A.5 Lab #2: PyMOL Visualizations

You will be using PyMOL extensively in the second half of the dry lab.

A.5.1 Task #1: identifying secondary structures using PyMOL

In the second portion of the lab, you are the given three unnamed .pdb files for the following secondary structures:

  1. Anti-parallel \(\beta\)-sheet
  2. Parallel \(\beta\)-sheet
  3. \(\alpha\)-helix

Once you’ve opened all three files in PyMOL, you will need to:

  1. Take screenshots of the stick visualization of each secondary structure (include these in your lab report).
  2. Identify which visualization corresponds to which secondary structure.
  3. Explain your rationale for 2 in your lab report.

You will then need to pick three amino acid pairs from each secondary structure and perform the following tasks using PyMOL’s wizard function:

  1. Measure their \(\psi\) and \(\phi\) dihedral angles
  2. Measure their O-H-N bond angles
  3. Measure their hydrogen bond lengths (in Angstroms)

Finally, use Microsoft Excel (or a suitable program) to construct a Ramachandran plot using the \(\psi\) and \(\phi\) dihedral angles that you’ve measured earlier (see my lab report to see what your plot should look like).

A.5.2 Task #2: visualizing neuraminidase

Neuraminidase is an enzyme that is present on the surface of the influenza virus. The drug zanamivir is an inhibtor of neuraminidase. Prof. Mu will give you a .pdb file of the neuraminidase enzyme with a zanamivir moiety interacting with it.

First, take a screenshot of the cartoon visualization of neuraminidase - be sure that the cartoon visualization is colored according to the main chains of the proteins! Then, take a screenshot of the stick visualization of zanamivir (present inside the .pdb file for neuraminidase). Also be sure to generate a three-dimensional surface view of zanamivir interacting with neuraminidase (see my lab report for reference); include all three screenshots in your lab report.

You will then need to find several (i.e., as many as you can find) direct interactions (i.e., drug-protein interactions) and indirect interactions (i.e., hydrogen bonding between a water molecule and the neuraminidase and zanamivir structures) in the .pdb file using PyMOL.

Once done, write a brief conclusion reflecting on what you have learned and taken away from this lab.