Homework #5

--Sequence comparison/Homology Search--

1.

 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:

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

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 in multiple alignment form.
  3. Please predict its secondary structure.
  4. Please show its charge distribution.
  1. BLASTP and PDB protein is used to find proteins sharing homology with the unknow sequence.
    One of the results is shown :

      
Accession: pdb|CARDIOTOXIN|2CRS__  Cardiotoxin iii (NMR, 13 structures)
         pdb|CARDIOTOXIN|2CRS__  Cardiotoxin iii (NMR, 13 structures)
                                             
Length = 60
Score = 329 (158.8 bits)
Expect = 1.5e-44
P = 1.5e-44
Identities = 56/60 (93%)
Positives = 60/60 (100%)
Query:   1 LKCNKLVPLFYKTCPAGKNICYKMFMVATP
           LKCNKLVPLFYKTCPAGKN+CYKMFMVATP
Subject: 1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATP
           
           KLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 60
           K+PVKRGCIDVCPKSSLLV+YVCCNTD+CN
           KVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
    So it is a new toxin!

  2. MSASHADE is used to find the homology of 5 candicates.
    The result is shown as

  3. GARNIER(GOR1) is used to predict the secondary stucture of the protein in question.
    The result is shown as 
    
Garnier plot of toxin
 60 aa; DCH = 0, DCS = 0
 
           .   10    .   20    .   30    .   40    .   50    .   60
       LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN
 helix H                         HHHH                              
 sheet     EEEEEEEEE      EEEEEEE           EEEEE    EEEEEEE       
 turns  TTT          TTTTT           T TTTTT     TTTT       TTTTTTT
 coil               C                 C                            


 Residue totals: H:  5   E: 28   T: 25   C:  2
        percent: H: 11.4 E: 63.6 T: 56.8 C:  4.5

  4. SAPS is used to find the charge distribution of the protein in quetion.
    The result is shown as 
    
CHARGE DISTRIBUTIONAL ANALYSIS
 
    0+00+00000  0+00000+00  00+0000000 
    LKCNKLVPLF  YKTCPAGKNI  CYKMFMVATP

    +000++000-  000+00000+  000000-+00
    KLPVKRGCID  VCPKSSLLVR  YVCCNTDKCN

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

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