Chem 436, Prof. Gelb

Protein Graphics Exercise

In this exercise, you will download a protein stucture file from the Protein Database, then use PyMol, a simple molecular graphics program, to create an image illustrating the relationship between the structure and function of that protein.

Introduction

Protein structural data is available at several different sites that are accessible over the Internet. One of the most widely used is the Protein Database. The most widely used format for protein structural data is known as the "Protein Database" format. These files contain the x, y, and z coordinates of each of the non-hydrogen atoms in the protein, as well as a variety of additional data about the protein itself, including secondary structural features. Such files are in text format and are recognizable by their extension ".pdb" following the actual file name. Such .pdb files can be read by a variety of protein graphics programs such as PyMol, RasMol, or RasMac, or more powerful, unix-based graphics packages such as InsightII. Files can be viewed directly through a Browser interface using a variety of viewers or plug-ins (e.g. VRML, RasMol, Chime) or downloaded from these databases for storage and later viewing and manipulation.

Download PyMol and install on your computer. It should be free.

There are lots of people around that know how to use PyMol.  You can also get help by searching the internet for user guide info.

Find and download the protein structural file

Using your web browser (Netscape or Internet Explorer) go to the Protein DataBank. Use the Search function to find the pdb file for the cobra venom phospholipase A2 containing a bound transition-state analog inhibitor, the pdb ID is 1POB.Following the directions given, download the pdb file to your computer and open it with PyMol.

Create a static image

Use PyMol to display only the following residues: 1) the active-site bound inhibitor, 2), the catalytic calcium ion, 3) the catalytic histidine residue, 4) the catalytic aspartic acid that is H-bonded to the histidine residue, 5) all of the amino acid residues that are ligands to the calcium ion. Display the residues only from a single monomer (there are 2 protein monomers in the crystallographic assymetric unit). Color each amino acid residue and the inhibitor a different color .

Create a image file to your computer from PyMol (for example .png file).

To get homework credit for this, submit your .png file to the Chem 436 TA by email.  Put chem 436 png file in the subject heading of your email so the TA can recognize it immediately.

Deadline to submit the .png file to your TA is end of the 5 week of the qtr.