dimerization interaction in the neck region
      • Multiple polar interactions suggest that it is highly stable
    • 2C shows the dimerization intearction between the PDs
      • Only one interaction between Glu139 and Glu175'
        • Weak interaction supports theory that conformational change is characterized by rotation of PDs
    • 2D shows that there is no interaction between PD heads during open conformation
  • Figure 3
    • Shows the cryo-EM map of the RBD-ACE2-B0AT1 complex
    • Color scheme is the same as previous figures
      • Red and Gold - RBD protomers
      • RBD can be seen interacting with PD, as explained in introduction and by previous research
    • Mixture produced only the closed conformation of the complex
  • Figure 4
    • Shows the interaction between the PDs and RBD of the RBD-ACE2-B0AT1 complex
    • There are three clusters of polar interactions
      • Multiple polar interactions at the N and C termini of the alpha1 helix primarily coordinate RBD
        • Interactions with alpha2 helix loop 3-4 also contribute
          • Loop 3-4 is the connection between antiparallel strands beta3 and beta4
    • Middle of alpha1 reinforces the interaction with two polar residues
    • Interaction is similar to the one between RBD of SARS-CoV and ACE2
  • Figure 5
    • Shows a comparison of the RBD-ACE2 interface for RBD from SARS-CoV and SARS-CoV-2
    • The interfaces of the two viruses with ACE2-PD is generally similar
    • Differences can be seen at the N and C termini, but most are found in the middle of the alpha1 helix bridge
      • Differences are alterations in polar residues
        • Most prominent is Val404 SARS-CoV with Lys417 in SARS-CoV-2

Discussion

  • Previous studies have shown that the S protein of SARS-CoV-2 has a trimeric structure with one RBD in the up confirmation and two in the down confirmation
    • The same study suggested that the RBD must have the up confirmation to bind to the receptor
    • This study confirmed these conclusions
  • Previous studies have found that B0AT1 interacts with a coronavirus receptor
    • This study suggests that B0AT1 can play a regulatory role in enteric infections by some coronaviruses
  • The authors recommend to explore the idea that B0AT1 can suppress SARS-CoV-2 infection by blocking ACE2 cleavage
  • Other future directions could involve exploring what and how different polar residues can strengthen the interactions between RBD and ACE2-PD
    • This is based on the findings associated with Figure 5
      • Comparing the complexes with RBDs from SARS-CoV and SARS-CoV-2 revealed that differences in residues cause differences in affinity
        • e.g. Val404 and Lys317
  • This study emphasizes the importance of sequencing the full structure of ACE2, and how it can play a role in treating COVID-19 patients
    • Understanding the structure function relationship between ACE2-PD and RBD-SARS-CoV-2 could reveal potential drug targets

Caveat Emptor

The study clearly presented its results and reasonably arrived to their conclusions with the evidence provided. The figures provided and the authors' use of them made their conclusions and interpretations easy to understand and visualize. The results in this paper also provide a foundation to better understand the structure function relationship between SARS-CoV and ACE2. This is best exemplified in the difference in affinity of SARS-CoV and SARS-CoV-2, likely due to a variation in polar residues. However, the study did not account for any other factors that might influence the interaction between S1 and ACE2, which the authors acknowledged.

Journal Club Presentation

Presentation

Scientific Conclusion

The purpose of this assignment was to learn more about the structure-function relationship between ACE2 and SARS-CoV-2 to prepare for future research projects. A study done by Yang et al. hoped to sequence the full-length human ACE2 to understand the structure-function relationship between the virus and the enzyme. They discovered that the RBD of SARS-CoV-2 interacts with the PD domain of ACE2 through three clusters of polar interactions. Their results also suggest that the polar residues in these clusters determine the strength of the interaction. This prompts future research to explore these residues to better understand the structure-function relationship and possibly even a way to exploit them for treatment.

Acknowledgements

  • My homework partners for this week were Carolyne Egekeze and Karina Vescio
    • We worked together to prepare a journal club presentation on Yang et al., communicated via email and working on Google Slides
  • The paper discussed for this assignment is "Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2" by Yan et al.
  • I followed the instructions on BIOL368/S20:Week 11 to complete this assignment
    • The citation for Yang et al. was copied from the assignment page
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jmenzago (talk) 23:06, 15 April 2020 (PDT)

References

Assignments

Individual Journal Entries

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