Questions: i. How does the consensus sequence for SARS-CoV (the 2003 virus) shown in the figure above compare to the results of Fan et al. described in the first paragraph on this page? ii. How does the consensus sequence for SARS-CoV-2 compare with the consensus sequence for SARS-CoV? Which positions are most conserved in terms of protease binding to substrate? What are the chemical characteristics of those conserved regions?

Solution Steps

• The consensus sequence for SARS-CoV (2003 virus) is shown in the figure with the sequence logo.
• The sequence logo indicates the most common amino acids at each position in the sequence.
• The height of each letter in the stack represents the frequency of that amino acid at that position.

• Fan et al. purified the 3CL^pro from the SARS coronavirus and examined the substrate preference.
• They found that an oligopeptide where Leu in P2 was replaced with Phe was cleaved at 40% of the rate compared to the consensus sequence.
• The consensus sequence in the figure shows Leu at the P2 position, consistent with Fan et al.'s findings.

• The consensus sequence for SARS-CoV-2 is also shown in the figure.
• Comparing the sequences, both SARS-CoV and SARS-CoV-2 have similar conserved regions, particularly at the P1 (Gln) and P2 (Leu) positions.
• The chemical characteristics of these conserved regions include the presence of hydrophobic (Leu) and polar (Gln) amino acids, which are crucial for protease binding to the substrate.

Final Answer