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Question

1. To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using Web-based protein databases and three-dimensional molecular viewing utilities such as Jmol, a free and user- friendly molecular viewer that is compatible with most browsers and operating systems. In this exercise you will examine the interactions between the enzyme SARS CoV2 main protease and in complex with inhibitor Telaprevir. Use the PDB identifier 6ZRT to explore the structure of the protease-inhibitor complex. To answer the following questions, use the information of the Structure Summary page at the Protein Data Bank (PDB) (www.rcsb.org), and view the structure using Jmol or a similar viewer.

A) How many amino acids are in the primary structure of the SARS CoV-2 protease?

B) Identify how many binding site residues does the protease have. What are these residues? Which amino acid in protease binding site binds to the inhibitor.

C) What types of secondary structures are found in the protease? How many of each?

D) Identify specific amino acids residues in each of the above secondary structures (list them; use toggle section mode, arrow, of Jmol).

E) Attach the snapshot of your protease-inhibitor structure when viewed in 3D View in PDB.

Answer 1

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