Non: Week 13

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Course Work
Assignments Journal Pages Shared Class Journal Pages
BIOL368/S20:Week 1 BIOL368/S20:Class Journal Week 1
BIOL368/S20:Week 2 Non: Week 2 BIOL368/S20:Class Journal Week 2
BIOL368/S20:Week 3 Non: Week 3 BIOL368/S20:Class Journal Week 3
BIOL368/S20:Week 4 Non: Week 4 BIOL368/S20:Class Journal Week 4
BIOL368/S20:Week 5 Non: Week 5 BIOL368/S20:Class Journal Week 5
BIOL368/S20:Week 6 Non: Week 6 BIOL368/S20:Class Journal Week 6
BIOL368/S20:Week 8 Non: Week 8 BIOL368/S20:Class Journal Week 8
BIOL368/S20:Week 10 Non: Week 10 BIOL368/S20:Class Journal Week 10
BIOL368/S20:Week 11 Non: Week 11 BIOL368/S20:Class Journal Week 11
BIOL368/S20:Week 13 Non: Week 13 BIOL368/S20:Class Journal Week 13
BIOL368/S20:Week 14 Non: Week 14 BIOL368/S20:Class Journal Week 14


The purpose of this week's lab to use various tools to explore the protein structure of the SARS-CoV-2 spike protein.

Combined Methods/Results

  1. First, I copied the FASTA sequence of the SARS-CoV-2 spike protein from the Week 13 Protocol into the NCBI Open Reading Frame Finder.
    • The website generated the following screenshot:
    • The most likely reading frame is the first one ORF1 because it encompasses the entirety of the gene.
    • This was confirmed by going to NCBI protein record which generated the same protein code as the Reading frame.
  2. Next I went to the UnitProt database to look up information on the SARS-CoV protein.
    • Searching for "SARS-CoV" generated 833 results.
    • I looked at P59594 as a reference to see what types of information could be accessed.
      • For that database page, you could find info about the function, taxonomy, sub-cellular location, pathology, PTM processing, interactions, structure, family, domains, sequence, and similar proteins.
  3. Then, I used PredictProtein to predict the structure of the surface glycoprotein of SARS-CoV-2 mentioned in Data S1 of the Walls et al. article.
    • It generated the following screenshot:
 >YP_009724390.1 surface glycoprotein [Severe acute respiratory syndrome coronavirus 2] 
  1. Finally, I viewed the structure of the glycoprotein from the article, specifically 6VYB.
    • The following screenshot of the structure was generated, mirroring the perspective of Fig. 3D of the Walls, et al. article:
    • The N terminus is A46

while the C terminus is S1146.

    • The sequence chain image from RCSB shows all of the secondary structure features. They do not really match up with the prediction from PredictProtein.

    • The article mentions 14 amino acids that are important for ACE2 binding: T402, R426, Y436, Y440, Y442, L472, N473, Y475, N479, Y484, T486, T487, G488, and Y491.

Research Question

  1. What question will you answer about sequence-->structure-->function relationships in a SARS-CoV-2 protein?
    • What makes ACE2 the most optimal receptor for SARS-CoV-2/SARS-CoV binding?
  2. What sequences will you use? I want you to take advantage of sequence data available to perform a multiple sequence alignment as part of your project.
    • SARS-CoV-2 spike protein; SARS-CoV spike protein;
    • different ACE2 sequences, from different organisms?
    • other common receptors utilized by viruses
  3. What protein tools will you use for analysis and answering your question?
    • RCSB, UniProt,


Scientific Conclusion

There are a variety of free online tools that allow for indepth analysis of protein structure and sequence. It is very hard to predict the structure of a protein.


  • I worked with my partners Jenny and Carolyn in figuring out what our topic of analysis should be.
  • I used the Week 13 Protocol for this assignment.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Non (talk) 22:35, 22 April 2020 (PDT)