135. X, Y and Z correspond to three different conformers of an 18-residue peptide, where X: α helix, Y: β strand
and Z: 310 helix. Which of the following correspond to the conformers in the decreasing order of end to end
distance?
1. Y, Z, X

2. X, Y, Z
3. Z, X, Y
4. Y, X, Z

Question

X, Y, and Z correspond to three different conformers of an 18-residue peptide, where X: α helix, Y: β strand, and Z: 310 helix. Which of the following correspond to the conformers in the decreasing order of end-to-end distance?

1. Y, Z, X

2. X, Y, Z

3. Z, X, Y

4. Y, X, Z

Detailed Explanation

Peptides can adopt different secondary structures, each with unique spatial arrangements. The end-to-end distance in these conformers refers to the distance between the first and last residues in the peptide chain, which is influenced by the specific type of secondary structure the peptide adopts.

Let’s explore the characteristics of each conformer:

1. α Helix (X):

   • The α helix is a right-handed helical structure where each residue forms hydrogen bonds with the fourth residue along the chain.

   • It has a tight, coiled structure with a typical rise per residue of about 1.5 Å.

   • Due to the compact nature of the helix, the end-to-end distance is relatively shorter compared to other secondary structures like β-strands.

2. β Strand (Y):

   • The β strand is a zigzag or extended structure where the peptide chain stretches out, with hydrogen bonds forming between adjacent strands in the β-sheet.

   • The peptide backbone in a β strand is extended, leading to a longer end-to-end distance compared to an α helix, as the strand is relatively more extended.

3. 310 Helix (Z):

   • The 310 helix is a right-handed helix that is slightly more compact than the α helix. Each turn of a 310 helix involves three residues (hence the “310” name) and has a shorter rise per residue compared to the α helix.

   • The end-to-end distance is slightly longer than the α helix, but not as long as the β strand, due to its more compact, spiral-like structure.

Correct Answer: 1. Y, Z, X

• Y (β strand) will have the longest end-to-end distance because the strand is fully extended and not coiled.

• Z (310 helix) will have a shorter end-to-end distance than Y but longer than X, as the 310 helix is more compact than the β strand but still forms a helical structure.

• X (α helix) will have the shortest end-to-end distance, as the α helix is a tightly coiled structure with a smaller rise per residue.

Thus, the decreasing order of end-to-end distances is: β strand (Y), 310 helix (Z), α helix (X).

Conclusion

In the given peptide sequence, the β strand (Y) has the longest end-to-end distance, followed by the 310 helix (Z), with the α helix (X) having the shortest. Understanding these structural differences is crucial when studying protein folding and stability.