.. _enzymes: ================== Enzyme definitions ================== All default available enzymes (`enzymes_definition.py`) are listed bellow. For each of them, there is the equivalent in `RPG` grammar. In the following, nomenclature of `Schechter and Berger `_ is used. 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 '|': .. code-block:: none ...P3-P2-P1-|-P1'-P2'-P3'... In **RPG**, this nomenclature is represented as: .. code-block:: none ...(P3)(P2)(P1)(,)(P1')(P2')(P3')... ----------------- Available enzymes ----------------- ================== ================== ================== 1: :ref:`arg-c` 2: :ref:`asp-n` 3: :ref:`bnps` 4: :ref:`brom` 5: :ref:`casp1` 6: :ref:`casp2` 7: :ref:`casp3` 8: :ref:`casp4` 9: :ref:`casp5` 10: :ref:`casp6` 11: :ref:`casp7` 12: :ref:`casp8` 13: :ref:`casp9` 14: :ref:`casp10` 15: :ref:`chymh` 16: :ref:`chyml` 17: :ref:`clost` 18: :ref:`cnbr` 19: :ref:`enter` 20: :ref:`fxa` 21: :ref:`ficin` 22: :ref:`form` 23: :ref:`gluc` 24: :ref:`glue` 25: :ref:`gran` 26: :ref:`hydro` 27: :ref:`iodo` 28: :ref:`lysc` 29: :ref:`lysn` 30: :ref:`neut` 31: :ref:`ntcb` 32: :ref:`pap` 33: :ref:`peps13` 34: :ref:`peps2` 35: :ref:`prol` 36: :ref:`protk` 37: :ref:`staphI` 38: :ref:`therm` 39: :ref:`throm` 40: :ref:`thromsg` 41: :ref:`tev` 42: :ref:`tryps` 43: :ref:`asp-n2` 44: :ref:`proa` 45: :ref:`elast` 46: :ref:`alp` ================== ================== ================== .. _arg-c: Arg-C ..... Arg-C proteinase preferentially cleaves after R (`P1`) **RPG definition:** cleaving rule: * ``(R,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ArgC .. _asp-n: Asp-N ..... Asp-N Sequencing Grade preferentially cleaves before C or D (`P1'` ) **RPG definition:** cleaving rule: * ``(,C or D)`` More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/ .. _bnps: BNPS-Skatole ............ BNPS-Skatole preferentially cleaves after W (`P1`) **RPG definition:** cleaving rule: * ``(W,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#BNPS .. _brom: Bromelain ......... Bromelain preferentially cleaves after K, A or Y (`P1`) **RPG definition:** cleaving rule: * ``(K or A or Y,)`` More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410479 .. _casp1: Caspase 1 ......... 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:** cleaving rule: * ``(F or W or Y or L)()(H or A or T)(D,)`` exception rule: * ``(F or W or Y or L)()(H or A or T)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp1 .. _casp2: Caspase 2 ......... 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:** cleaving rules: * ``(D)(V)(A)(D,)`` * ``(D)(E)(H)(D,)`` exception rules: * ``(D)(V)(A)(D,)(P or E or D or Q or K or R)`` * ``(D)(E)(H)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp2 .. _casp3: Caspase 3 ......... 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:** cleaving rules: * ``(D)(M)(Q)(D,)`` * ``(D)(E)(V)(D,)`` exception rules: * ``(D)(M)(Q)(D,)(P or E or D or Q or K or R)`` * ``(D)(E)(V)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp3 .. _casp4: Caspase 4 ......... 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:** cleaving rules: * ``(L)(E)(V)(D,)`` * ``(W or L)(E)(H)(D,)`` exception rules: * ``(L)(E)(V)(D,)(P or E or D or Q or K or R)`` * ``(W or L)(E)(H)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp4 .. _casp5: Caspase 5 ......... Caspase 5 preferentially cleaves after D (`P1`) preceded by (W/L)EH. **RPG definition:** cleaving rule: * ``(W or L)(E)(H)(D,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp5 .. _casp6: Caspase 6 ......... 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:** cleaving rule: * ``(V)(E)(I or H)(D,)`` exception rule: * ``(V)(E)(I or H)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp6 .. _casp7: Caspase 7 ......... 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:** cleaving rule: * ``(D)(E)(V)(D,)`` exception rule: * ``(D)(E)(V)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp7 .. _casp8: Caspase 8 ......... 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:** cleaving rule: * ``(I or L)(E)(T)(D,)`` exception rule: * ``(I or L)(E)(T)(D,)(P or E or D or Q or K or R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp8 .. _casp9: Caspase 9 ......... Caspase 9 preferentially cleaves after D (`P1`) preceded by LEH. **RPG definition:** cleaving rule: * ``(L)(E)(H)(D,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp9 .. _casp10: Caspase 10 .......... Caspase 10 preferentially cleaves after D (`P1`) preceded by IEA. **RPG definition:** cleaving rule: * ``(I)(E)(A)(D,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Casp10 .. _chymh: Chymotrypsin high specificity ............................. 