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. 2016 Jul 26;7(6):459–477. doi: 10.1080/21655979.2016.1208868

Table 1.

In silico proteolytic cleavage site analysis for P1-polyprotein, VP1 and glutathione reductase (GOR) using primarily the P1 and P2 substrate positions within amino acid sequences.

Protease        
Cysteine protease P1-polyprotein GOR Cleavage Preferential Cleavage
Papain (C25, H159, N175) VP1 chain – AR157, 200, LR67, 145, YR179, TR114, 172, PR189, DR38, SR138, QR26VP2 chain – TR18, 54, MR102, PR151, DR13, ER60VP3 chain – R56, R120, R212, R218, PR34, DR72VP4 chain – none AR37, 45, LR224, 478, IR127, 218, WR97, SR109 AR↓, VR↓, LR↓, IR↓, FR↓, WR↓, YR↓, TR↓, MR↓, PR↓, DR↓, SR↓, ER↓, QR↓ (A, V, L, I, F, W, Y – hydrophobic amino acids in P2 position)(↓ no Val after cleavage sites)
  VP1 chain - VK81, 210, IK169, MK181, EK96, QK204VP2 chain – FK63, IK198, DK2, SK217, QK134VP3 chain – AK84, 118, TK67, PK20, 134, SK154VP4 chain – SK70 VK252, 255, 324, 397, 452, LK247, IK100, YK357, TK120, 296, 412, 457, MK420, PK66, 137, DK221, 310, SK212, 361, EK102 AK↓, VK↓, LK↓, IK↓, FK↓, WK↓, YK↓, TK↓, MK↓, PK↓, DK↓, SK↓, EK↓, QK↓
  VP1 chain – IH195, YH108, PH123, SH59, QH29VP2 chain – AH157, VH174, TH65, PH145, DH87VP3 chain – AH141, LH108, IH144, TH191 VP4 chain – TH58 AH351, VH75, IH389, 434, 467, YH408, MH80, PH151, 164, DH82, SH52, 122, 374 AH↓, VH↓, LH↓, IH↓, FH↓, WH↓, YH↓, TH↓, MH↓, PH↓, DH↓, SH↓, EH↓, QH↓
  VP1 chain – AE184, VE16, LE77, TE175, 198, PE95VP2 chain – AE40, 59, VE108, LE11, 52, 82, TE5, 192, PE128, PE137, EE6VP3 chain – AE49, 146, 176, 220, FE58, 210, ME131VP4 chain – none AE41, VE50, 201, LE184, 239, IE124, 141, 394, FE355, TE236, 384, DE317, 386, 442, SE77, 472, EE185, 237, 428, 473, QE5 AE↓, VE↓, LE↓, IE↓, FE↓, WE↓, YE↓, TE↓, ME↓, PE↓, DE↓, SE↓, EE↓, QE↓
