BIOL361 Lecture 9: Assessing the assumption of Normality

Please Explain how to solve this problem.

Like alpha helices, beta sheets often have one side facing the surface of the protein and one side facing the interior, giving rise to an amphiphilic sheet with one hydrophobic surface and one hydrophilic surface. From the sequences listed below, pick the one that could form a strand in an amphiphilic beta sheet. Think about the way side chains are arranged in a strand of a beta sheet. (See Table 8, page 966, for one-letter amino acid code; the mnemonic in problem 3-18 might also be helpful.)
A. A L S C D V E T Y W L I
B. D K L V T S I A R E F M
C. D S E T K N A V F L I L
D. T L N I S F Q M E L D V
E. V L E F M D I A S V L D

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1. a. Consider the following sequences, which are pieces of a larger, independently folding polypeptide. Which sequence is more likely to form an alpha helix, and which is more likely to form a beta-hairpin—a two-stranded antiparallel beta-sheet in which the strands are separated by a turn?

Sequence A: I F I C T T G P N A T V I C V F V

Sequence B: M D R L M E A M A K L D H L L A E

b. How do the structures of the residues I, V, and T versus L and M contribute to the conformational preferences of these two sequences?

c. Which residues likely form the turn between the stands in the beta-hairpin? Why are these residues suited for this structure?

An amphipathic protein helix is lying flat one the surface of a lipid bilayer membrane. Which of the following sets of amino acids would most likely face away from the lipid bilayer and towards water?

A. S-W-I-L-T

B. F-G-I-L-P

C. A-C-D-E-H

D. I-L-M-F-V

E. Y-W-W-L-R