Table 3.
Analysis of cleavage sites of known caspase 3 substrates with GraBCas
| Caspase 3 substrate | Acc_number | Known cleavage site | Score by GraBCas | P6–P2′ of cleavage site |
|---|---|---|---|---|
| ADD1: adducing 1 (alpha) | NP_001110 | DDSD (633) | 0,357 | TGDDSDAA |
| APAF1: apoptotic protease activating factor | NP_001151 | SVTD (271) | 0,462672 | DKSVTDSV |
| ARHGDIB: Rho GDP dissociation inhibitor (GDI) beta | NP_001166 | DELD (19) | 22,4 | DDDELDSK |
| ATP2B4: ATPase, Ca++ transporting, plasma membrane 4 | NP_001675 | DEID (1080) | 71,4 | GLDEIDHA |
| BAD: BCL2-antagonist of cell death | NP_004313 | EQED (14) | 0,001632 | PSEQEDSS |
| BAX: BCL2-associated X protein | NP_004315 | FIQD (33) | 0,002142 | QGFIQDRA |
| BCL2: B-cell CLL/lymphoma 2 | NP_000624 | DAGD (34) | 0,0357 | EWDAGDVG |
| BCL2L1: BCL2-like 1 | NP_001182 | HLAD (61) | 0,027846 | SWHLADSP |
| BCL2L1: BCL2-like 2 | NP_001182 | SSLD (76) | 0,274176 | HSSSLDAR |
| BIRC2: baculoviral IAP repeat-containing 2 | NP_001157 | ENAD (372) | 0,111384 | GEENADPP |
| BLM: Bloom syndrome | NP_000048 | TEVD (415) | 5 | LLTEVDFN |
| BRCA1: breast cancer 1, early onset | NP_009225 | DLLD (1154) | 3,4272 | PDDLLDDG |
| CAMK4: calcium/calmodulin-dependent protein kinase IV | NP_001735 | YWID (31) | 0,0084966 | PDYWIDGS |
| CAMK4: calcium/calmodulin-dependent protein kinase IV | NP_001735 | PAPD (176) | 0,0144942 | ATPAPDAP |
| CDC2L1: cell division cycle 2-like 1 (PITSLRE proteins) | NP_001778 | YVPD (391) | 0,0124236 | GDYVPDSP |
| CDC6: CDC6 cell division cycle 6 homolog (Saccharomyces cerevisiae) | NP_001245 | SEVD (442) | 4 | VISEVDGN |
| CDC6: CDC6 cell division cycle 6 homolog (S.cerevisiae) | NP_001245 | LVRD (99) | 0,0055692 | RRLVFDNQ |
| CDKN1A: cyclin-dependent kinase inhibitor 1A (p21, Cip1) | NP_000380 | DHVD (112) | 18,7 | EEDHVDLS |
| CSEN: calsenilin, presenilin binding protein, EF hand transcription factor | NP_038462 | DSSD (64) | 0,4284 | GSDSSDSE |
| CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa | NP_001895 | DLMD (764) | 0,0153 | AQDLMDGL |
| CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa | NP_001895 | YPVD (751) | 10 | ADYPVDGL |
| CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa | NP_001895 | ADID (83) | 0,18207 | QVADIDGQ |
| CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa | NP_001895 | TQFD (115) | 0,37128 | PSTQFDAA |
| CTNNB1: catenin (cadherin-associated protein), beta 1, 88 kDa | NP_001895 | SYLD (32) | 0,22848 | QQSYLDSG |
| DFFA: DNA fragmentation factor, 45 kDa, alpha polypeptide | NP_004392 | DAVD (224) | 35,7 | EVDAVDTG |
| DFFA: DNA fragmentation factor, 45 kDa, alpha polypeptide | NP_004392 | DETD (117) | 37,8 | DVDETDSG |
| DRPLA: dentatorubral-pallidoluysian atrophy (atrophin-1) | NP_001931 | DSLD (109) | 6,8544 | DLDSLDGR |
| EIF2S1: eukaryotic translation initiation factor 2, subunit 1 alpha, 35 kDa | NP_004085 | AEVD (301) | 1 | ENAEVDGD |
| EIF2S1: eukaryotic translation initiation factor 2, subunit 1 alpha, 35 kDa | NP_004085 | DGDD (304) | 0,0085 | EVDGDDDA |
