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活性肽胃肠稳定性预测

已有 1484 次阅读 2018-9-23 14:49 |系统分类:科研笔记

        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)。

image.png

        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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