  VP1 chain – IN49, FN164, YN131, TN103, PN91, 143, DN100, EN17, QN46VP2 chain – AN202, VN166, 190, IN149, FN117, TN153, 207, PN47VP3 chain – LN152, IN106, FN31, TN43, 179, SN88VP4 chain – IN23, TN61, DN41, SN48, QN13, 32, 64 AN425, LN111, 301, FN95, WN71, YN365, TN233, PN294, DN462, EN240, 395, QN116 AN↓, VN↓, LN↓, IN↓, FN↓, WN↓, YN↓, TN↓, MN↓, PN↓, DN↓, SN↓, EN↓, QN↓
  VP1 chain – AQ153, IQ25, TQ23, PQ45VP2 chain – VQ57, IQ133, YQ139, TQ27, PQ196, DQ170VP3 chain – AQ76, 96, VQ181, FQ188, TQ100VP4 chain – YQ31, TQ37, MQ28, SQ12, QQ29 LQ445, IQ306, FQ182, 319, YQ115, MQ436, PQ6,9, SQ167 AQ↓, VQ↓, LQ↓, IQ↓, FQ↓, WQ↓, YQ↓, TQ↓, MQ↓, PQ↓, DQ↓, SQ↓, EQ↓, QQ↓
  VP1 chain – AS69, FS74, YS137, TS3, 162, PS58, ES7VP2 chain – VS44, TS24, 49, 72, PS216, DS74, 97, QS28VP3 chain – AS172, 204, LS163, FS158, YS102, MS80, 87, DS70VP4 chain – AS73, IS44, FS69, 77, TS56, SS6, 74, QS5, 15 AS20, 35, 172, VS108, 143, 264, LS207, 259, 299, IS231, FS249, 373, YS400, TS134, 177, 214, 402, PS89, 161, DS228, 360, SS471, ES51, 166 AS↓, VS↓, LS↓, IS↓, FS↓, WS↓, YS↓, TS↓, MS↓, PS↓, DS↓, SS↓, ES↓, QS↓
  VP1 chain – AT128, 171, VT12, 43, 174, LT87, 113, YT120, TT2, 13, 14, 102, PT105, 161, 197, ST70, ET22, 185, QT212VP2 chain – AT38, VT33, 71, 110, LT16, 95, 141, 188, IT159, WT178, TT8, 17, 23, 26, MT155, PT85, 206, ST25, ET7, 53VP3 chain – VT16, 65, IT190, FT42, 112, 156, YT99, 168, 170, TT17, 66, 178, PT53, 115, DT149, ET177VP4 chain – AT9, TT55, 60, DT36, 54, ST52, 57 AT156, 456, VT267, 411, LT119, 339, 383, IT176, FT133, 404, YT148, MT277, PT139, 369, 469, ST162, 232, 401, QT307 AT↓, VT↓, LT↓, IT↓, FT↓, WT↓, YT↓, TT↓, MT↓, PT↓, DT↓, ST↓, ET↓, QT↓
  VP1 chain – AG5, VG63, YG19, 166, EG84VP2 chain – AG212, VG31, 113, 164, FG76, YG35, 92, SG45, 50, EG193VP3 chain – AG93, 206, YG12, 27, TG113, 150, PG39, 129, DG10, 196, SG103, EG59, QG182VP4 chain – AG3, LG39, FG81, TG10, 19, SG16, 45, 78, EG50 AG16, 196, 204, 242, 346, VG62, 194, 330, 381, 432, LG43, 55, 174, 210, 304, 439, IG27, 290, 378, YG86, 392, TG157, MG454, PG170, 188, 271, DG179, SG31, 144, 260, EG92, QG10, 437, 446 AG↓, VG↓, LG↓, IG↓, FG↓, WG↓, YG↓, TG↓, MG↓, PG↓, DG↓, SG↓, EG↓, QG↓
