Homework 9
Mac Lee, a student in the department of Life Sciences, was bitten by a snake in the backyard of life science building. He was so angry! Thus, he killed the snake and purified several toxins from its venoms. He sequenced one of the toxin, got this sequence:
1 L K C N K L V P L F Y K T C P A G K N I C Y K M F M V A T P
31 K L P V K R G C I D V C P K S S L L V R Y V C C N T D K C N
(1) Is this a new toxin? Please help him to identify this toxin.
(2) Can you find proteins that share sequence homology with this toxin? Show them (at least 10 sequences) in multiple alignment form (in color).
(3) He would like to see 3D structure of this toxin. Please help him to make the model.
Answer
1.Using Basic BLAST of NCBI, we find scores of cytotoxin 3 - Chinese cobra, CYTOTOXIN 3 PRECURSOR (CARDIOTOXIN ANALOGUE III) (CTX III) (CARDIOTOXIN C-10) (CYTOTOXIN IV) and CARDIOTOXIN PRECURSOR are hightest. But their identities are 93%. Maybe it is a new protein. Click here to get more informations.
2.We use biological workbench to search the protein that share sequence homology with the toxin. Using protein information resource(PIR) as our databse and the all values are setted default, we find the result show below:
.
3.I send the amino acid sequence to SWISS-MODEL, and use RasMol tool to show 3-D structure.
