HOMEWORK#5

Sequence comparison / Homology search

• due on 12/17

• Shirley Lee, a student in department of Life Sciences, was bitten by a snake in the backyard of life science building. She was so angry! Thus, she killed the snake and purified several toxins from its venoms. She 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.

  (1)Answer:No,it is not a new toxin.It is the cytotoxin 3 of Chinese Cobra.

  (2) Can you find proteins that share sequence homology with this toxin? Show them in multiple alignment form.

  (2)Answer:

  (3) Please predict its secondary structure.

  (3)Answer:The secondary sturcture is in the following:

  
         The predic secondary structure is

            .   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                            

  
  

  (4) Please show its charge distribution.

  (4)Answer:

  CHARGE DISTRIBUTIONAL ANALYSIS
   
         1  0+00+00000 0+00000+00 00+0000000 +000++000- 000+00000+ 000000-+00
  
  A. 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