Biochemistry COVID question.

Question

I need an in depth answer to this. I am stuck at this and need help

. Compare the sequences of S proteins between SARS-CoV, SARS-CoV2 and MERS-CoV (start by using the “Nature” paper with S protein alignment). What are the conserved, semiconserved and non-conserved amino acids?

This is the link with the sequences.

I am confused how to compare the sequences

https://www.nature.com/articles/s41591-020-0820-9,

Answer 1

Hi Esh,

Figure 1 shows two expansions of the primary protein sequence (the amino acids in order that they appear in the protein) in the S (spike) subunit. One expansion is for the O-linked glycans, and one for the receptor binding domain. In each of these regions, the amino acids are shown using their single letter code. You can look up on line which amino acid corresponds to which single letter code. The authors have also color coded the amino acids for easy identification. To compare the sequences, look along the line for each labeled sequence (for example, the Human SARS CoV is on the top line in both). The sites where all sequence have the same amino acid are highly conserved, sites where some sequences are the same and some are different are semi-conserved, and sites where most or all vary are not conserved.

Hope this helps!

Scarlett