diff --git a/docs/enzymes.rst b/docs/enzymes.rst index 6635b6ab66160232666a02fbdf36b246b3533cf3..513e8637de4dfb4ce0fe93dd29feebdfa929c99d 100644 --- a/docs/enzymes.rst +++ b/docs/enzymes.rst @@ -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:**