CHEM C130 Midterm: mcbC100A-fa2015-mt1-Kuriyan-soln
Document Summary
The a-form double helix in rna has a narrow major groove, so an alpha helix cannot enter it readily. Helix 3 exposes polar/charged sidechains to the membrane environment. These sidechains lose interactions with water, and cannot regain good hydrogen bonding interactions with each other, since they are located 2 turns apart. So, on their own, the proteins are unstable in the membrane. Presumably, the proteins are able to dimerize so that the d and e sidechains form hydrogen bonds with each other. This compensates for the loss of interactions with water. The e and d sidechains have to be neutral in order to hydrogen bond. If they were charged, they would have an even stronger penalty for insertion into the membrane. So, they are harder to deprotonate, and so the pka values become higher. If we assume that the helix is straight, there are 35/1. 5 = 23. 3 residues in the membrane.
