Table 1. Identity of the degradomic protein targets for calpain-2 and capase-3, and differentially regulated proteins after TBI.
Protein names or abbreviations are listed in the far left column. Their template and lane location are listed on the second column. Swiss Pro ID and predicted MMs are also listed. Where a protein is altered in levels in one of the three conditions (calpain-2, capase-3 or TBI), the fold-change of the parent protein is indicated in the 3 columns on the far right. Since the majority of proteins showed decreased levels in the treatment group versus control (naive), the fold-change always indicates decrease as the default. When a protein level is increased (for some proteins in TBI), the fold-change increase is indicated with a (+) sign and the fold-change is given inside brackets. Also, we have used high stringency inclusion criteria. Only proteins with a band decrease or increase of at least 1.5-fold in all 9 possible comparisons between 3 treatment replicas and 3 control replicas are shown. *, Fold changes for each treatment group are given against controls (naïve). AKAP220, A-kinase anchoring protein; Arp, actin-related protein; ASAP1, Arf GTPase-activating protein; BRMP2, amphiphysin; c-Cbl, casitas B-lineage lymphoma; CtBP1, C-terminal-binding protein 1; cdk2, cyclin-dependent kinase2; DRBP76, double-stranded RNA-binding nuclear protein76; GABA-B-R2, γ-aminobutyric acid-B-receptor2; GS27, Golgi SNARE 27; GSTP, GTP-binding protein appearing to be essential for the G1 to S phase transition of the cell cycle; hPRP17, human homologue of yeast Prp17; MEF2D, myocyte-enhancer-binding factor 2D; mGluR1, metabotropic glutamate receptor1; MEK, MAPK/ERK kinase; Munc-18, non-neuronal syntaxin binding protein; MYPT1, myosin phosphatase target protein1; Nck, Nck adaptor protein 1; Nek2, NIMA (never in mitosis A)-related kinase; NES1, serine protease inhibitor kallikrein; nNOS, neuronal nitric oxide synthase; NSP1, non-structural protein 1; PEX19, peroxisome assembly factor 19; PKC, protein kinase C; PMCA2, plasma membrane calcium pump isoform2; RIP2/RICK (receptor-interacting protein kinase2/Rip-like interacting caspase-like apoptosis-regulatory protein kinase; SCAMP1, secretory carrier-associated membrane protein1; SCAR-1, suppressor of cAMP receptor-1; SLK, Ste20-like kinase; Smg/GDS, stimulatory GDP/GTP exchange protein; TBP, TATA box-binding polypeptide; TFIIS, transcription factor IIS; TNIK, Traf2 and Nck-interacting kinase.
| Protein | Lane | Swiss Pro ID | MM (kDa) | Calpain-2* (fold-decrease) | Caspase-3* (fold-decrease) | TBI* [fold-decrease/(increase)] |
|---|---|---|---|---|---|---|
| Template A | ||||||
| AKAP220 | 1 | Q62924 | 220 | >10 | >10 | >10 |
| Amphiphysin | 1 | Q95163 | 125 | >10 | ||
| ASAP1 | 39 | Q9QWY8 | 130 | >10 | ||
| BRMP2 | 15 | O08539 | 96/89 | >10 | 7.31 | |
| CaMPK-II | 36 | P11275 | 52 | 5.23 | 5.67 | |
| CASK | 3 | Q62915 | 120 | (+5.8) | ||
| Dynactin | 19 | Q13561 | 50 | >10 | >10 | >10 |
| Endopeptidase | 29 | P42676 | 80 | >10 | ||
| GABA-BR2 | 36 | O088871 | 130 | >10 | >10 | >10 |
