HOMEWORK#9

Sequence comparison / model building

• due on 6/2

• 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.

    Yes, it is a new toxin.  The given amino acid sequence resembles Cardiotoxin 3 from Taiwan Cobra but differs at four positions [(I20L),(L32V),(R50K),(K58R)].

pir||H3NJ3F cytotoxin 3 - Chinese cobra >pir||JK0222 cytotoxin 10 - monocled
            cobra >pir||B40667 cardiotoxin isoform 3, cytotoxin isoform 3,
            CTX-3 - Naja naja >bbs|127032 cardiotoxin isoform 3, cytotoxin
            isoform 3, CTX-3 [Naja naja=Formosan cobra, ssp. atra, venom,
            Peptide, 60 aa] >pdb|2CRS|   Cardiotoxin Iii (Nmr, 13 Structures)
            >pdb|2CRT|   Cardiotoxin Iii (Nmr, Minimized Average Structure)
            >prf||0406231A toxin,cardio [Naja atra]
            Length = 60

 Score = 329 (156.6 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 56/60 (93%), Positives = 60/60 (100%)

Query:
   1LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN60
   LKCNKLVPLFYKTCPAGKN+CYKMFMVATPK+PVKRGCIDVCPKSSLLV+YVCCNTD+CN
Sbjct:
  1LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN60
 
 

(2) Can you find proteins that share sequence homology with this toxin? Show them (at least 10 sequences) in multiple alignment form (in color).
 There are umpteem number proteins having sequence homology with this toxin.
Among that 10 sequences were taken and Clustlaw is used to show multiple alignment. Due to heavy rush in Biology Work Bench, that site is not utlized.

The alignment  

(3) He would like to see 3D structure of this toxin. Please help him to make the model.

 

 The structure of the given amino acid sequnce is very differ from that of CTX III, having a alpha helix at C terminal and a broken beta sheet.