HOMEWORK#7

 

• David Liu, a student in 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 L C Y K M F M V A T P

  31 K V P V K R G C I D V C P K S S L L V K Y V C C N T D R 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 in multiple alignment form.

  (3) Please predict its secondary structure.

  (4) Please show its charge distribution.

   

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(1).Ans :

The Protein is CARDIOTOXIN III of TAIWAN COBRA.

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(2).Ans :

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(3).Ans : Secondary Structure :

60 aa; DCH = 0, DCS = 0

      1   .   10    .   20    .   30    .   40    .   50    .   60
      LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
helix H                 HHH     HHHH                              
sheet     EEEEEEEEE        EEEEE      E E  EEEEE    EEEEEEEE      
turns  TTT          TTTT            T  T TT     TTTT        TTTTTT
coil               C                 C                            

 H : helix 
 E : sheet 
 T : turns 
 C : coil  

 Residue totals: H:  8   E: 29   T: 21   C:  2
     percent(%): H: 18.2 E: 65.9 T: 47.7 C:  4.5 

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(4).Ans : Charge Distribution:

1  0+00+00000 0+00000+00 00+0000000 +000++000- 000+00000+ 000000-+00



CHARGE CLUSTERS.


Positive charge clusters (cmin = 13/30 or 18/45 or 22/60):  none

Negative charge clusters:  not evaluated (frequency of - < 5%, too low)

Mixed charge clusters (cmin = 15/30 or 20/45 or 25/60):  none