  VP1 chain – YF73, SF34, 163VP2 chain – LF67, 143, FF62, PF162, DF42, SF75, EF214, QF116, 147 VP3 chain – VF30, LF187, IF3, TF54, 90, 157, MF111, DF209, QF77VP4 chain – AF76, LF80, WF68 AF132, VF372, LF354, FF181, DF460, SF226, 403, EF78, 318 AF↓, VF↓, LF↓, IF↓, FF↓, WF↓, YF↓, TF↓, MF↓, PF↓, DF↓, SF↓, EF↓, QF↓
  VP1 chain – noneVP2 chain – PW177VP3 chain – EW147VP4 chain – DW67 LW287, MW70 AW↓, VW↓, LW↓, IW↓, FW↓, WW↓, YW↓, TW↓, MW↓, PW↓, DW↓, SW↓, EW↓, QW↓
  VP1 chain – AY107, VY130, LY178, YY72, TY71, 186, PY119VP2 chain – AY100, VY91, 200, LY138, TY34, SY98, QY171VP3 chain – AY125, VY26, YY98, TY169, PY63, 161, DY167, QY97, 101VP4 chain – YY26, QY30 AY106, IY114, 327, TY399, MY407, DY23, 85, 364, SY21, EY356 AY↓, VY↓, LY↓, IY↓, FY↓, WY↓, YY↓, TY↓, MY↓, PY↓, DY↓, SY↓, EY↓, QY↓
  VP1 chain – AL98, 117, VL126, 151, LL66, 177, 192, IL51, TL61, 159, 213, PL112, 191, DL53, 76, 86, 148, EL176VP2 chain – LL10, 81, 122, IL15, TL9, 142, 179, PL187, SL94, EL83, 129, 137, QL140VP3 chain – AL199, VL74,202, LL45, FL55, 91, YL162, SL81, EL211, QL37VP4 chain – AL83, LL84, QL38 AL209, 337, VL223, 246, LL286, 338, IL153, TL258, ML444, DL298, SL173, 215, 300, EL42, 186, 238, QL183 AL↓, VL↓, LL↓, IL↓, FL↓, WL↓, YL↓, TL↓, ML↓, PL↓, DL↓, SL↓, EL↓, QL↓
  VP1 chain – LM54, IM36VP2 chain – AM125, YM101VP3 chain – FM110, YM122, DM79, SM34VP4 chain – YM27 VM69, 276, 419, LM216, FM79, TM278, PM406, SM229, 265, EM202, 443 AM↓, VM↓, LM↓, IM↓, FM↓, WM↓, YM↓, TM↓, MM↓, PM↓, DM↓, SM↓, EM↓, QM↓
Cathepsin L VP1 chain – KR182, KH82, KQ203, KA97, 110, 170VP2 chain – KK3, KR135, KE218, KT4, KG89 VP3 chain – KH85, KT21, 68, 135, KF155, KA119, 194VP4 chain – KL71 KK67, 146, 256, KR103, 413, KE101, 253, 358, 427, KS121, KT213, 257, 398, 415, KG311, 325, KF94, 248, KY147, KA336, 458, KL54, 303, 349, 362, KM453 KK↓, KR↓, KH↓, KE↓, KN↓, KQ↓, KS↓, KT↓, KG↓, KF↓, KW↓, KY↓, KA↓, KL↓, KM↓,
  • ▪

