Analysis of a nonapeptide, Compound N, gave the following amino acid composition

Question

Analysis of a nonapeptide, Compound N, gave the following amino acid composition:

Ala, Arg, Asp, Gly x 2, Gln, Leu, Val x 2

Treatment of Compound N with the Edman reagent led to an octapeptide Compound O, with the following amino acid composition:

Ala, Arg, Asp, Gly x 2, Gln, Val x 2

Treatment of both Compound N and Compound O with the enzyme DPAP gave the following mixtures of peptides:

N ---DPAP---> (Arg, Gly), (Gln, Ala), (Leu, Val), (Val, Asp), Gly

O ---DPAP---> (Ala, Gly), (Gly, Val), (Asp, Gln), (Val, Arg)

DPAP cleaves a peptide after every second residue from the amino terminus. Determine the amino acid sequence of Compound N.

Explanation / Answer

Compound N:

Ala, Arg, Asp, Gly x 2, Gln, Leu, Val x 2

After treatment with Edman reagent

Compound O:

Ala, Arg, Asp, Gly x 2, Gln, Val x 2

Since Leu is not present in the peptide sequence after Edman degradation, it is the N terminal amino acid.

After we treat N and O with DPAP, we obtain the following residues

N ---DPAP---> (Arg, Gly), (Gln, Ala), (Leu, Val), (Val, Asp), Gly

O ---DPAP---> (Ala, Gly), (Gly, Val), (Asp, Gln), (Val, Arg)

Now, starting with Leu

(Leu,Val) is an obtained peptide

After Leu is removed from the sequence, Val will be the new N terminal amino acid

Hence we look for a peptide in O to overlap with (Leu,Val) in N.

The overlap is done so that the second amino acid in a peptide from N is the same as the first amino acid from a peptide in O, thus the subsequent peptide sequence is obtained

N: (Leu,Val)

O: (Val,Arg)

Similarly we proceed with alternating N, O fragments to obtain the overlap sequence

N: (Leu,Val)

O: (Val,Arg)

N: (Arg,Gly)

O: (Gly,Val) {We use this Gly, since the other being a lone amino acid is clearly the C terminus of N}

N: (Val,Asp)

O: (Asp,Gln)

N: (Gln,Ala)

O: (Ala,Gly)

N: Gly

So, the peptide sequence obtained is

N: Leu,Val,Arg,Gly,Val,Asp,Gln,Ala,Gly.

P.S: The overlap process shown may not come out properly in the final answer, but i can clear any doubts if you just comment below.

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