Table 1.
Previously uncharacterized caspase-3 substrates isolated from round 3 of selection
| Number | Protein name | Selected SOR/full length | Tested FL or LF* | Cut by caspase-3? |
|---|---|---|---|---|
| 1 | ADNP | 824–929/1102 | ||
| 2 | AFTIPHILIN | 108–208/908 | ||
| 3 | AGGF1 | 504–592/714 | 442–714 | Y |
| 4 | ALS2C13 | 120–223/345 | ||
| 5 | ANKRD1 | 26–97/319 | 1–319 | Y |
| 6 | ARGAP21 | 1400–1498/1957 | ||
| 7 | ARGEF12 | 683–776/1544 | ||
| 8 | ARL13B | 304–368/428 | ||
| 9 | BCAS1 | 244–301/584 | 1–584 | Y |
| 10 | BNIP2 | 4–79/314 | 1–314 | Y |
| 11 | BTAF1 | 124–241/1849 | 1–472 | Y |
| 12 | BRWD3 | 1588–1641/1802 | 688–1384 | Y |
| 13 | C10ORF6 | 336–446/1173 | ||
| 14 | C12ORF11 | 585–696/706 | ||
| 15 | C219 | 599–711/1907 | 493–974 | Y |
| 16 | CCDC47 | 79–192/483 | 1–483 | Y |
| 17 | CDC10 | 92–240/417 | 1–417 | N |
| 18 | CEP1 | 1333–1438/2325 | ||
| 19 | CGNL1 | 630–725/1302 | 446–912 | Y |
| 20 | CHD3 | 602–696/1966 | ||
| 21 | CLU | 116–213/501 | 53–501 | Y |
| 22 | COG5 | 450–575/839 | ||
| 23 | DGKB | 354–453/773 | ||
| 24 | DHX38 | 7–99/1227 | 1–674 | Y |
| 25 | DNM1 | 547–647/851 | ||
| 26 | DYN | 2738–2830/5171 3384–3480/5171 | ||
| 27 | EEF1B2 | 59–168/225 | 1–225 | N |
| 28 | EPRS | 921–1022/1512 | 693–1315 | N |
| 29 | ESRRBL1/HIPPI | 275–389/429 | 1–429 | Y |
| 30 | FILIP1 | 709–848/1213 | ||
| 31 | FLJ21908 | 351–457/665 | ||
| 32 | FUS | 273–357/526 | ||
| 33 | GAPVD1 | 1051–1163/1487 | 940–1487 | Y |
| 34 | GOLGA4 | 681–819/2230 | ||
| 35 | GOLGB1 | 1833–1978/3259 | 1095–1701 | Y |
| 36 | HSPA4 | 640–784/840 | 1–840 | N |
| 37 | HYPB | 781–900/2061 | 688–1263 | Y |
| 38 | INO80 | 1322–1391/1556 | 1207–1556 | Y |
| 39 | KIF21A | 558–655/1661 | ||
| 40 | JARID1A | 1589–1685/1690 | 1131–1690 | Y |
| 41 | KIAA0423 | 871–974/1720 | 593–1180 | Y |
| 42 | KIAA0864 | 159–263/1402 | ||
| 43 | KIDIN220 | 221–301/1771 | 1–627 | Y |
| 44 | LMO7 | 1085–1184/1349 | 553–1271 | Y |
| 45 | LOC22998 | 684–803/1083 | ||
| 46 | M11S1 | 80–165/709 | 54–709 | Y |
| 47 | MACF1 | 1661–1757/5430 4126–4240/5430 | 1427–2062 | Y |
| 48 | MATRIN3 | 636–739/847 | ||
| 49 | MLL3 | 810–910/4025 | 560–1126 | Y |
| 50 | MNAB | 1033-1113/1191 | 652-1191 | Y |
| 51 | MORF15 | 145–292/362 | 1–362 | N |
| 52 | MPP8 | 432–513/860 | ||
| 53 | MYO18A | 1943–2047/2054 | ||
| 54 | NAPLl3 | 97–181/506 | 1–506 | Y |
| 55 | NDUFS1 | 240–328/727 | 1–727 | Y |
| 56 | NEB | 832–928/6669 | 550–1058 | Y |
| 57 | NEXN | 309–355/505 | 1–505 | Y |
| 58 | NUCB2 | 175–269/420 | 1–420 | Y |
| 59 | PCF11 | 319–442/1555 | 1–713 | Y |
| 60 | PDZGEF1 | 329–439/1499 | 130–950 | Y |
| 61 | PHACTR2 | 511–592/634 | 1–634 | Y |
| 62 | PHTF2 | 267–365/785 | ||
| 63 | PIK3R1 | 501–631/724 | ||
| 64 | PIK3R3 | 64–215/461 | 1–461 | Y |
| 65 | PJA2 | 131–237/708 | 1–708 | Y |
| 66 | PPP1R12A | 833–916/1030 | ||
| 67 | PSIP2 | 69–148/530 | 1–530 | Y |
| 68 | PSMC1 | 251–323/440 | 1–440 | |
| 69 | PSMC3 | 269–348/439 | 1–439 | |
| 70 | PSRC2 | 317–395/1989 | ||
| 71 | RNF6 | 128–227/685 | 1–685 | Y |
| 72 | S100PBP | 85–188/408 | ||
| 73 | SALL1 | 97–134/1324 | ||
| 74 | SCG3 | 78–138/468 | 1–468 | Y |
| 75 | SERBP1 | 180–256/402 | ||
| 76 | SHOC2 | 191–308/582 | 1–582 | Y |
| 77 | SLC4A1AP | 711–782/796 | 1–796 | Y |
| 78 | SMARCA1 | 856–923/1054 | ||
| 79 | SMC5 | 807–910/1101 | ||
| 80 | SORBS1 | 389–525/816 | 1–816 | Y |
| 81 | SPARCL1 | 257–335/664 | 1–664 | Y |
| 82 | SSFA2 | 439–534/1256 | ||
| 83 | SRP54 | 358–436/504 | 1–504 | Y |
| 84 | STAC3 | 259–363/364 | 1–364 | N |
| 85 | SYTL2 | 686–797/1256 | ||
| 86 | TAF15 | 99–171/589 | ||
| 87 | TFG | 23–145/400 | 1–400 | Y |
| 88 | UTP11L | 109–196/253 | 1–253 | N |
| 89 | UTP14C | 305–395/766 | 1–766 | Y |
Only selected fragments whose specific cleavage by caspase-3 has been confirmed by SDS/PAGE are listed. Column 3 shows the range of the shortest overlap region (SOR) and the size of the full-length protein. Column 4 shows the range of the TNT-generated full length (FL) or of large fragment (LF) that had been tested in caspase-3 cleavage reaction (the results are listed in column 5). The GenBank accession numbers of these proteins are listed in SI Table 4. Y, yes; N, no. Bold text represents full-length proteins that were specifically cleaved by caspase-3, whereas italicized text represents large fragments from very large proteins that were specifically cleaved by caspase-3.
*Motif Scan (http://myhits.isb-sib.ch/cgi-bin/motif_scan) and Protein Blast were used for the prediction of domains, motifs, and patterns. The Hierarchical Neural Network method (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html) was used for the prediction of secondary structures.