BIOCHEMISTRY HELP

Question

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 has. What are these residues? Which amino acid in the 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). (3 pts) E) Attach the snapshot of your protease-inhibitor structure when viewed in 3D View in PDB.

Answer 1

I love exercise-based questions! They impart practical skills. As part of my own lab's research, we often use the interactive protein structure viewing tool at RCSB PDB. This multi-part question is a little tricky in that you actually don't need to interact with the 3-D structure in Jmol to answer most of it. Here, I can describe my general approach to answering each part:

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

The primary structure (aka amino acid sequence) is provided on the main page (Structure Summary) under "Macromolecule Content" and can be confirmed under the Structure tab.

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

This information can be retrieved under the Sequence tab. The table row labels and are pretty intuitive to navigate. During a tutoring lesson I would walk a student through how to find this information quickly and confirm that it is correct.

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

Secondary structures for proteins are (i) alpha helices and (ii) beta strands, which form sheets. These can be found easily under the Sequence tab.

(D) Identify specific amino acids residues in each of the above secondary structures (list them; use toggle section mode, arrow, of Jmol). (3 pts)

Once you write down the secondary structures you looked up under Sequence, you can navigate to the Structure tab, use your mouse to highlight the residues of interest in the text sequence at the top, and then save that selection as a feature.

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

If you really want to impress your instructor, you can set all the helices in one color, and the beta strands as a different color, convert the inhibitor molecule to a space-filled (atoms as clouds) model, then when you save the snapshot use a program like Powerpoint (or any image editing tool) to add a color key.