Question

22. Consider an alpha helix with sequence VLADWMAVELA, and consider the hydrogen bonds that are required in order to form the alpha helix. A. Fill in all of the hydrogen bonds that must form between a given residue's backbone N-H backbone C-O, or R group, indicating what the hydrogen bonding partner for each will be. For example, the C-O of V1 is a hydrogen bond acceptor of the W5 N-H hydrogen bond donor, reflected in the appropriate squares under V1 and W5. Note: some squares may be left blank: record only those interactions that are required to satisty the definition of an alpha helix. 10 11 V1 Backbone N-H R group B. Are there any backbone C-Ogroups or N-H groups whose hydrogen bonding capacity remains unsatisfied? What is the significance of this fact? C. Proline residues are often found at the termini of helices. Why? D. The figure at right contrasts an alpha helix with another type of peptide helix, the 310 helix. Note the differences in hydrogen bonding patterns between backbone atoms. As you did in part A above, record the hydrogen bonds between backbone N-H and C-O groups that are necessary to form a 3- helix. Canonical 3(10) helix Canonical a-helx V1 Backbone N-H Buckbone C o D4 R group E. The frequency of 310-helices is much lower than that of alpha helices. Can you make an argument for this observation based on the orientation of sidechains? Would a 310-helix configuration be favorable for the peptide sequence VLADWMAVELA? Canonical a-helix Canonical 3(10) helix

Answer 1

Answer 22.A have been answered.

Answer 22.B)

1. Proline and Glycine can be considered as the amino acids whose hydrogen binding potential remains unsatisfied.
2. Both of them basically cannot form hydrogen bonds. In case of proline, the amide group is merged in the cyclic form and hence is not involved in formation of the Hydrogen bonds. Glycine on the other hand do not have side chain which restricts their potential to form stable hydrogen bonds.

Answer 22.C)

1. Proline residues are seen at the N-terminal end of a peptide chain configuring an alpha helix.
2. Basically, the hydrogen providing amide group is found in the cyclic structure and thus cannot link with the acceptor (C=O) to form the bond.
3. The hydrogen from C=O group at 1st position binds with Hydrogen from N-H at the fourth position as a part of intrachain binding which keeps the N-terminal vacant which cannot form any linkage or bond. Due to this, there needs to be availability of such an amino acid that would not initiate bond formation or remain unpaired. Proline thus remains attached to N-terminal end.