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:** cleaving rule: * ``(F or Y or W,)`` exception rules: * ``(F or Y or W,)(P)`` * ``(W,)(M)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym .. _chyml: Chymotrypsin low specificity ............................. 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:** cleaving rule: * ``(F or L or Y or W or M or H,)`` exception rules: * ``(F or L or Y or W or M or H,)(P)`` * ``(W,)(M)`` * ``(M,)(Y)`` * ``(H,)(D or M or W)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Chym .. _clost: Clostripain ........... Clostripain (Clostridiopeptidase B) preferentially cleaves after R (`P1`). **RPG definition:** cleaving rule: * ``(R,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Clost .. _cnbr: CNBr .... CNBr preferentially cleaves after M (`P1`). **RPG definition:** cleaving rule: * ``(M,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#CNBr .. _enter: Enterokinase ............ Enterokinase preferentially cleaves after K (`P1`) preceded by D/E in `P2`, `P3`, `P4` and `P5`. **RPG definition:** cleaving rule: * ``(D or E)(D or E)(D or E)(D or E)(K,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Enter .. _fxa: Factor Xa ......... 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:** cleaving rule: * ``(A or F or I or L or V or W or G or T)(D or E)(G)(R,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Xa .. _ficin: Ficin ..... Ficin preferentially cleaves after G, S, E or Y (`P1`) preceded by A, V, I, L ,F, Y or W in `P2`. **RPG definition:** cleaving rule: * ``(A or V or I or L or F or Y or W)(G or S or E or Y,)`` More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410578 .. _form: Formic acid ........... Formic acid preferentially cleaves after D (`P1`). **RPG definition:** cleaving rule: * ``(D,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#HCOOH .. _gluc: Glu-C ..... Glu-C Sequencing Grade preferentially cleaves after D or E (`P1`). **RPG definition:** cleaving rule: * ``(D or E,)`` More information: https://france.promega.com/resources/pubhub/using-endoproteinases-asp-n-and-glu-c-to-improve-protein-characterization/ .. _glue: Glutamyl endopeptidase ...................... Glutamyl endopeptidase preferentially cleaves after E (`P1`). **RPG definition:** cleaving rule: * ``(E,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Glu .. _gran: Granzyme B .......... Granzyme B preferentially cleaves after D (`P1`) preceded by IEP. **RPG definition:** cleaving rule: * ``(I)(E)(P)(D,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#GranB .. _hydro: Hydroxylamine ............. Hydroxylamine (NH2OH) preferentially cleaves after N (`P1`) followed by G in `P1'`. **RPG definition:** cleaving rule: * ``(N,)(G)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Hydro .. _iodo: Iodosobenzoic acid .................. Iodosobenzoic acid preferentially cleaves after W (`P1`). **RPG definition:** cleaving rule: * ``(W,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Iodo .. _lysc: Lys-C ..... LysC Lysyl endopeptidase (Achromobacter proteinase I) preferentially cleaves after K (`P1`). **RPG definition:** cleaving rule: * ``(K,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysC .. _lysn: Lys-N ..... LysN Peptidyl-Lys metalloendopeptidase preferentially cleaves before K (`P1'` ). **RPG definition:** cleaving rule: * ``(,K)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#LysN .. _neut: Neutrophil elastase ................... Neutrophil elastase preferentially cleaves after A or V (`P1`). **RPG definition:** cleaving rule: * ``(A or V,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Elast .. _ntcb: NTCB .... NTCB +Ni (2-nitro-5-thiocyanobenzoic acid) preferentially cleaves before C (`P1'` ). **RPG definition:** cleaving rule: * ``(,C)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#NTCB .. _pap: Papain ...... Papain preferentially cleaves after R or K (`P1`) preceded by A, V, I, L ,F, Y or W in `P2`. It will not cleave if followed by V in `P1'`. **RPG definition:** cleaving rule: * ``(A or V or I or L or F or Y or W)(R or K,)`` exception rule: * ``(A or V or I or L or F or Y or W)(R or K,)(V)`` More information: https://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=16410606 .. _peps13: Pepsin pH 1.3 ............. 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:** cleaving rule: * ``(,F or L,)`` exception rules: * ``(,F or L)(P)`` * ``(R)(,F or L)`` * ``(P)()(,F or L)`` * ``(H or K or R)()()(,F or L)`` * ``(F or L,)()(P)`` * ``(P)(F or L,)`` * ``(H or K or R)()(F or L,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps .. _peps2: Pepsin pH >=2 ............. 