3. Answer ALL parts a)-e). The diagram below illustrates the interactions between two a-helices within a larger protein

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3 Answer All Parts A E The Diagram Below Illustrates The Interactions Between Two A Helices Within A Larger Protein 1 (52.39 KiB) Viewed 67 times

3. Answer ALL parts a)-e). The diagram below illustrates the interactions between two a-helices within a larger protein structure at pH 7.0. Side chain interactions occur between residues directly opposite one another as shown (L1 interacts with I, E1 with E2 etc...) N-terminus A₁ CH₂ K₁ ⒸNH₂ D OH Protein A₂ CH₂ K₂ bil C-terminus Aqueous solution a) In the primary sequence, how many amino acid residues apart must I and Y be to display on the same face of the a-helix as shown? [1] b) There are two interactions between the side chains of these two a-helices that would be disruptive to this structure. i) Identify the amino acid side chain pairs involved, briefly justifying your answer in each case. [4] ii) Suggest a replacement amino acid for one half of each pairing from b) i) that will give a fully attractive set of interactions between these two a-helices. [2] c) Classify the three most significant attractive non-covalent interactions between these two helices. Indicate the amino acid side chains involved and briefly justify your answer in each case. [6] d) If the pH is increased to 12 explain how and why the interaction between the two a-helices would change. [4] e) Using only natural amino acids, suggest a replacement for two amino acids that would enable a covalent cross-link to form between the helices. Illustrate your answer with a reaction scheme. [3] H₂NO