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活性肽胃肠稳定性预测
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最近初学活性肽，要预测若干肽的胃肠稳定性。但对胃肠蛋白酶的酶解位点所知甚少，幸运的是，在peptide cutter找到了答案。通过Schechter和Berger（1967,1968）创建的模型来描述酶特异性酶解位点。根据该模型，将底物中氨基酸残基，以切割键为起点，沿N端方向依次命名为P1，P2，P3，P4等。 同样，将C端方向残基被命名为P1'，P2'，P3'，P4' 等（下图）。
蛋白酶特异性酶解规律来自Keil（1992），Barrett等人（1998）也验证了这些规律，最后网站给出汇总表如下。其中，胰凝乳蛋白酶（high specificity ）位点：F-|-x，Y-|-x（x不能是P）；W-|-x（x不能是M、P）。胃蛋白酶（pH 1.3）位点：x-y-F-|-x1-y1，x-y-L-|-x1-y1（x不能是H、K、R，或y不能是P，或y1不能是P）；x-y-z-F-|-z1，x-y-z-L-|-z1（x不能是H、K、R，或y不能是P，或z不能是R，或z1不能是P）。胰蛋白酶位点：K-|-x，R-|-x（x不能是P，但W-K-|-P和M-K-|-P可以被水解）；以下例外不能水解：C或D-K-|-D，C-K-|-H或Y，C-R-|-K，R-R-|-H或R。当然，也可以用peptide cutter在线酶解进行预测。
Enzyme name | P4 | P3 | P2 | P1 | P1' | P2' |
Arg-C proteinase | - | - | - | R | - | - |
Asp-N endopeptidase | - | - | - | - | D | - |
BNPS-Skatole | - | - | - | W | - | - |
Caspase 1 | F, W, Y, or L | - | H, A or T | D | not P, E, D, Q, K or R | - |
Caspase 2 | D | V | A | D | not P, E, D, Q, K or R | - |
Caspase 3 | D | M | Q | D | not P, E, D, Q, K or R | - |
Caspase 4 | L | E | V | D | not P, E, D, Q, K or R | - |
Caspase 5 | L or W | E | H | D | - | - |
Caspase 6 | V | E | H or I | D | not P, E, D, Q, K or R | - |
Caspase 7 | D | E | V | D | not P, E, D, Q, K or R | - |
Caspase 8 | I or L | E | T | D | not P, E, D, Q, K or R | - |
Caspase 9 | L | E | H | D | - | - |
Caspase 10 | I | E | A | D | - | - |
Chymotrypsin-high specificity (C-term to [FYW], not before P) | - | - | - | F or Y | not P | - |
- | - | - | W | not M or P | - | |
Chymotrypsin-low specificity (C-term to [FYWML], not before P) | - | - | - | F,L or Y | not P | - |
- | - | - | W | not M or P | - | |
- | - | - | M | not P or Y | - | |
- | - | - | H | not D,M,P or W | - | |
Clostripain (Clostridiopeptidase B) | - | - | - | R | - | - |
CNBr | - | - | - | M | - | - |
Enterokinase | D or E | D or E | D or E | K | - | - |
Factor Xa | A,F,G,I,L,T,V or M | D or E | G | R | - | - |
Formic acid | - | - | - | D | - | - |
Glutamyl endopeptidase | - | - | - | E | - | - |
GranzymeB | I | E | P | D | - | - |
Hydroxylamine | - | - | - | N | G | - |
Iodosobenzoic acid | - | - | - | W | - | - |
LysC | - | - | - | K | - | - |
Neutrophil elastase | - | - | - | A or V | - | - |
NTCB (2-nitro-5-thiocyanobenzoic acid) | - | - | - | - | C | - |
Pepsin (pH1.3) | - | not H,K, or R | not P | not R | F or L | not P |
- | not H,K, or R | not P | F or L | - | not P | |
Pepsin (pH>2) | - | not H,K or R | not P | not R | F,L,W or Y | not P |
- | not H,K or R | not P | F,L,W or Y | - | not P | |
Proline-endopeptidase | - | - | H,K or R | P | not P | - |
Proteinase K | - | - | - | A,E,F,I,L,T,V,W or Y | - | - |
Staphylococcal peptidase I | - | - | not E | E | - | - |
Thermolysin | - | - | - | not D or E | A,F,I,L,M or V | - |
Thrombin | - | - | G | R | G | - |
A,F,G,I,L,T,V or M | A,F,G,I,L,T,V,W or A | P | R | not D or E | not DE | |
Trypsin (注意例外) | - | - | - | K or R | not P | - |
- | - | W | K | P | - | |
- | - | M | R | P | - | |
Enzyme name | P4 | P3 | P2 | P1 | P1' | P2' |
例外：
Enzyme name | P4 | P3 | P2 | P1 | P1' | P2' |
Trypsin | - | - | C or D | K | D | - |
- | - | C | K | H or Y | - | |
- | - | C | R | K | - | |
- | - | R | R | H or R | - |
References
Schechter I. & Berger A. On the size of the active site in proteases. I. Papain. Biochemical and Biophysical Research Communication (1967) 27: 157.
Schechter I. & Berger A. On the active site of proteases. 3. Mapping the active site of papain; specific peptide inhibitors of papain. Biochemical and Biophysical Research Communication (1968) 32: 898.
Keil, B. Specificity of proteolysis. Springer-Verlag Berlin-Heidelberg-NewYork (1992)
Barrett A., Rawlings N.D., Woessner J.F. Handbook of proteolytic enzymes. Academic Press (1998)
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