This exam is to be worked on independently. You may not discuss any aspect of this exam with anyone except Professor Martin - not other students, not other faculty, no one.
Question 2
a) Look at the following surface representations:
Toggle between the two surface views. Explain what you think is the difference between the two views (something more deep than "one is smoother than the other"). Explain why one view is "better" than the other.
Answer: (10 points) You might reasonably surmise that the tighter surface is using van der Waals radii, while the "fatter" view is likely something like the solvent accessible surface (indeed this is what they are). The latter more accurately reflects the surface of the protein in that we're never concerned about He and H2 making van der Waals contact, but rather, we're interested in how larger (small) molecules and proteins interact. Some of you seemed to miss the point that these are just two different views of reality - remember, the molecule is what it is - these are just different ways for us to think about that reality.
b) Given your understanding of protein structure, explain why this molecule is unlikely to adopt this precise structure as a monomer in solution.
Answer:
(15 points) The stretch from 32 to about 40 is sticking out in solution - no hydrophobic core (though some of it is hydrophobic), nothing to stabilize that structure (except likely in the crystal structure, contacts with other molecules). This is not stable in that one conformation regardless of whether the stretch were hydrophobic or hydrophilic - no core.