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

parent e861cb78
......@@ -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.
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
-----------------
......@@ -29,7 +33,7 @@ Available enzymes
Arg-C
.....
Arg-C proteinase proteinase preferentially cleaves after R
Arg-C proteinase proteinase preferentially cleaves after R (`P1`)
**RPG definition:**
......@@ -47,7 +51,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC
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:**
......@@ -65,7 +69,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-
BNPS-Skatole
............
BNPS-Skatole preferentially cleaves after W
BNPS-Skatole preferentially cleaves after W (`P1`)
**RPG definition:**
......@@ -83,7 +87,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS
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:**
......@@ -105,7 +109,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1
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:**
......@@ -129,7 +133,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2
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:**
......@@ -153,7 +157,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3
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:**
......@@ -177,7 +181,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4
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:**
......@@ -195,7 +199,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5
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:**
......@@ -217,7 +221,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6
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:**
......@@ -239,7 +243,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7
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:**
......@@ -261,7 +265,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8
Caspase 9
.........
Caspase 9 preferentially cleaves after D preceded by LEH.
Caspase 9 preferentially cleaves after D (`P1`) preceded by LEH.
**RPG definition:**
......@@ -279,7 +283,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9
Caspase 10
..........
Caspase 10 preferentially cleaves after D preceded by IEA.
Caspase 10 preferentially cleaves after D (`P1`) preceded by IEA.
**RPG definition:**
......@@ -297,7 +301,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10
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:**
......@@ -320,7 +324,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
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:**
......@@ -345,7 +349,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym
Clostripain
...........
Clostripain (Clostridiopeptidase B) preferentially cleaves after R.
Clostripain (Clostridiopeptidase B) preferentially cleaves after R (`P1`).
**RPG definition:**
......@@ -363,7 +367,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost
CNBr
....
CNBr preferentially cleaves after M.
CNBr preferentially cleaves after M (`P1`).
**RPG definition:**
......@@ -381,7 +385,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr
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:**
......@@ -399,7 +403,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter
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:**
......@@ -417,7 +421,7 @@ https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa
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:**
......@@ -435,7 +439,7 @@ https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-
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:**
......@@ -452,7 +456,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Lys-N
.....
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K.
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'`).
**RPG definition:**
......@@ -469,7 +473,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
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:**
......@@ -486,7 +490,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
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:**
......@@ -513,7 +517,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
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:**
......@@ -540,7 +544,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
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.
......@@ -567,9 +571,9 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
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:**
......@@ -590,9 +594,7 @@ More informations: see thrombin cleavage kit of
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
This thrombin is defined in several kit (see links)
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.
**RPG definition:**
......
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