| GSTP2 | 33 | O88180 | 88 | 4.77 | ||
| Integrin-α3 | 22 | Q62470 | 135 | >10 | >10 | >10 |
| M-calherin | 34 | P10287 | 130 | >10 | ||
| mGluR1 | 19 | P23385 | 133 | >10 | ||
| Munc-18 | 3 | Q99PV2 | 68 | >10 | >10 | |
| MYPT1 | 29 | Q9DBR7 | 130 | 3.38 | 3.93 | 5.00 |
| nNOS | 7 | P29475 | 155 | >10 | ||
| PKC-β | 18 | P05771 | 80 | >10 | 7.31 | |
| PKC-ϵ | 10 | Q02156 | 90 | 6.50 | ||
| PKC-γ | 30 | P05129 | 80 | >10 | 3.30 | >10 |
| PMCA2 | 17 | P11506 | 133 | >10 | >10 | >10 |
| Psme3 | 29 | Q12920 | 36 | (+4.7) | ||
| Rabphilin-3A | 23 | P47709 | 75 | >10 | >10 | |
| SNAP-25 | 7 | P13795 | 25 | >10 | >10 | >10 |
| Synapsin-IIa | 13 | Q63537 | 74 | >10 | 1.70 | 10.10 |
| Synapsin-1 | 23 | Q62910 | 140 | >10 | >10 | |
| Synaptotagmin | 11 | P21579 | 65 | 2.91 | 1.50 | |
| Template B | ||||||
| α-Actinin | 9 | AAA51582 | 104 | (+8.41) | ||
| Adaptin | 29 | P17426 | 112 | >10 | 6.12 | |
| Bad | 30 | Q61337 | 23 | 10.80 | 3.23 | 3.00 |
| β-Catenin | 5 | Q02248 | 92 | >10 | >10 | >10 |
| Cathepsin L | 22 | P07711 | 43 | 7.18 | >10 | 7.71 |
| Ceruloplasmin | 37 | Q61147 | 150 | (>+10) | ||
| Dynamin | 26 | P21575 | >100 | 10.69 | >10 | 4.41 |
| Ki-67 | 8 | P46013 | 395 | >10 | >10 | |
| MEF2D | 3 | Q63943 | 70 | >10 | >10 | |
| Nck | 2 | P16333 | 47 | >10 | ||
| NSP1 | 24 | Q9Y2X4 | 72 | >10 | >10 | >10 |
| p150Glued | 26 | P28023 | 150 | >10 | >10 | >10 |
| p190 | 3 | Q13017 | 190 | >10 | >10 | >10 |
| PKC-α | 25 | P17252 | 82 | 3.67 | >10 | |
| SII/TFIIS | 32 | P23193 | 38 | >10 | >10 | >10 |
| Smac/Diablo | 6 | Q9NR28 | 22 | >10 | >10 | >10 |
| DRBP76 | 7 | Q13906 | 90 | >10 | ||
| Template C | ||||||
| Arp-3 | 18 | P32391 | 50 | >10 | >10 | |
| CaMPK-IV | 12 | Q16566 | 60 | 3.11 | 2.63 | 4.26 |
| c-Cbl | 9 | P22681 | 120 | >100 | ||
| cdk2 | 9 | P24941 | (>+10) | |||
| hPRP-17 | 15 | O60508 | 66 | 3.33 | 2.36 | |
| MEK2 | 5 | P51955 | 46 | >10 | ||
| NES1 | 38 | O43520 | 30 | (>+10) | ||
| p55-Cdc | 8 | Q9BW56 | 55 | >10 | ||
| Profilin | 28 | P07737 | 15 | >10 | >10 | |
| RIP2/RICK | 26 | AAH04553 | 61 | 2.59 | ||
| α/β-SNAP | 21 | P54920 | 35/36 | >10 | 13.79 | |
| Syntaxin 6 | 7 | Q63635 | 31 | 3.81 | ||
| Striatin | 22 | P70483 | 110 | 9.31 | 3.01 | 6.51 |
| TBP | 26 | P20226 | 37 | (+7.31) | ||
| TNIK | 38 | Q9UKE5 | 150 | 2.59 | ||
| Template D | ||||||
| Catenin/p120 | 32 | P30999 | 120 | >10 | >10 | >10 |
| GS27 | 10 | O14653 | 27 | (>+10) | ||
| p190-B | 28 | Q13017 | 195 | >10 | >10 | >10 |
| PEX19 | 29 | P40855 | 38 | 6.31 | ||
| RONa | 27 | Q04912 | 40 | >10 | ||
| SCAMP1 | 38 | O15126 | 36 | 7.40 | ||
| Synapsin-Ia | 38 | P09951 | 80 | >10 | 9.90 | |
| ATP synthase | 21 | P15999 | 55 | >10 | 5.84 | >10 |
| βII-Spectrin | 8 | Q01082 | 240 | >10 | >10 | 6.30 |
| β-Raf | 25 | P15056 | 95/72 | >10 | >10 | 2.71 |
| Clathirin heavy chain | 39 | P11442 | 120 | >10 | >10 | 7.43 |
| CtBP1 | 26 | Q91W16 | 48 | >10 | >10 | |
| NSF | 13 | P46459 | 82 | >10 | 3.30 | 2.59 |
| SCAR-1 | 4 | Q92588 | 80 | >10 | 7.50 | 3.23 |
| SLK | 13 | NP_055535 | 125 | 4.00 | ||
| Smg/GDS | 13 | CAA45067 | 57 | (>+10) |