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Commit c5eea95a authored by Nicolas MAILLET's avatar Nicolas MAILLET
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Properly define P1 P1' etc

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...@@ -7,6 +7,10 @@ All default available enzymes (`enzymes_definition.py`) are listed bellow. ...@@ -7,6 +7,10 @@ All default available enzymes (`enzymes_definition.py`) are listed bellow.
For each of them, there is the equivalent in `RPG` grammar. For each of them, there is the equivalent in `RPG` grammar.
On the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. According to it, amino acids before the cleavage site are designated as `P1`, `P2`, `P3`, etc in the N-terminal direction, and as `P1'`, `P2'`, `P3'`, etc in the C-terminal direction. For example, with cleavage site represented as '|'::
...P3-P2-P1-|-P1'-P2'-P3'...
----------------- -----------------
Available enzymes Available enzymes
----------------- -----------------
...@@ -29,7 +33,7 @@ Available enzymes ...@@ -29,7 +33,7 @@ Available enzymes
Arg-C Arg-C
..... .....
Arg-C proteinase proteinase preferentially cleaves after R Arg-C proteinase proteinase preferentially cleaves after R (`P1`)
**RPG definition:** **RPG definition:**
...@@ -47,7 +51,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC ...@@ -47,7 +51,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
Asp-N Asp-N
..... .....
Asp-N Sequencing Grade preferentially cleaves before C or D Asp-N Sequencing Grade preferentially cleaves before C or D (`P1'`)
**RPG definition:** **RPG definition:**
...@@ -65,7 +69,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu- ...@@ -65,7 +69,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-
BNPS-Skatole BNPS-Skatole
............ ............
BNPS-Skatole preferentially cleaves after W BNPS-Skatole preferentially cleaves after W (`P1`)
**RPG definition:** **RPG definition:**
...@@ -83,7 +87,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS ...@@ -83,7 +87,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
Caspase 1 Caspase 1
......... .........
Caspase 1 preferentially cleaves after D preceded by H, A or T in `P2` and preceded by F, W, Y or L in `P4`. It will not cleave if D is followed by P, E, D, Q ,K or R Caspase 1 preferentially cleaves after D (`P1`) preceded by H, A or T in `P2` and preceded by F, W, Y or L in `P4`. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -105,7 +109,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1 ...@@ -105,7 +109,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
Caspase 2 Caspase 2
......... .........
Caspase 2 preferentially cleaves after D preceded by DVA or DEH. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 2 preferentially cleaves after D (`P1`) preceded by DVA or DEH. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -129,7 +133,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2 ...@@ -129,7 +133,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
Caspase 3 Caspase 3
......... .........
Caspase 3 preferentially cleaves after D preceded by DMQ or DEV. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 3 preferentially cleaves after D (`P1`) preceded by DMQ or DEV. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -153,7 +157,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3 ...@@ -153,7 +157,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
Caspase 4 Caspase 4
......... .........
Caspase 4 preferentially cleaves after D preceded by LEV or (W/L)EH. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 4 preferentially cleaves after D (`P1`) preceded by LEV or (W/L)EH. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -177,7 +181,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4 ...@@ -177,7 +181,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
Caspase 5 Caspase 5
......... .........
Caspase 5 preferentially cleaves after D preceded by (W/L)EH. Caspase 5 preferentially cleaves after D (`P1`) preceded by (W/L)EH.
**RPG definition:** **RPG definition:**
...@@ -195,7 +199,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5 ...@@ -195,7 +199,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
Caspase 6 Caspase 6
......... .........
Caspase 6 preferentially cleaves after D preceded by VEI or VEH. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 6 preferentially cleaves after D (`P1`) preceded by VEI or VEH. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -217,7 +221,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6 ...@@ -217,7 +221,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
Caspase 7 Caspase 7
......... .........
Caspase 7 preferentially cleaves after D preceded by DEV. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 7 preferentially cleaves after D (`P1`) preceded by DEV. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -239,7 +243,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7 ...@@ -239,7 +243,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
Caspase 8 Caspase 8
......... .........
