Download Prob_Set_2_2007

Problem Set #2 Chem 200B
- due Wednesday Feb 21 in class 1) Pick out a protein of known structure that is central to your research or is
connected to your research interests. Download the coordinates from the Protein
Data Bank (www.rcsb.org) and use a rendering program such as Chimera,
Rasmol, Pymol, Molmol, iMol (Macs) etc. to generate a ribbon diagram. Classify
the protein – e.g., alpha, beta, alpha/beta, alpha+beta, membrane protein or
other. Be prepared to briefly (< 1 minute) describe your interest and the
structure of this chosen protein in class on Wednesday (Feb. 21).
2) Design a protein from scratch. Yes, you read correctly – I would like you to use
what you now know to design a protein to take on a specific fold. You may
choose any fold motif you wish, but if you want a suggestion, I recommend a
four-helix bundle. If you choose a bundle, things to consider are: length of the
helical segments (check recent work from the M. H. Hecht lab), residues that
favor helical structure, construction of amphipathic helices, appropriate
sequences for turns, selection of residues exposed to the aqueous medium, etc.
Please give a step-by-step rationale for your design and your chosen sequence.
Please feel free to select other motifs such as a TIM barrel or beta sandwich.
3) The strength of the hydrogen bond and its contribution to protein stability has
been a matter of controversy. Find three fairly recent publications (say within
the last five to ten years) that attempt to quantify the energetics associated with
forming a hydrogen bond. What do you conclude from your readings? Please
write a short statement – say half page – citing the appropriate references that
support your conclusion.