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

Purpose

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] 
 MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHV
 SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF
 LGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPI
 NLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYN
 ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV
 YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
 YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF
 PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL
 PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLT
 PTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLG
 AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGI
 AVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
 LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIG
 VTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDI
 LSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM
 SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT
 FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVA
 KNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
 SEPVLKGVKLHYT

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.

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

1. • 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, Phylogeny.fr

Data/Files

• PredictProtein
• Structure
• N-Terminus
• C-Terminus
• Secondary Structures

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.

Acknowledgements

• 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)

References

• Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. DOI: 10.1016/j.cell.2020.02.058
• OpenWetWare. (2020). BIOL368/S20:Week 13. Retrieved April 20, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_13
• ExPASy(2020). SIB Swiss Institute of Bioinformatics. Retrieved April 22, 2020, from https://web.expasy.org/translate/
• Cn3D. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. Retrieved April 22, 2020, from http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
• PredictProtein (2020). RostLab. Retrieved April 22, 2020, from https://open.predictprotein.org/
• UniProtKB - P59594 (2020). National Center for Biotechnology Information (NCBI). Retrieved April 22, 2020, from https://www.uniprot.org/uniprot/P59594
• 6VYB. RSCB. Retrieved April 22, 2020, from https://www.rcsb.org/structure/6VYB