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In: Biology

The ubiquitin protein from the malaria parasite was treated with chymotrypsin, and the resulting fragments were...

The ubiquitin protein from the malaria parasite was treated with chymotrypsin, and the resulting fragments were sequenced. A second sample of the polypeptide was treated with trypsin, and the fragments were sequenced. What is the sequence of the polypeptide?

Chymotrypsin fragments:

AGKQLEDGRTLSDY

IPPDQQRLIF

VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI

NIQKESTLHLVLRLRGGMQIF

Trypsin Fragments:

LR

AK

EGI

IQDK

LIFAGK

QLEDGR

TLTGK

IPPDQQR

GGMQIFVK

TLSDYNIQK

ESTLHLVLR

Expert Solution

The sequence is

IPPDQQRLIF AGKQLEDGRTLSDY NIQKESTLHLVLRLRGGMQIF VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI

Chymotrypsin cleavage site is
NH-R-R'-CO
R= phenylalanine (F), Tyrosine (Y), tryptophan (W)
R' is not proline (P)
The cleavage site of trypsin is
NH-R-CO
R= Lysine (K) or arginine (R)
In both the digestion we can see a fragment snding with Isoleucine (I). It is not a cleavage site of both the enzymes. Hence it is considered as the carboxy terminal of the polypeptide. Using this fragment (VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI) we shall predict the sequence.

We shall consider the first 2 amino acid "VK" in VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI for our analysis. Look for sequence ending with VK in trypsin.
We have GGMQIFVK. Now look for this sequence QIF in carboxy terminus of chymotrypsin fragments. We have this NIQKESTLHLVLRLRGGMQIF. Hence this fragment will come before the terminal sequence.

NIQKESTLHLVLRLRGGMQIF VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI

Again look for NIQK in the trypsin fragment. We have TLSDYNIQK. Look for TLSDY in chymotrypsin fragments. We have AGKQLEDGRTLSDY.

The sequence becomes
AGKQLEDGRTLSDY NIQKESTLHLVLRLRGGMQIF VKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI

Finally look for AGK in trypsin fragments and it is LIFAGK. Look for LIF in chymotrypsin fragments and it is IPPDQQRLIF.

Hence the answer is IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLDVEPSDTEIN-VKAKIQDKEGI

gladiator answered 1 year ago

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