    Generally the same as papain with these additional specificities

  • ▪

    Exceptions at the P2 position with respect to papain are EXaa,QXaa, TXaa, AXaa where Cathepsin-L does not have specificity for
  VP1 chain – noneVP2 chain – WT178VP3 chain – noneVP4 chain – WF68 WR97, WN71, WA288 WK↓, WR↓, WH↓, WE↓, WN↓, WQ↓, WS↓, WT↓, WG↓, WF↓, WW↓, WY↓, WA↓, WL↓, WM↓
  VP1 chain – HK109, 202, HE83, HT30, 60VP2 chain – HK88, 175, HQ146, HT22, HL66, 80VP3 chain – HG192, HF109, HA145, HM86VP4 chain – HT59 HK53, 390, HR352, HE165, HS76, HA83, 130, 409, HM435 HK↓, HR↓, HH↓, HE↓, HN↓, HQ↓, HS↓, HT↓, HG↓, HF↓, HW↓, HY↓, HA↓, HL↓, HM↓
  VP1 chain – FI35VP2 chain – HI158, SI132, FI148VP3 chain – SI159VP4 chain – SI21, II22 HI123, 152, 313, PI377, YI198, VI26, 99, II126, LI154, MI217, 230, 279 KI↓, HI↓, DI↓, SI↓, PI↓, FI↓, WI↓, YI↓, VI↓, II↓, LI↓, MI↓  
  VP1 chain – KV42, 155, DV32, PV11, 209, FV40, WV89, IV206, LV62VP2 chain – KV173, 199, HV210, DV107, SV30, FV43, 163, WV70, VV56, 181, LV123, 180, MV126VP3 chain – KV29, DV47, 174, PV5, 25, 215, WV184, YV64, VV201, LV15, MV123VP4 chain – none KV68, 222, DV282, 332, SV191, PV275, 341, YV107, VV49, 371, 431, IV193, 315, LV25, 475, MV266, 422 KV↓, HV↓, DV↓, SV↓, PV↓, FV↓, WV↓, YV↓, VV↓, IV↓, LV↓, MV↓  
Cathepsin H VP1 chain – R26, 27, 38, 67, 114, 124, 135, 138, 145, 157, 172, 179, 182, 189, 200, K41, 81, 96, 109, 154, 169, 181, 202, 204, 210, F34, 39, 73, 163, W88, L51, 53, 61, 65, 66, 76, 86, 98, 112, 115, 117, 126, 144, 148, 151, 159, 176, 177, 191, 192, 213, Y18, 71, 72, 107, 119, 130, 136, 165, 178, 186
VP2 chain – R13, 18, 54, 60, 77, 102, 135, 151, 167, K2, 3, 63, 88, 134, 172, 175, 198, 217, F42, 61, 62, 67, 75, 116, 143, 147, 162, 214, W69, 105, 177, L9, 10, 15, 51, 66, 80, 81, 83, 94, 121, 122, 129, 137, 140, 142, 179, 187, Y34, 36, 91, 98, 100, 138, 168, 171, 200
VP3 chain – R34, 40, 56, 72, 120, 212, 218, K20, 28, 67, 84, 118, 134, 154, 193, 207, F3, 30, 41, 54, 57, 77, 90, 109, 111, 155, 157, 187, 209, W147, 183, L14, 37, 44, 45, 55, 74, 81, 91, 94, 107, 151, 162, 186, 199, 202, 211, 213, Y11, 26, 63, 97, 98, 101, 121, 125, 161, 167, 169
VP4 chain – K70, F68, 76, 80, W67, L38, 71, 79, 83, 84, Y25, 26, 30 		R3, 37, 38, 45, 97, 103, 109, 127, 189, 218, 224, 272, 291, 347, 352, 413, 478K53, 66, 67, 93, 100, 102, 120, 137, 145, 146, 212, 221, 247, 252, 255, 256, 296, 302, 310, 324, 335, 348, 357, 361, 390, 397, 412, 414, 416, 420, 426, 429, 452, 457F78, 87, 94, 132, 180, 181, 226, 248, 318, 354, 372, 403, 447, 460,W70, 96, 287L24, 33, 42, 54, 110, 118, 153, 173, 183, 186, 206, 209, 215, 223, 238, 246, 258, 261, 273, 285, 286, 298, 300, 303, 337, 338, 349, 353, 362, 382, 438, 444, 474Y21, 23, 85, 106, 114, 147, 197, 327, 356, 364, 391, 399, 407 R↓, K↓, F↓, W↓, L↓, Y↓  
Cathepsin B VP1 chain – RR27VP2 chain – noneVP3 chain – noneVP4 chain – none RR38 RR↓
  • ▪

