A protein biochemist attempted to determine the amino acid sequence of a decapeptide. Use the results from the trypsin, chymotrypsin, and cyanogen bromide treatments to suggest the amino acid sequence of this decapeptide. Trypsin digestion gave two fragments, containing the following residues (not in order): T1: Ala, Arg, Phe, Pro, Thr, Trp, Tyr T2: Lys, Met, Val Chymotrypsin digestion gave three fragments with the following residues (not in order): CT1: Ala, Arg, Phe, Pro CT2: Thr, Trp CT3: Lys, Met, Tyr, Val N-terminal analysis of the CT1 tetrapeptide indicated that the N-terminal amino acid was Ala. The cyanogen bromide gave only one single amino acid, methionine, and a nanopeptide.

**I know that Trypsin cleaves after Lys and Arg, but not on the N-side of Pro. Chymotrypsin cleaves after Phe, Trp, and Tyr, but not on the N-side of Pro. Cyanogen bromide cleaves after Met. My professor also told me that it begins with Met, & ends with Lys.

Before I start, let me make one thing clear before we start solving this...I know its says that it will not cleave if it's on the N-side of Proline. HOWEVER, this does not mean the WHOLE N-side...just the immediate N-side Amino Acid. This misunderstanding really screwed me over when I was trying to solve this question.

Ok, so let's start with 10 blanks:

X-X-X-X-X-X-X-X-X-X

Cyanogen bromide cleaves after methionine and leaves a nonapeptide so methionine must be the first one

Met-X-X-X-X-X-X-X-X-X

The information from the trypsin digestion lets us know the first part of the sequence. Since Trypsin cleaves the C side of Lys and Arg, Lys must be the last amino acid

Met-Val-Lys-X-X-X-X-X-X-X

CT3 has Lys, Met, Tyr, and Val and since Met, Val, and Lys are the first three amino acids, Tyr must be the fourth:

Met-Val-Lys-Tyr-X-X-X-X-X-X

Since chymotrypsin cleaves after Tyr and Trp and the sequence is only Thr-Trp, I just put it in next. This is kinda like a "gimme" sequence.

Met-Val-Lys-Tyr-Thr-Trp-X-X-X-X

(we don't have to worry for Trp to be next to Pro since we were told that Ala is the first Amino Acid of CT1's sequence)

All we are missing now is Ala, Arg, Phe, and Pro. Since Ala is the first amino acid of the CT1, that means:

Met-Val-Lys-Tyr-Thr-Trp-Ala-X-X-X

Now this is the part where it can be tricky to explain. This is spot where you can get multiple answers depending on where you look at first or what process of elimination you are using...

There are 4 possible ways to end this sequence...Phe-Arg-Pro, Arg-Phe-Pro, Arg-Pro-Phe, or Phe-Pro-Arg. HOWEVER, Arg-Phe-Pro and Phe-Arg-Pro CANNOT work.

Why?

For Phe-Arg-Pro:

If this was the case then there should have been a CT4: Arg-Pro

For Arg-Phe-Pro:

Then there should have been a T3: Phe-Pro

So your two answers can be:

Met-Val-Lys-Tyr-Thr-Trp-Ala-Phe-Pro-Arg OR Met-Val-Lys-Tyr-Thr-Trp-Ala-Arg-Pro-Phe