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 has been answered already.

Answer 26)

1. ​​​​​​The only type of bond that is possible in the formation of beta sheet is the backbone-backbone hydrogen bond as can also be seen in case of alpha helical structure.
2. The bond formation occurs between he hydrogen atom from C=O group of one amino acid of one beta strand and other hydrogen atom from N-H group of other amino acid from second beta strand.
3. Side chains are usually oriented in a same direction and hence their occurrence in the form of bonding is not possible as they orient themselves according to the phi-psi angle.
4. Backbone and side chain bonding is also not possible.The groups specific to side chain can vary depending on the presence of a particular amino acid which in turn will prevent the formation of a pleaded structure that can be seen in case of beta sheet.
5. Single beta strand interactions are not favoured.

Sidech ain sidechaia bond B ackb Backbone one- sidechain bond bond Beta strand Absent Absent Abic Beta sheet Prelent Absent
​​​​​​​