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:** cleaving rule: * ``(,F or L or W or Y,)`` exception rules: * ``(,F or L or W or Y)(P)`` * ``(R)(,F or L or W or Y)`` * ``(P)()(,F or L or W or Y)`` * ``(H or K or R)()()(,F or L or W or Y)`` * ``(F or L or W or Y,)()(P)`` * ``(P)(F or L or W or Y,)`` * ``(H or K or R)()(F or L or W or Y,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Peps .. _prol: Proline-endopeptidase ..................... Proline-endopeptidase preferentially cleaves after P (`P1`) preceded by H, K or R in `P2` but will not cleaves if followed by P in `P1'`. **RPG definition:** cleaving rule: * ``(H or K or R)(P,)`` exception rule: * ``(H or K or R)(P,)(P)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Pro .. _protk: Proteinase K ..................... Proteinase K preferentially cleaves after F, W, Y, T, E, A, V, L or I (`P1`). The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids. **RPG definition:** cleaving rule: * ``(F or W or Y or T or E or A or V or L or I,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#ProtK .. _staphI: Staphylococcal peptidase I .......................... Staphylococcal peptidase I preferentially cleaves after E (`P1`). It will not cleave after E in `P1` preceded by E in `P2`, but cleaves after E in `P1` followed by E in `P1'`. **RPG definition:** cleaving rule: * ``(E,)`` exception rule: * ``(E)(E,)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Staph .. _therm: Thermolysin ........... Thermolysin preferentially cleaves before A,F,I,L,M or V (`P1'` ) when not followed by P in `P2'` nor preceded by D or E in `P1`. **RPG definition:** cleaving rule: * ``(,A or F or I or L or M or V)`` exception rules: * ``(,A or F or I or L or M or V)(P)`` * ``(D or E)(,A or F or I or L or M or V)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Therm .. _throm: Thrombin (PeptideCutter) ........................ 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 or T in `P3` and `P4`. It will not cleave after R followed by D/E in `P1'` or `P2'`. It is not strictly coherent with the definition in PeptideCutter, as in this software there are differences between definition, summary and behavior of this enzyme. **RPG definition:** cleaving rules: * ``(G)(R,)(G)`` * ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)`` exception rules: * ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)`` * ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)()(D or E)`` .. warning:: the following combined exception ``(A or F or I or L or V or W or G or T)(A or F or I or L or V or W or G or T)(P)(R,)(D or E)(D or E)`` cannot be used instead, as it will cleave on [...](R,)(D or E). More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Throm https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288055/ .. _thromsg: Thrombin SG ......................... This thrombin (Sequencing Grade) 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 in `P2'`. This thrombin is defined in several kits (see below). **RPG definition:** cleaving rule: * ``(L)(V)(P)(R,)(G)(S)`` More information: see thrombin cleavage kits of `Abcam `_, `BioVision `_, `Merck `_ or `Novagen `_. .. _tev: Tobacco etch virus protease ........................... Tobacco etch virus protease (TEV) preferentially cleaves after Q (`P1`) when followed by G or S in `P1'` and preceded by Y in `P3` and E in `P6`. **RPG definition:** cleaving rule: * ``(E)()()(Y)()(Q,)(G or S)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#TEV .. _tryps: Trypsin ....... 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:** cleaving rules: * ``(K or R,)`` * ``(W)(K,)(P)`` * ``(M)(R,)(P)`` exception rules: * ``(K or R,)(P)`` * ``(C)(K,)(D)`` * ``(D)(K,)(D)`` * ``(C)(K,)(H)`` * ``(C)(K,)(Y)`` * ``(C)(R,)(K)`` * ``(R)(R,)(H)`` * ``(R)(R,)(R)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#Tryps .. _asp-n2: Asp-N Endopeptidase ................... Asp-N Sequencing Grade preferentially cleaves before D (`P1'` ) **RPG definition:** cleaving rule: * ``(,D)`` More information: https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html#AspN .. _proa: ProAlanase .......... ProAlanase Sequencing Grade preferentially cleaves after A or P (`P1`). **RPG definition:** cleaving rule: * ``(A or P,)`` More information: https://france.promega.com/products/mass-spectrometry/proteases-and-surfactants/proalanase-mass-spec-grade?catNum=VA2161 .. _elast: Elastase ........ Elastase preferentially cleaves after A, V, S, G, L, or I (`P1`). **RPG definition:** cleaving rule: * ``(A or V or S or G or L or or I,)`` More information: https://france.promega.com/products/mass-spectrometry/proteases-and-surfactants/elastase/?catNum=V1891 .. _alp: aLP ... α-Lytic Protease preferentially cleaves after T, A, S or V (`P1`) **RPG definition:** cleaving rule: * ``(T or A or S or V,)`` More information: https://www.neb.com/en/products/p8113-a-lytic-protease#Product%20Information