Homework 5

(1) No, it is not a new toxin, because the sequence can be found in the
protein~~~ Cardiotoxin iii (100% fit), and there are two kinds of it,
which are showed below:
2crs (NMR 13 structures)

2crt (minimized average structure)
(2) Here are the proteins which have the similar sequence with the toxin :
Cardiotoxin iii (NMR minimized average structure)
Cardiotoxin iii (NMR 13 structures)
Cardiotoxin ii (NMR 12 structures)
Cardiotoxin ii (NMR minimized average structure)
Cardiotoxin ctx i (NMR 11 structures)
Cardiotoxin v=4===II== (toxin III)
Cardiotoxin gamma (NMR minimized average structure)
Toxin gamma (cardiotoxin)
Cardiotoxin v=4===II== (toxin III)
Toxin gamma (cardiotoxin) 

@The toxin's sequence:
LKCNKLVPLFYKTCPAGKNLCYKMFMVA--KVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
@2CRT__:
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
@2CRS__:
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
@1CRF__:
LKCNKLVPLFYKTCPAGKNLCYKMFMVSNLTVPVKRGCIDVCPKNSALVKYVCCNTDRCN
@1CRE__:
LKCNKLVPLFYKTCPAGKNLCYKMFMVSNLTVPVKRGCIDVCPKNSALVKYVCCNTDRCN
@2CDX__:
LKCNKLIPIASKTCPAGKNLCYKMFMMSDLTIPVKRGCIDVCPKNSLLVKYVCCNTDRCN
@1CDT_A:
LKCNKLIPIAYKTCPEGKNLCYKMMLASKKMVPVKRGCINVCPKNSALVKYVCCSTDRCN
@1CXN__:
LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN
@1TGX_A:
LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN
@1CDT_B:
LKCNKLIPIAYKTCPEGKNLCYKMMLASKKMVPVKRGCINVCPKNSALVKYVCCSTDRCN
@1TGX_C:
LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN
(3) secondary structure (toxin and cardiotoxin iii ~~2crt) :
1.Garnier plot of toxin
     58 aa; DCH = 0, DCS = 0
            .   10    .   20    .   30    .   40    .   50
       LKCNKLVPLFYKTCPAGKNLCYKMFMVAKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
 helix H                 HHHHHHHHHHHHH                           
 sheet     EEEEEEEEE                      EEEEE    EEEEEEEE      
 turns  TTT          TTTT             TTTT     TTTT        TTTTTT
 coil               C                                            

 Residue totals: H: 14   E: 22   T: 21   C:  1
        percent: H: 33.3 E: 52.4 T: 50.0 C:  2.4
2.Garnier plot of Cardiotoxin iii (NMR, minimized average structure)
     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
(4) 
   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

B. HIGH SCORING (UN)CHARGED SEGMENTS.