Lurbinah Week 14

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Lizzy Urbina

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Assignments


Weekly Assigments

Class Journal Assigments

Purpose

The purpose of this week's assignment was to further analyzed using the information provided by Wan et al. (2020) paper to investigate the structure-function relationship of the ACE2 receptor. Our investigation was based on: Can 2019-nCoV bind to certain species ACE2 receptor?

Methods and Results Combined

Sequence and Data Collection of ACE2 Receptor

  • Collected ACE2 receptor sequences from 19 different species using Uniprot
    • We gather data fro different species and very diverse groups of animals
    • Some species were included in Wan et al. (2020) (Civet, Bat, Mouse, Rat, Pig, Orangutan)
    • Some species were not included in Wan et al. (2020) (Platypus, Sperm whale, Pig, Horse, Giant Panda, Elephant, Dog, Red Fox, Chicken, Turtles, Chameleons, Zebrafish, Opossum)
  • ACE2 receptor sequence was obtained in FASTA form

Phylogenic tree

  • Phylogeny.fr was used to elaborate a phylogenetic tree using the sequences of all the species' ACE2 receptor
  • The following tree was created.

  • There was no pattern shown with the data used.
    • Humans and mice were closely related and humans get the novel virus and mice do not. Therefore, we had to look at the data from another angle

Sequence Analysis of ACE2 Alpha Helix

  • iCn3D was used to identify the area where 2019-nCoV binds to.
    • We found that it was a sequence part of the ACE2 alpha helix
  • The picture in the are highlighted showed the sequences that are closer and 2019-nCoV binds to.

Species Sequences Analysis

  • The sequence of the ACE2 alpha-helix of the 19 species was recorded in the picture below.

  • We use human as our positive control since it is known that humans can get infected by the virus
  • We use mouse our negative control since it is known that humans can't get infected by the virus
  • Later, we identify the residues that are different
    • Six residues were found to be different
    • The picture below shows the comparison of the sequences

  • We chose to further analyze 5 species

  • Horse-4 out of 6 residues were different to our positive control
    • I=>T=non polar to polar
    • D=>E=both - charged
    • H=>S=+ charged to polar
    • F=>S= nonpolar to polar
    • Horses are known to get inffected by other strains of coronavirus
  • Platypus-6 out of 6 residues were different to our positive control
    • T=>-=loss of amino acid
    • I=>P=both hydrophobic, change of shape
    • D=>T,= - charged to uncharged
    • K=>Q= + charged to uncharged
    • H=>K= both + charged, change of shape
    • F=>S= hydrophobic to polar
    • Platypus results are expected sice it was our outlayer.
  • Civet-5 out of 6 residues were different to our positive control
    • I=>T = nonpolar to polar
    • D=> E = both - charged
    • K=>T = + charge to polar
    • H=>Y = + charge to polar
    • F=> S = nonpolar to polar
    • Wan et al (2020) have predicted that civet's wont be able to get infected, however there are other cat species being infected by the novel virus.
  • Bat-3 out of 6 residues were different to our positive control
    • I=> T = nonpolar to polar
    • H=> T = + charged to polar
    • F=> S = nonpolar to polar
    • Bats are known to be carriers of coronavirus.
  • Orangutan-All residues were conserved
    • This could be expected since Orangutan is known to be 97-98% similar to human DNA
  • The following file has all the different sequences of all the species we originally sequenced for ACE2 alpha-helix

File:MAP 19 Sequences Comparison.pdf

Residues Summary Table

  • The following table summarized the changes among the ACE2 alpha-helix sequences
  • Our criteria to determine whether 2019-nCoV would be able to bind to ACE2 receptor was the following
    • 3 or more residues conserved when compared to our positive control it is likely that 2019-nCoV would be able to bind to ACE2 of that specie
    • Less than 3 residues conserved when compared to our positive control it is less likely that 2019-nCoV would be able to bind to ACE2
  • The highlighted species in the following were found to be less likely to get infected by the novel virus

Analysis of Position 13

  • In Wan et al. (2020) position 31 was considered integral in binding
    • In our sequences position 13is equivalent to position 31 in Wan et al.'s paper
  • The following table shows the two species that are different in position 13

    • These results correlate with our prediction according to our criteria that these two species' ACE2 receptor would be less likely to bind to 2019-nCoV

Disscussion and Future Research

  • Our predictions can give an idea if the virus can bind to a particular ACE2 receptor
    • However, we just looked at the helix that directly binds the virus. It is important to keep in mind that other parts of the ACE2 structure could bind to the virus, or the virus can mutate itself to bind to more species.
  • Civets were able to have SARS-CoV-1, but predicted to not bind to SARS-2.
    • This shows the diversity among the coronavirus family, and how a virus can mutate itself as it happened in SARS-CoV-1 to bind to civet's receptor.
    • Additionally, it is known that other cat species can get infected by the virus.
  • Future research could include looking at other hotspots in the ACE2 receptor

Data and Files

Final Powepoint Presentation

File:MAP Final Presentation Bioinformatics.pdf

Conclusion

According to our research, we found that orangutan, horse, and bat would be more likely to get infected by the virus. Additionally, we found that the hotspot in position 13 according to Wan et al. paper matches our prediction that platypus and civet won't be able to get infected by the novel virus. We based our research on the finding that 2019-nCoV binds to the ACE2 receptor in the alpha-helix sequence.

Acknowledgments

I worked with my homework partners Madeleine B. King, Maya, and Karina Vescio to work on the research project, analyze data, worked on the PowerPoint, and meeting on Wednesday, April 29, 2020, to practice

  • I copied and modified the protocol for Week 14 assignment
  • The foundation of this research is based Wan et al. (2020) paper
  • I used my partner's files Madeleine B. King, Maya added to this entry.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Lurbinah (talk) 23:57, 29 April 2020 (PDT)

References

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