Homework #1 Due February 18
The goal of this homework assignment is to get you to examine some protein structures in detail and to think about protein structure and function. To visualize protein structures, several programs are available. Rasmol is still probably the most common molecular graphics program. It's available for just about every platform and it has fast, although not particular beautiful, graphics. A good alternative is Pymol, which has nice ray tracing graphics and is becoming more full featured all the time. For publication quality graphics, Molscript (or the Bobscript variant) and Raster3D are still probably the best and most flexible programs. These programs create still images, however, not interactive displays. You can find links to these, and more, molecular graphics and rendering tools on the links page of my home page (http://www.soe.ucsc.edu/~rohl/rohllab/).
Your first task is to dowload, install and become familiar with the use of at least one of these programs. Explore the PDB web site (www.rcsb.org) to obtain some PDB files. You should learn how to rotate and zoom, how to display the molecule in different representations (i.e. wireframe with all the bonds shown; space filling or cpk, cartoons with arrows for strands and helices for sheets, etc), how to select individual residues, and how to output images in different graphics formats. Rasmol also lets you measure distance, torsion angles. Some programs, like MolMol will also do some structure analysis such as calculation of Ramachandran plots, contact maps, and structural superpositions.
For your homework assignment, pick two proteins of known structure and use the molecular graphics tools to make images that illustrate something interesting for each of these proteins. If you have no clue what proteins to select, I suggest you start by browsing through SCOP until you find something that piques your interest. Or browse through the PDB using functional keywords. You might also try looking through databases that catalog protein-protein interactions or protein conformational changes to get some ideas. Do NOT just take images that can be made by various websites that provide methods to map function on structure, illustrate conformational changes or do something similar. You should create these images yourself using the molecular graphics programs you've chosen
For a protein, you might choose to illustrate how the structure affects or enables the protein's function. If your protein is an enzyme, where is the active site? If it interacts with other proteins or with other macromolecules, what's known about how these interactions occur? There may be more than one structure that's relevant to your protein. The structure of the protein in complex with a substrate or binding partner may be known, or maybe there's some dynamic behavior (i.e. a conformational change) that's interesting.
An alternative to illustrating functional aspects of a protein is to illustrate features of the structure itself that are interesting or unusual. You could choose to compare and contrast a few homologous structures, highlighting the similarities and/differences. You can use SCOP to find structural neighbors of your protein and online structual alignment programs like DALI to compare structures yourself. Maybe there's some aspect of this protein's putative evolutionary history that can be illustrated. Look in the PDB file itself for some clues about interesting aspects about the structure.
Be creative. I'm not expecting you to discover anything new about these proteins, just learn something interesting about them and illustrated it well. If you want some ideas to inspire you, check out the 'Molecule of the Month' feature at the RCSB site. Also, most of the molecular graphics programs homepages have sample images that demonstrate their capabilities. If you're uncertain as to how much work to do, keep in mind that your class project is 50% of your grade; this assignment will be 15% of your grade. Remember that the goal is to illustrate something interesting about the protein, not just to make pretty pictures. Two informative pictures for a protein are much better than five uninformative ones. And don't forget that you'll need explanations to accompany your images.
You can hand in this assignment either by email or as an URL to a web page. If you make a web page, do not make any plugins (Chime, etc) necessary to view your page.