821605 homework 5

MOS Homework 5


* David Liu, a student in department of Life Sciences, got bit 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. 
View Answer <1>
(2) Can you find proteins that share sequence homology with this toxin?

Show them in multiple alignment form. 
 View Answer <2>

(3) Please predict its secondary structure. 
View Answer <3>

(4) Please show its charge distribution.
View Answer <4>

ANS

(1) Toxin Identification

The toxin was searched by NCSA Biology Workbench. The sequence is not a new protein. It has 100% homology with

Q02454 cardiotoxin precursor(from genebank)
P01444 cytotoxin 3 precusor(from genebank)
2CRS and 2CRT cardiotoxin(from pdbbank)

The toxin is cardiotoxin III, from Taiwan cobra venom. It has 60 residues. The figure is 2CRT from PDB .

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(2) Use the sequence find several proteins that share sequece homology from PIR databank. Most of them are cardiotoxin or cytotoxin.
View sequences alignment

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(3) Predict its secondary structure by GARNIER and ChOFAS

Chou-Fasman plot of toxin

 60 aa;                .         .         .         .         .         .
       LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
 helix <--------->        <------------->       <-------->
 sheet     EEEEEEEEE      EEEEEEEEEE        EEEE     EEEEEEEEE
 turns                  T           T     T       TT



 helix
 sheet
 turns

 Residue totals: H: 36   E: 32   T:  5
        percent: H: 60.0 E: 53.3 T:  8.3

Garnier plot of toxin

 60 aa; DCH = 0, DCS = 0

           .   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



 helix
 sheet
 turns
 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) View its charge distribution by SAPS CHARGE DISTRIBUTIONAL ANALYSIS

           0+00+00000 0+00000+00 00+0000000  +000++000-  000+00000+ 000000-+00
           LKCNKLVPLF YKTCPAGKNL CYKMFMVATP KVPVKRGCID VCPKSSLLVK  YVCCNTDRCN
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

B. HIGH SCORING (UN)CHARGED SEGMENTS.

______________________________________
High scoring positive charge segments:

score=   2.00 frequency=   0.183  ( KR )
score=   0.00 frequency=   0.000  ( BZX )
score=  -1.00 frequency=   0.783  ( LAGSVTIPNFQYHMCW )
score=  -2.00 frequency=   0.033  ( ED )

 Expected score/letter:  -0.483
 - now scoring for positive charge segments;    Average information/letter:   0.430
 Minimal length of displayed segments set to:  20

M_0.01= 13.07  (cv=  7.77, lambda=  0.52686, k=  0.16371, x=  5.30;
                90% confidence interval for segment length:  23 +-  25)
M_0.05=  9.97  (x=  2.20)

# of segments (>=20 residues) exceeding M_0.05: none

______________________________________
High scoring negative charge segments:

score=   2.00 frequency=   0.033  ( ED )
score=   0.00 frequency=   0.000  ( BZX )
score=  -1.00 frequency=   0.783  ( LAGSVTIPNFQYHMCW )
score=  -2.00 frequency=   0.183  ( KR )

 Expected score/letter:  -1.083
 - now scoring for negative charge segments;    Average information/letter:   3.490
 Minimal length of displayed segments set to:  20

M_0.01=  4.94  (cv=  2.54, lambda=  1.61122, k=  0.47671, x=  2.40;
                90% confidence interval for segment length:   3 +-   3)
M_0.05=  3.92  (x=  1.38)

# of segments (>=20 residues) exceeding M_0.05: none

___________________________________
High scoring mixed charge segments:

score=   1.00 frequency=   0.217  ( KEDR )
score=   0.00 frequency=   0.000  ( BZX )
score=  -1.00 frequency=   0.783  ( LAGSVTIPNFQYHMCW )

 Expected score/letter:  -0.567
 - now scoring for mixed charge segments;    Average information/letter:   1.051
 Minimal length of displayed segments set to:  20

M_0.01=  6.07  (cv=  3.19, lambda=  1.28520, k=  0.40993, x=  2.89;
                90% confidence interval for segment length:  11 +-   9)
M_0.05=  4.80  (x=  1.62)

# of segments (>=20 residues) exceeding M_0.05: none

________________________________
High scoring uncharged segments:

score=   1.00 frequency=   0.783  ( LAGSVTIPNFQYHMCW )
score=   0.00 frequency=   0.000  ( BZX )
score=  -8.00 frequency=   0.217  ( KEDR )

 Expected score/letter:  -0.950
 - now scoring for uncharged segments;    Average information/letter:   0.173
 Minimal length of displayed segments set to:  20

M_0.01= 32.53  (cv= 20.56, lambda=  0.19916, k=  0.10900, x= 11.97;
                90% confidence interval for segment length:  54 +-  44)
M_0.05= 24.34  (x=  3.79)

# of segments (>=20 residues) exceeding M_0.05: none

C. CHARGE RUNS AND PATTERNS.

pattern  (+)|  (-)|  (*)|  (0)| (+0)| (-0)| (*0)|(+00)|(-00)|(*00)|
lmin0     5 |   3 |   6 |  29 |  10 |   6 |  10 |  11 |   6 |  12 |
lmin1     6 |   4 |   7 |  36 |  12 |   7 |  12 |  14 |   8 |  14 |
lmin2     7 |   4 |   8 |  39 |  13 |   8 |  14 |  15 |   9 |  16 |

There are no charge runs or patterns exceeding the given minimal lengths.

Run count statistics:

  +  runs >=   3:   0
  -  runs >=   3:   0
  *  runs >=   4:   0
  0  runs >=  20:   0

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