Caspase 8 preferentially cleaves after D preceded by (I/L)ET. It will not cleave if D is followed by P, E, D, Q ,K or R. Caspase 8 preferentially cleaves after D (`P1`) preceded by (I/L)ET. It will not cleave if D is followed by P, E, D, Q ,K or R in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -261,7 +265,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8 ...@@ -261,7 +265,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
Caspase 9 Caspase 9
......... .........
Caspase 9 preferentially cleaves after D preceded by LEH. Caspase 9 preferentially cleaves after D (`P1`) preceded by LEH.
**RPG definition:** **RPG definition:**
...@@ -279,7 +283,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9 ...@@ -279,7 +283,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
Caspase 10 Caspase 10
.......... ..........
Caspase 10 preferentially cleaves after D preceded by IEA. Caspase 10 preferentially cleaves after D (`P1`) preceded by IEA.
**RPG definition:** **RPG definition:**
...@@ -297,7 +301,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10 ...@@ -297,7 +301,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
Chymotrypsin high specificity Chymotrypsin high specificity
............................. .............................
This chymotrypsin preferentially cleaves after F, Y or W if not followed by P. It will not cleave after W followed by M. This chymotrypsin preferentially cleaves after F, Y or W (`P1`) if not followed by P in `P1'`. It will not cleave after W followed by M in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -320,7 +324,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym ...@@ -320,7 +324,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
Chymotrypsin low specificity Chymotrypsin low specificity
............................. .............................
This chymotrypsin preferentially cleaves after F, L, Y, W, M or H if not followed by P. It will not cleave after W followed by M. It will not cleave after M followed by Y. It will not cleave after H followed by D/M/W. This chymotrypsin preferentially cleaves after F, L, Y, W, M or H (`P1`) if not followed by P in `P1'`. It will not cleave after W followed by M in `P1'`. It will not cleave after M followed by Y in `P1'`. It will not cleave after H followed by D/M/W in `P1'`.
**RPG definition:** **RPG definition:**
...@@ -345,7 +349,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym ...@@ -345,7 +349,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
Clostripain Clostripain
........... ...........
Clostripain (Clostridiopeptidase B) preferentially cleaves after R. Clostripain (Clostridiopeptidase B) preferentially cleaves after R (`P1`).
**RPG definition:** **RPG definition:**
...@@ -363,7 +367,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost ...@@ -363,7 +367,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
CNBr CNBr
.... ....
CNBr preferentially cleaves after M. CNBr preferentially cleaves after M (`P1`).
**RPG definition:** **RPG definition:**
...@@ -381,7 +385,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr ...@@ -381,7 +385,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
Enterokinase Enterokinase
............ ............
Enterokinase preferentially cleaves after K preceded by D/E in `P2`, `P3`, `P4` and `P5`. Enterokinase preferentially cleaves after K (`P1`) preceded by D/E in `P2`, `P3`, `P4` and `P5`.
**RPG definition:** **RPG definition:**
...@@ -399,7 +403,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter ...@@ -399,7 +403,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
Factor Xa Factor Xa
......... .........
Factor Xa preferentially cleaves after R preceded by G in `P2`, D/E in `P3` and A/F/I/L/V/W/G/T in `P4`. Factor Xa preferentially cleaves after R (`P1`) preceded by G in `P2`, D/E in `P3` and A/F/I/L/V/W/G/T in `P4`.
**RPG definition:** **RPG definition:**
...@@ -417,7 +421,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa ...@@ -417,7 +421,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
Glu-C Glu-C
..... .....
Glu-C Sequencing Grade preferentially cleaves after D or E. Glu-C Sequencing Grade preferentially cleaves after D or E (`P1`).
**RPG definition:** **RPG definition:**
...@@ -435,7 +439,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu- ...@@ -435,7 +439,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-
Lys-C Lys-C
..... .....
LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K. LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K (`P1`).
**RPG definition:** **RPG definition:**
...@@ -452,7 +456,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -452,7 +456,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Lys-N Lys-N
..... .....
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K. LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'`).
**RPG definition:** **RPG definition:**
...@@ -469,7 +473,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -469,7 +473,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
NTCB NTCB
.... ....
NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C. NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C (`P1'`).
**RPG definition:** **RPG definition:**
...@@ -486,7 +490,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -486,7 +490,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Pepsin pH 1.3 Pepsin pH 1.3
............. .............
