Visualizing Proteins with Jsmol
This tutorial focuses on protein structure and the intramolecular forces that are involved in protein folding and stability. This section is an introduction to a variety of ways of depicting proteins, as well as some common color schemes used in depicting proteins. All the proteins used in this tutorial have had their structures determined using X-ray crystallography or NMR. These structures are deposited in the Protein Data Bank (PDB) for use by researchers, educators and students. The PDB accession numbers are provided for each protein in this tutorial, in case you want to explore the proteins further.
Throughout the tutorial, clicking on the buttons will launch a Jmol (Jsmol) image of the protein on the screen at the right.
Once a protein appears in the Jmol window, wait until the image stops moving before pushing a button to execute another script. You may spin the protein (left mouse button click and drag), or, if you wish, you may use Jmol commands to explore the protein further. A Jmol Quick Reference Sheet and Jmol Training Guide are available if you want to play with the images. (WARNING: This can be a lot of fun!)
If you hover over an atom in Jmol, a popup window will identify the atom in the format:
[ASN]108:B CA #1888
where
[ASN] is the 3 letter amino acid abbreviation (or 1 letter nucleotide, if it is a nucleic acid)
108: is the residue number
B identifies the chain name in the pdb file
CA identifies the atom type. (CA is the code for the alpha carbon)
#1888 identifies the atom number in the pdb file.
There are three common formats for displaying proteins; each is used to show different features of the protein. Shown below is insulin (2HIU.pdb), a hormone that regulates blood sugar levels.
Spacefill Spacefill depicts all atoms at their relative diameter.
Backbone This display only shows the central carbon atom (the alpha carbon) of each amino acid, with a solid line connected adjacent amino acids. It is sometimes called the alpha carbon backbone.
Ball and Stick This view shows each of the atoms as balls, with sticks to indicate the bonding between atoms.
Combination Display Each representation has advantages and disadvantages.
Color can be used effectively to communicate information about protein structure.
Color Chains Some proteins, such as insulin (2HIU.pdb), consist of more than one peptide chain. Here the chains are colored differently to visualize how they interact.
Color Structure This view displays secondary structure of a zinc finger protein (1ZAA.pdb). Zinc finger motifs are often found in proteins that bind to DNA (shown here in pale blue). Here alpha helices are colored red and beta pleated sheets are colored yellow.
CPK Coloring This standardized coloring scheme uses a specific color for each type of atom. In this scheme:
Carbon is gray (or sometimes black)
Oxygen is red
Nitrogen is blue
Hydrogen is white
Sulfur is yellow
Zinc is brown
User Defined Color Scheme This is an image of GATA-1 and FOG-1, proteins important in regulating which genes are turned on in development. This model was designed by the 2011 Mount Mary CREST Team. They colored the two protein backbones differently, then added important sidechains in CPK coloring. You'll learn more about these proteins later in the tutorial.
Here are some other examples of user defined color schemes. The possibilities are endless!
User Defined Color Scheme: Blue
User Defined Color Scheme: Purple and Green
You now know enough about how proteins are depicted to explore the four levels of protein structure. Enjoy the journey into the world of molecular visualization!