Jennymchua Week 13 Assignment
The purpose of this week's assignment is to analyze the SARS-CoV-2 spike protein using biological database tools and identify key identifiers and ways to distinguish it between SARS-CoV.
How do you know which of the six frames is the correct reading frame (without looking up the answer)?
- The longest frame would probably be the correct reading frame, as long as it starts with the start codon AUG (Met).
- Confirmed via NCBI protein record.
If you search on the keywords "SARS-CoV" (which refers to the first SARS virus), in the main UniProt search field, how many results do you get?
- 818 results.
Use the entry with accession number "P59594" which corresponds to the reference entry for the SARS-CoV spike protein. What types of information are provided about this protein in this database entry?
This entry has information on its function, names and taxonomy, subcellular location, pathology and biotech, PTM and processing, interaction, structure, family and domains, sequence, similar proteins, cross-references, entry information, and anything miscellaneous that does not fit within the aforementioned categories.
Paste a screenshot of the results from the SARS-CoV-2 spike protein amino acid sequence using PredictProtein server.
How does this information relate to what is stored in the UniProt database for the SARS-CoV spike protein?
Like UniProt, PredictProtein also includes information on subcellular localization, structure, similar proteins, and other miscellaneous information. Though, I do like how PredictProtein offers information such as the effect(s) of point mutation, as this could be helpful in tracking what could happen if the virus were to mutate.
Create a view of the protein from your paper recreates one of the figures from your paper. You may not be able to get this to be exactly the same in terms of colors or backbone style, but you should try to rotate the to be the same view as the article.
I tried to rotate the 3D image from NCBI so that the RBD was shown in the upper right quadrant in the down position similar to that shown in Wrapp et al. Figure 2A.
Find the N-terminus and C-terminus of each polypeptide tertiary structure.
N-termini were located
Locate all the secondary structure elements. Do these match the predictions made by the PredictProtein server?
The alpha helices (spirals) and beta sheets (arrows) matched the predictions made by PredictProtein.
Locate particular amino acids that were discussed in your paper, show a screenshot that highlights them.
Amino acids that were discussed in Wrapp et al. include SS (signal sequence); S2' (S2' protease cleavage site); FP (fusion peptide); HR1 (heptad repeat 1); CH (central helix); CD (connector domain); HR2 (heptad repeat 2); TM, (transmembrane domain); and CT (cytoplasmic tail).
Data and files
All files were uploaded throughout the Methods/Results section as part of answers.
Screenshot of converted spike protein sequence in ExPASY Translate tool. Screenshot of SARS-CoV-2 spike protein amino acid sequence using PredictProtein. View of the prefusion 2019-nCoV glycoprotein spike from NCBI. View of the 2019-nCoV RBD down protomer from Wrapp et al. Primary structure of amino acids referenced in Wrapp et al.
By comparing the structures and sequences of the 2019-nCoV spike protein using different biological databases (as well as the information these databases provided), we were able to see the different parts and structures of the protein in a three-dimensional view. Going forward, the visual information could be key in helping to determine the structure-function relationship of the virus's protein and our human ACE2 receptor for the final research projects.
Beginning your research project
What question will you answer about sequence-->structure-->function relationships in a SARS-CoV-2 protein?
We are interested in the structure/function relationship of ACE2 as a SARS-CoV-2 receptor. Therefore, what about the structure or sequence of ACE2 makes it a SARS-CoV-2 receptor? Why not another one?
What sequences will you use?
We will use the sequence QHD43416.1: spike protein (Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1) as well as an ACE2 sequence.
What protein tools will you use for analysis and answering your question?
We will use NCBI and UniProt.
- I worked with my homework/rest of the semester partners Carolyn and Nathan via Zoom and in a group chat throughout the week to discuss our final research project.
- I emailed Dr. Dahlquist twice regarding some questions I had with the assignment.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
- ExPASy. (2020). Translate. Retrieved April 20, 2020 from https://web.expasy.org/translate/.
- NCBI. (2020). PDB ID 6VSB: Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up. Retrieved April 20, 2020 from https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?&mmdbid=184713&bu=1&showanno=1.
- NCBI. (2020). Surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]. Retrieved April 20, 2020 from https://www.ncbi.nlm.nih.gov/protein/1791269090.
- OpenWetWare. (2020). BIOL368/S20:Week 13. Retrieved April 20, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_13.
- PredictProtein. (2020). PredictProtein Open. Retrieved April 20, 2020 from https://open.predictprotein.org/.
- RCSB Protein Data Bank. (2020). 6VSB. Retrieved April 20, 2020 from https://www.rcsb.org/structure/6VSB.
My user page
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- 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.