Chymotrypsin is a well-studied proteolytic enzyme that functions in our digestive tract where it assists in the hydrolysis of proteins that we eat. It readily cleaves the peptide bonds adjacent to aromatic amino acids tyrosine, phenylalanine and tryptophan. Its mechanism of action is well-understood and is often taught in undergraduate biochemistry courses as an example of the enzyme catalysis. The active site of chymotrypsin has two interesting structural features:
You saw that it was quite easy to color structures by selecting desired chains or residues with mouse. However, in a typical case, you may not know where the residues of interest are in a complex structure such as a protein molecule. Here the powerful command-line becomes very helpful. You will learn how to use the PyMOL commands by creating an image that illustrates the following aspects of the chymotrypsin mechanism:
A suitable structure of chymotrypsin with a bound inhibitor is found in the PDB file 1AFQ. Open this file in PyMOL by using the PDB Loader Service under Plugin menu. The structure looks pretty complex, so let's simplify the view by displaying parts that are important for your assignment. The information under Ligand Chemical Component on the PDB website reveals that the inhibitor has residue name 0fg. We want to show this ligand, and the catalytic residues in some detail while displaying the rest of the protein as a transparent surface. To accomplish this, you can type the following commands into the command line:
hide
select inhi, resn 0fg show sticks, inhi show sphere, inhi color forest, inhi cmd.disable('inhi')
select active, (resi 57,195,102) show sticks, active color marine, active cmd.disable('active')
create prtn, (chain a,b,c) show surface, prtn
This gets you the basic elements in place, and now you just need to alter the settings for surface color, transparency, and sphere scale to have an aesthetically pleasing image. You can change these settings from Edit All ... under the Settings menu. Or you can simply type set transparency, 0.5 to make all surfaces 50% transparent. Next, rotate and zoom the structure into a position that best illustrates what you want to show. Finally, you may raytrace the image with the command ray to provide a more photorealistic look and save it as a PNG file on your hard disk.
The structure and function of chymotrypsin are further described in a Chime-based tutorial from the UC Davis. Please note that you need a Chime plug-in to see this structure. The plug-in is not installed on SGI computers.
A gallery of PyMOL images with associated PDB files and scripts (you can run these from File > Run) is available at www.chem.ucsb.edu/~molvisual.