HOMEWORK#8

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* David Liu, same guy from last homework, also isolated a cDNA clone from snake venom library. The nucleotide sequence of this cDNA clone is shown here:

AAAACCATCAAATATGTTATGCTGGAATGCAACGAACTGATCCCGCTGTTC

TACGAAACCTGCCCGGCTGGTGAAAACATCTGCTACGAAATGTTCATGGTT

GCTACCCCGAAAGTTCCGTGCGAACGTGGTTGCATCGACGTTTGCCCGGAA

TCTTCTCTGATCGTTAAATACGTTTGCTGCAACACCGACCGTTGCCAGTAAT

CCAGCGCCTGATCTCTCGAAATAAAAGCCGCATTG

(1) Please help him to find its corresponding polypeptide sequence (DNA -> Protein translation).

MLECNELIPL FYETCPAGEN ICYEMFMVAT PKVPCERGCI DVCPESSLIVKYVCCNTDRCQ

(2) Please help him to calculate pI/Mw of this polypeptide,perform the trypsin cutting , analyze the cutting pattern and report the fragments with molecular weight over 500 Dalton.

MLECNELIPL FYETCPAGEN ICYEMFMVAT PKVPCERGCIDVCPESSLIVKYVCCNTDRCQ

Molecular weight: 6917.13

Theoretical pI: 4.29

3699.66 1- 32 MLECNELIPLFYETCPAGENICYEMFMVATPK

1462.73 38- 51 GCIDVCPESSLIVK

973.39 52- 59 YVCCNTDR

603.29 33- 37 VPCER

(3) Please help him to identify this toxin. Is it a new toxin?

The most relative sequence:

Score = 296 (142.8 bits), Expect = 2.8e-38, P = 2.8e-38

Identities = 48/59 (81%), Positives = 58/59 (98%)

Query: 2 LECNELIPLFYETCPAGENICYEMFMVATPKVPCERGCIDVCPESSLIVKYVCCNTDRC 60

L+CN+L+PLFY+TCPAG+N+CY+MFMVATPKVP +RGCIDVCP+SSL+VKYVCCNTDRC

22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRC80

Not identify!

I think it is a new toxin.

(4) Please help him to use Prosite scanning tool to find out possible functions or pattern of this polypeptide.

1 PDOC00005 PS00005 PKC_PHOSPHO_SITE (Protein kinase C phosphorylation site)

Number of matches: 2

1 30-32 TPK

2 57-59 TDR

2 PDOC00245 PS00272 SNAKE_TOXIN (Snake toxins signature)

38-58 GCIDVCPESSLIVKYVCCNTD

(5) David would like to see its structure. Could you help him to find structure of this toxin or make a model if it is a new protein? Show structure on your homwpage ( 3 different views).