This pepsin preferentially cleaves around F or L. It will not cleave before F or L followed by P. It will not cleave before F or L preceded by R in `P2` or P in `P3` or H/K/R in `P4`. It will not cleave after F or L followed by P in `P2'`. It will not cleave after F or L preceded by P in `P2` or H/K/R in `P3`. This pepsin preferentially cleaves around F or L (`P1` or `P1'`). It will not cleave before F or L in `P1'` followed by P in `P2'`. It will not cleave before F or L in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F or L in `P1` followed by P in `P2'`. It will not cleave after F or L in `P1` preceded by P in `P2` or H/K/R in `P3`.
**RPG definition:** **RPG definition:**
...@@ -513,7 +517,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -513,7 +517,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Pepsin pH >=2 Pepsin pH >=2
............. .............
This pepsin preferentially cleaves around F, L, W or Y. It will not cleave before F, L, W or Y followed by P. It will not cleave before F, L, W or Y preceded by R in `P2` or P in `P3` or H/K/R in `P4`. It will not cleave after F, L, W or Y followed by P in `P2'`. It will not cleave after F, L, W or Y preceded by P in `P2` or H/K/R in `P3`. This pepsin preferentially cleaves around F, L, W or Y (`P1` or `P1'`). It will not cleave before F, L, W or Y in `P1'` followed by P in `P2'`. It will not cleave before F, L, W or Y in `P1'` preceded by R in `P1` or P in `P2` or H/K/R in `P3`. It will not cleave after F, L, W or Y IN `P1` followed by P in `P2'`. It will not cleave after F, L, W or Y in `P1` preceded by P in `P2` or H/K/R in `P3`.
**RPG definition:** **RPG definition:**
...@@ -540,7 +544,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -540,7 +544,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thrombin (PeptideCutter) Thrombin (PeptideCutter)
........................ ........................
This thrombin preferentially cleaves after R. Optimum cleavage is when R is preceded and followed by G. Cleavage also occurs when R is preceded by P in `P2` and A/F/I/L/V/W/G/T in `P3` and `P4`. It will not cleave after R followed by D/E in `P1'` or `P2'`. This thrombin preferentially cleaves after R (`P1`). Optimum cleavage is when R is preceded and followed by G (`P2` and `P1'`). Cleavage also occurs when R is preceded by P in `P2` and A/F/I/L/V/W/G/T in `P3` and `P4`. It will not cleave after R followed by D/E in `P1'` or `P2'`.
It not strictly coherent with the definition as differences exist in PeptideCutter between definition, summary and behavior of this enzyme. It not strictly coherent with the definition as differences exist in PeptideCutter between definition, summary and behavior of this enzyme.
...@@ -567,9 +571,9 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h ...@@ -567,9 +571,9 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thrombin Sequencing Grade Thrombin Sequencing Grade
......................... .........................
This thrombin preferentially cleaves after R preceded by P in `P2`, V in `P3` and L in `P4` and followed by G in `P1'` and S `P2'`. This thrombin preferentially cleaves after R (`P1`) preceded by P in `P2`, V in `P3` and L in `P4` and followed by G in `P1'` and S `P2'`.
This thrombin is defined in several kit (see links) This thrombin is defined in several kit (see below).
**RPG definition:** **RPG definition:**
...@@ -590,9 +594,7 @@ More informations: see thrombin cleavage kit of ...@@ -590,9 +594,7 @@ More informations: see thrombin cleavage kit of
Trypsin Trypsin
....... .......
Trypsin preferentially cleaves after K or R. It will not cleave after K followed by P in `P1'` except if W in `P2`. It will not cleave after R followed by P in `P1'` except if M in `P2`. It will not cleave CKD, DKD, CKH, CKY, CRK, RRH nor RRR Trypsin preferentially cleaves after K or R (`P1`). It will not cleave after K followed by P in `P1'` except if W in `P2`. It will not cleave after R followed by P in `P1'` except if M in `P2`. It will not cleave CKD, DKD, CKH, CKY, CRK, RRH nor RRR.
This thrombin is defined in several kit (see links)
**RPG definition:** **RPG definition:**
......
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