    Generally the same as papain and Cathepsin-L with these additional specificities

  • ▪

    Exceptions at the P2 position with respect to papain and Cathepsin-L are PXaawhere Cathepsin B does not have specificity for
  VP1 chain – RP190, HP196, NP104, TP44, AP94, VP57, 90, 142, LP118, 160VP2 chain – KP176, NP150, GP46, FP144, 215, AP186, 195, 205, VP127, 161, LP84, VP3 chain – DP19, 24, EP132, NP32, TP136, GP114, AP127, VP62, IP160, LP38,VP4 chain – SP7 KP138, HP375, 468, DP136, EP6, QP8, TP163, 340, 405, GP11, FP88, AP150, VP65, IP169, 280, 368, LP187, 274, MP160 KP↓, RP↓, HP↓, DP↓, EP↓, NP↓, QP↓, SP↓, TP↓, GP↓, FP↓, WP↓, YP↓, AP↓, VP↓, IP↓, LP↓, MP↓
  VP1 chain – GE6, GG20, 64, GA93, 167, GL65VP2 chain – GR77, GH21, GE213, GN114, GS93, GG119, GP46, GW105, GY36, GA194, GL51VP3 chain – GK193, 207, GR40, GT104, GG13, GP114, GT104, GG13, GP114, GY11, GL94, 151, GM130VP4 chain – GN17, GQ4, GS11, 20, 47, 51, GG46, GL79 GK93, 145, 335, GR189, 272, 347, GH129, 312, GS30, 211, GT57, GG29, 32, 56, 158, GP11, GF87, 180, 447, GY197, GA17, 44, 171, 195. 455, GL33, 261, 382, 438, GM159 GK↓, GR↓, GH↓, GE↓, GN↓, GQ↓, GS↓, GT↓, GG↓, GP↓ GF↓, GW↓, GY↓, GA↓, GL↓, GM↓
  VP1 chain – NQ47, NT101, NG92, 132, NP104, NY18, 165, NL144VP2 chain – NR167, NQ115, NT48, 191, NG20, 104, 118, NP150, NM154
VP3 chain – NQ36, NS153, NT89, NP32, NL44, 107VP4 chain – NE49, NN24, 65, NQ14, NS33, NT18, 62, NY25, NA42 		NK302, 426, NN117, 366, NT72, 295, 321, 463, NW96, NA112, 241, NL118 NK↓, NR↓, NH↓, NE↓, NN↓, NQ↓, NS↓, NT↓, NG↓, NP↓ NF↓, NW↓, NY↓, NA↓, NL↓, NM↓  
  VP1 chain – RH201, RN139, RQ28, RT158, RG146, RP190, RY136, RA183, RL115, RM180VP2 chain – RE136, RN19, RT152, RF61, RY168VP3 chain – RN35, RF41, RY121, RA219, RL213VP4 chain – none RK348, 414, RH219, RQ4, RS225, RG128, RA39, R110, 273, 353 RK↓, RH↓, RE↓, RN↓, RQ↓, RS↓, RT↓, RG↓, RP↓ RF↓, RW↓, RY↓, RA↓, RL↓, RM↓  
Legumain VP1 chain – TN103VP2 chain – AN202, TN153, 207VP3 chain – TN43, 179, LN152VP4 chain – TN61 AN425, TN233, 322, LN111, 301 AAN↓, AN↓, TN↓, LN↓ Based on optimal sequences for schistosome (C197, N197C) and human legumains, and cruzain 49
Serine protease        
Trypsin (H57, D102, G193, S195) VP1 chain – K41, 81, 96, 109, 154, 169, 181, 202, 204, 210, R26, 27, 38, 67, 114, 124, 135, 138, 145, 157, 172, 179, 182, 189, 200
VP2 chain – K2, 3, 63, 88, 134, 172, 175, 198, 217, R13, 18, 54, 60, 77, 102, 135, 151, 167
VP3 chain – K20, 28, 67, 84, 118, 134, 154, 193, 207, R34, 40, 56, 72, 120, 212, 218
VP4 chain – K70 		K53, 66, 67, 93, 100, 102, 120, 137, 145, 146, 212, 221, 247, 252, 255, 256, 296, 302, 310, 324, 335, 348., 357, 361, 390, 397, 412, 414, 416, 420, 426, 429, 452, 457, R3, 37, 38, 45, 97, 103, 109, 127, 189, 218, 224, 272, 291, 347, 352, 413, 478 K↓, R↓  

Amino acids are designated by the single-letter code

Cleavage sites are designated by arrows (↓)

Numbers appearing after amino acids refer to the position of potential cleavage

Highly abundant cleavage sites are highlighted in yellow

Highly scarce cleavage sites are highlighted in turquoise

Cleavage sites occurring at the end of a protein sequence are highlighted in gray