Given the following sequences N-terminal to C-terminal of the resulting fragments, deduce the sequence of the original peptide.

Question

A sample of an unknown peptide was divided into two aliquots. One aliquot was treated with trypsin; the other was treated with cyanogen bromide. Given the following sequences (N-terminal to C-terminal) of the resulting fragments, deduce the sequence of the original peptide.

Trypsin treatment

Asn—Thr—Trp—Met—Ile—Lys

Gly—Tyr—Met—Gln—Phe

Val—Leu—Gly—Met—Ser—Arg

Cyanogen bromide treatment

Gln—Phe

Val—Leu—Gly—Met

Ile—Lys—Gly—Tyr—Met

Ser—Arg—Asn—Thr—Trp—Met

Answer 1

This is a great problem, let’s break it down step-by-step!

Trypsin cleaves after Lys (K) and Arg (R), while cyanogen bromide (CNBr) cleaves after Met (M). The trick here is to look for overlaps between the fragments from both treatments and piece the puzzle together.

From CNBr, you have these chunks:

Val—Leu—Gly—Met

Ser—Arg—Asn—Thr—Trp—Met

Ile—Lys—Gly—Tyr—Met

Gln—Phe

From trypsin:

Asn—Thr—Trp—Met—Ile—Lys

Gly—Tyr—Met—Gln—Phe

Val—Leu—Gly—Met—Ser—Arg

By lining up the overlaps between the fragments (Met residues and cleavage sites help here), you can

deduce the original sequence:

Val—Leu—Gly—Met—Ser—Arg—Asn—Thr—Trp—Met—Ile—Lys—Gly—Tyr—Met—Gln—Phe

It takes a little peptide detective work, but I hope that helps!