Abstract: There are many ways one can portray atomic structures to elucidate particular aspects. The following is a review of the various display options and are all available on the MacIntosh using the freeware programs MolView and MolView Lite. MolView runs on all Macintoshes and can output object-oriented PICT, Quicktime, QuickDraw 3D, and DXF files. MolView Lite is a QuickDraw 3D 1.5 application that only runs on PowerMacs and can output PICT and QuickTime movies.

Structure Files

To begin analyzing protein structures, one needs to have an atomic coordinate file. Thousands of atomic structures are available on the WWW from the Brookhaven Database. This facility has become the major repository for protein structures. These are called 'PDB' files and are ASCII lists of the positions of the atoms in 3D space. For each atom, there are several pieces of associated information:

1) Residue Type: This is the most often name of the amino acid or nucleotide in the protein (e.g. ALA, PHE, PRO, GTP, etc.) to which this particular atom belongs.

2) Atom Type: This is the name of the atom itself. The first letter most often represents the elemental type, and the remaining characters give further nomenclature. For example, CA atoms are alpha carbons that lie in the backbone of the protein to which the sidechains are attached.

3) Residue Number: This is the number of that particular residue to which the atom belongs. This is often the amino acid number in the sequence. In the case of MolView, this number is often adjusted to accomidate proteins with more than one subunit.

4) X, Y, Z: This is the position of the atom in 3D cartesian coordinates.

5) B value: This is the last number in the line for each atom and represents the thermal motion of the atom. The average B value is normally about 14 square angstroms. The more flexible the atom, the higher the B value.

C-Alpha Backbone Diagrams

C-Alpha atoms (CA in the PDB file) are the carbon atoms to which the side chains are attached. These backbone plots are where lines are drawn to sequentially connect each of these atoms and effectively trace the backbone of the protein. Without the sidechains and other atoms blocking the view, one can easily see how the protein is folded. Below are two MolView versions of this type of diagram. The left figure is a simple line drawing where the model appears to fade into the background where the right figure is a MolView Lite rendering where the lines take on a tube-like appearance.

Space Filling and Surface Diagrams

When looking at a protein structure, the above c-alpha backbones are very informative as to the basic shape and folding pattern of a protein, but does not show you how it fills space. There are several ways to show the volume and surface characteristics of a protein. One way is a CPK diagram. In these plots, each atom is represented by a solid sphere that is equal to its Van der Waal radius (the volume of space occupied by the atom). One can also display this surface by rolling a probe about the surface of the protein. This is basically what a water molecule sees as the protein is in solution. In MolView, this surface can be represented by a series of dots that can be colored in a variety of ways. The following four diagrams are some different representations of these diagrams. The first figure is the c-alpha backbone of a protein, the second figure is a MolView CPK model, the third figure is a MolView Lite version of the same protein, and the final panel is a surface diagram where the surface is represented by color dots. The coloring scheme (one of several possiblilities) is based on amino acid types (hydrophobic=green, charged=red, polar=blue, and glycine=yellow). Therefore, this representation is not only useful to see what the outer surface of a protein looks like, but what is its chemical characteristic as well.

Ribbon Diagrams

Ribbon diagrams are one of the most popular ways to represent protein structures. In these diagrams, much of the structure is stripped away and the proteins fold is represented by cartoon figures. Alpha-helices are represented by either coiled ribbons or by thick tubes, beta-sheets are represented by arrows where the head of the arrow is placed at the carboxyl end of the strand, and 'random coils' are represented by lines or thin tubes. Below are two versions of a ribbon diagram generated by MolView and MolView Lite. In these figures, the ribbon is colored according to the rainbow (red->blue) as the chain is drawn from the amino to the carboxyl terminii. In MolView, there are many ways to color these diagrams.

Ball & Stick Models

Ball and stick models are another very popular way to represent atomic structures. In these figures, the atoms are represented by colored balls and the chemical bonds between them are represented by tubes. This often gives the viewer a somewhat better sense as to the chemical nature of the structural geometry. Below are two examples from MolView and MolView lite of a heme group (the oxygen carrying group of hemeglobin) where nitrogens are blue, oxygens are red, and carbons are yellow, and the iron is purple.

Colored Stick Models

There are actually many other ways to represent chemical interactions. In MolView, one can draw lines between two groups that may be sharing a hydrogen atom in a hydrogen bond (e.g. amide nitrogens and carbonyl oxygens). Also, one can draw the object in a color scheme similar to the B&S routine above, except the atoms are not represented by balls but just as colored sticks. This is useful when you want to convey the chemical interactions in a region, but it is a bit too crowded for a Ball&Stick representation.

Combining Techniques

When looking at a protein, one often uses combinations of these diagrams to highlight particular aspects of the protein. For example:

By using a combination of ribbon and CPK, we can clearly hightlight important aspects of the protein.

It is important to note that, while the rendered 3DMF versions look very nice, they are not always the best to use in all situations. For publication, class notes, or other printed matter, the object-oriented PICT files will yield sharper output for less money. For publication purposes, you can get high resolution with low cost by limiting the number of colors.

Finally...

Here at Purdue, we have created a series of inexpensive CD-ROM's containing images, movies, and tutorials of over 100 proteins. They are being distributed by W.C. Brown Publishers. For information contact, contact Dr. Clark Gedney at Purdue University. These tutorials highlight important aspects of these proteins while supplying files that are ready for exploration with MolView. So, even if you are a novice at looking at protein structures, these CD's can teach you the basics of protein structure structure to help you get started with your own exploration.