@@ -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'...
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Available enzymes
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@@ -29,7 +33,7 @@ Available enzymes
Arg-C
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Arg-C proteinase proteinase preferentially cleaves after R
Arg-C proteinase proteinase preferentially cleaves after R (`P1`)
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'`.
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'`.
LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K.
LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K (`P1`).
**RPG definition:**
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@@ -452,7 +456,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Lys-N
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LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K.
LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'`).
**RPG definition:**
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@@ -469,7 +473,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
NTCB
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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:**
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@@ -486,7 +490,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Pepsin pH 1.3
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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:**
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@@ -513,7 +517,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Pepsin pH >=2
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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:**
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@@ -540,7 +544,7 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thrombin (PeptideCutter)
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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.
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@@ -567,9 +571,9 @@ More informations: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.h
Thrombin Sequencing Grade
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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:**
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@@ -590,9 +594,7 @@ More informations: see thrombin cleavage kit of
Trypsin
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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.
