Homework9

1.這不是一個新的toxin，在ScanProsite下輸入這個toxin的sequence，即可得到 兩筆資料，其中一筆是關於蛇毒蛋白的，其相關資料如下：

Snake toxins signature --- 37-57 GCIDVCPKSSLLVRYVCCNTD

  1. Snake toxins belong to a family of proteins [1,2,3] which groups short
     and long neurotoxins, cytotoxins and short toxins, as well as a other
     miscellanous venom peptides.  Most of these toxins act by binding to 
     the nicotinic acetylcholine receptors in the postsynaptic membrane of
     skeletal muscles and prevent the  binding of acetylcholine, thereby 
     blocking the excitation of muscles.

  2. Snake toxins are proteins that consist of sixty to seventy five amino 
     acids.  Among the invariant residues are eight cysteines all involved 
     in disulfide bonds. A signature pattern was developed [4] which 
     includes our of these cysteines as well as a conserved proline thought
     to be important for the maintenance of the tertiary structure.   
     The second cysteine in the pattern is linked to the third one by a 
     disulfide bond.
2.理論上multiple sequence alignment應該是在workbench完成的，但是由於網路
速度過慢，再加上一試再試（先辛辛苦苦地將由BLAST查到的前十個homology最高的
protein sequence丟到work bench）試遍protein tool中的multiple sequence 
alignment，以及alignment tool中的所有功能，仍無法找到multiple alignment的方
法，所以只好靠著做電燈泡的精神，以手工方式完成此十一個sequence的比對，其結
果如下︰

LKCNKLVPLFYKTCPAGKNICYKMFMVATPKLPVKRGCIDVCPKSSLLVRYVCCNTDKCN 



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKNSLLVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSALVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMYMVATPKVPVKRGCIDVCPKSSLVLKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGRIDVCPKSSLLVKYVCCNTDRCN



LKCNKLIPIASKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN



LKCNKLIPLAYKTCPAGKNLCYKMFMVAAPKVPVKRGCIDACPKNSLLVKYVCCNTDRCN



LKCNKLVPLFYKTCPAGKNLCYKMFMVSNKMVPVKRGCIDVCPKSSLLVKYVCCNTDRCN

在我們想要比對的十個protein sequence中，藍色的residue表示positive（polarity 
or charge similarity），紅色的residue表示完全不相同的residue。


3.在swiss-prot將此protein sequence寄出後第二天，即可得到他們model出來的toxin
3D structure data，存成pdb檔後，即可利用rasmol得到其3D structure如下圖︰