Question

If the sequence Met-Lys-Glu-Ala-Phe-Leu-Gln is folded into an α-helix, the amino acid whose carbonyl group interacts with the amide hydrogen of Gln would be:

A. Glu

B. Ala

C. Phe

D. Leu

E. Lys

The answer is A. can you explain the answer

Answer 1

An α-helix is a secondary structure of a protein in which the polypeptide backbone is tightly wound around an imaginary axis drawn longitudinally through the middle of the helix, and the R groups of the amino acid residues protrude outward from the helical backbone. A single turn of an α-helix extends about 5.4 Å along the axis with each helical turn consisting of 3.6 amino acid residues.

The α-helix structure is stabilized by a hydrogen bond between the hydrogen atom attached to the nitrogen atom of a peptide linkage (amide hydrogen) and the carbonyl oxygen atom of the fourth amino acid on the N-terminal side of that peptide bond. Within the alpha helix, all the peptide bonds, except first and last in the polypeptide chain, participate in hydrogen bonding. Therefore, each successive turn of the alpha helix is held to adjacent turns by three to four hydrogen bonds.

When the given peptide sequence Met-Lys-Glu-Ala-Phe-Leu-Gln is folded into an α-helix, the amino acid whose carbonyl group interacts with the amide hydrogen of Gln would be Glu because it is the fourth amino acid residue on the N-terminal side of the peptide i.e. Met⁶-Lys⁵-Glu⁴-Ala³-Phe²-Leu¹-Gln.

The hydrogen bond formation between the amide hydrogen and the carbonyl oxygen of the 4th amino acid residue on the N-terminal side in an α-helix is shown in the figure below:

Incorrect options:

B. Ala - In the α-helix of peptide Met⁷-Lys⁶-Glu⁵-Ala⁴-Phe³-Leu²-Gln¹, Ala carbonyl group cannot interact with amide hydrogen of any amino acid residue as there is no fourth residue on the C-terminal side.

C. Phe - in the α-helix of peptide Met⁷-Lys⁶-Glu⁵-Ala⁴-Phe³-Leu²-Gln¹, Phe carbonyl group cannot interact with amide hydrogen of any amino acid residue as there is no fourth residue on the C-terminal side. However, the amide hydrogen of Phe will form H-bond with the carbonyl group of the Met residue.

D. Leu - in the α-helix of peptide Met⁷-Lys⁶-Glu⁵-Ala⁴-Phe³-Leu²-Gln¹, Leu carbonyl group cannot interact with amide hydrogen of any amino acid residue as there is no fourth residue on the C-terminal side. However, the amide hydrogen of Leu will form H-bond with the carbonyl group of the Lys residue.

E. Lys - in the α-helix of peptide Met⁷-Lys⁶-Glu⁵-Ala⁴-Phe³-Leu²-Gln¹, Lys carbonyl group will interact with amide hydrogen of Leu residue which is the fourth residue on the C-terminal side.