1) Pick a protein in the Brookhaven Protein Data Base (the "PDB") and download its entry. See the handout "Finding Files in the Brookhaven Protein Data Base" for tips on how to use Mosaic and ftp. Your structure should be solved using data of at least 2.5 resolution, and should have between 100 and 1000 residues. (As always, smaller is easier). In class, each group should present a short (~10- 15 min) introduction to the protein, including its function and its basic structural elements. You will have to read some papers for this, and look at the protein on the graphics system as described in 2) and 3) below. You may find helpful information in the header of the entry. We will use a display and model building program called Quanta for the remainder of the exercises. Quanta is menu-driven and relatively self-explanatory. Use the primer to guide you through the exercises. I have several sets of Quanta documentation (manuals) that you may borrow. Do not lose them!
2) Draw the protein, and its Ca trace. Measure its overall size and describe overall shape, as well as the size and shape of each subunit if there are more than one. If you have a catalytic or ligand-binding site, try to find it.
3) Identify the regular secondary structural elements a-helices and b-sheets in the protein using the Ca trace or the "main-chain atoms only". You may want to try a ribbon diagram, or a cartoon (arrows and cylinders - this is also called a Richardson diagram) to help find the helices and sheets. These representations are useful to understand how the protein is built, but you cannot use them to measure distances, angles, etc. You may also want to investigate the main-chain hydrogen bonding patterns to help find the helices and sheets. Once you have found some helices or sheets, turn off the cartoons and return to the Ca trace. Measure the lengths of the regular secondary structural elements, in and #residues.
4) Measure the phi-psi angles for 30 residues. Phi and psi are torsion (dihedral) angles that are defined by the positions of four atoms (i.e. for CH2R-C'H2R' t he C- C torsion angle is defined by the four atoms R,C,C',R'). Plot these values on a Ramachandran graph. Note which pairs correspond to residues in a- helices, b-strands, and loop regions.
5) Look at the location of the ionizable amino acids asp, glu, arg, lys, and his. One way to see this is to color the molecule according to residue type. Another is to draw the Ca trace with only some of the side chains displayed. Describe the locations (surface, buried, etc) of the ionizable residues. Do you have any salt bridges? Now draw all of the phe, val, leu and ile residues, and describe their locations. Where are the hydrophobic side chains located? Note that while particular amino acids do have a prefered location many exceptions are found.
6) Measure side chain torsion angles (c) for one of the following sets of residues: (leu, val, ile), (arg, met, lys), or (phe, trp, tyr). This is most easily done by making an object that has, ex. all of the leucines. Measure about 30 c's. Plot the distribution of c1 (and c2 if you have them). Draw Newman projections to explain the observed distribution of c angles.