Question

25. Consider two peptide sequences: LKAENDEAARAMSEA and CRAGGFPWDQPGTSN. Which of the two is more likely to adopt an alpha-helical structure? Why? 26. A beta strand is a stretch of residues in the extended conformation that can participate in a beta sheet. (In the figure at right, beta strands A and B participate in a two-strand sheet.) What sorts of hydrogen bonds are required for the formation of single beta strands and for the formation of beta sheets? backbone- backbone sidechain sidechain sidechain single beta strands beta sheets 27. The goal is to design a poptide that will form an alpha helix that is further stabilized by ionic interactions between R groups at pH - 7 (at right, the curved rectangle at the bottom represents an ionic interaction between R side chains) A. The peptide is going to be 12 amino acids long with a lysine at position 2. Which of the following positions would you predict to be the best place to put the amino acid that you want to form an ionic interaction with? Why? B. which of the following amino acids would you put at that position? why? C. what would happen to the stability of the helix in a pH-2.0 environment?

Answer 1

Answer 25)

1. Lets make comparison between both the peptide sequences. The difference lies in terms of Glycine (G) and Proline (P) which is seen in sequence 2.
2. Proline is basically an amino acid which when present in a protein structure, lacks hydrogen atom at the alpha-amino group due to which it cannot form hydrogen bond.
3. Glycine lacks side chain or in other words has a small side chain. So, due to this fact they cannot participate in Hydrogen binding. Thus, they are present in less number as residues. They are not able to stabilize the structure.
4. Due to these reasons, option 2 is not suited to adapt to an alpha-helices structure. Option 1 ( LKAENDEAARAMSEA ) is most suitable to form an alpha helix.