| FNTA: farnesyltransferase, CAAX box, alpha | NP_002018 | VSLD (59) | 0,137088 | GFVSLDSP |
| GCLC: glutamate-cysteine ligase, catalytic subunit | NP_001489 | AVVD (499) | 0,306 | GNAVVDGC |
| GSN: gelsolin (amyloidosis, Finnish type) | NP_000168 | DQTD (403) | 15,4224 | DPDQTDGL |
| HD: huntingtin (Huntington disease) | NP_002102 | DSVD (513) | 30,6 | WEAQRDSH |
| HNRPU: heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) | NP_004492 | SALD (100) | 0,319872 | GISALDGD |
| IL16: interleukin 16 (lymphocyte chemoattractant factor) | NP_004504 | SSTD (510) | 0,462672 | LNSSTDSA |
| IL18: interleukin 18 (interferon-gamma-inducing factor) | NP_001553 | LESD (36) | 0,0014 | ENLESDYF |
| KRT18: keratin 18 | NP_000215 | VEVD (238) | 2 | LTVEVDAP |
| MAPT: microtubule-associated protein tau | NP_005901 | DMVD (421) | 0,1 | SIDMVDSP |
| MDM2: Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) | NP_002383 | DVPD (361) | 12,4236 | GFDVPDCK |
| NFKBIA: nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha | NP_065390 | DRHD (32) | 0,3332 | LDDRHDSG |
| NUMA1: nuclear mitotic apparatus protein 1 | NP_006176 | DSLD (1712) | 6,8544 | SIDSLDLS |
| PAK2: p21 (CDKN1A)-activated kinase 2 | NP_002568 | SHVD (212) | 0,748 | GDSHVDGA |
| POLE: polymerase (DNA directed), epsilon | NP_006222 | DQLD (189) | 9,1392 | IADQLDNI |
| POLE: polymerase (DNA directed), epsilon | NP_006222 | DMED (1185) | 10 | APDMEDFG |
| PPP2R1A: protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform | NP_055040 | DEQD (218) | 1,4 | ASDEQDSV |
| PRKCD: protein kinase C, delta | NP_006245 | DMQD (329) | 0,0014 | GEDMQDNS |
| PRKCM: protein kinase C, mu | NP_002733 | CQND (378) | 5,712 | AECQNDSG |
| PRKCQ: protein kinase C, theta | NP_006248 | DEVD (354) | 100 | PLDEVDKM |
| PRKCZ: protein kinase C, zeta | NP_002735 | DGVD (239) | 0,0085 | VIDGMDGI |
| PRKCZ: protein kinase C, zeta | NP_002735 | EETD (210) | 1,512 | PSEETDGI |
| PRKDC: protein kinase, DNA-activated, catalytic polypeptide | NP_008835 | DEVD (2713) | 100 | PGDEVDNK |
| PSEN2: presenilin 2 (Alzheimer disease 4) | NP_000438 | DSYD (329) | 4,7124 | EEDSYDSF |
| RB1: retinoblastoma 1 (including osteosarcoma) | NP_000312 | DEAD (886) | 18,2 | GSDEADGS |
| RFC1: replication factor C (activator 1) 1, 145 kDa | NP_002904 | DEVD (722) | 100 | IMDEVDGM |
| ROCK1: Rho-associated, coiled-coil containing protein kinase 1 | NP_005397 | DETD (1113) | 37,8 | SADETDGN |
| SNRP70: small nuclear ribonucleoprotein 70 kDa polypeptide (RNP antigen) | NP_003080 | DGPD (341) | 3,451 | GPDGPDGP |
| SPTBN1: spectrin, beta, non-erythrocytic 1 | NP_003119 | DEVD (1457) | 100 | STDEVDSK |
| SPTBN1: spectrin, beta, non-erythrocytic 2 | NP_003119 | ETVD (2146) | 1,428 | MAETVDTS |
| VIM: vimentin | NP_003371 | DSVD (85) | 30,6 | KGDEVDGV |
The bold printed amino acids in the extended clevage site indicate hits detected by the high stringency filter. Numbers in brackets indicate clevage site position in the amino acid sequence.