Table 2.
List of the proteins that were selected for interactome analysis.
| Protein | Gene | Proteoform | Lost or gained domains and motifs |
|---|---|---|---|
| Q12904 Aminoacyl-tRNA synthetase complex–interacting multifunctional protein 1 Length: 312 AA | AIMP1 | Known UniProt isoform Q12904-2; N-terminal extension of 24 AA | Gain of three linear motifs according to ELM: binding motif for UBA3 adenylation (AA 17–24), SH3 ligand (AA 4–10), and SPAK/OSR1-docking motif (AA 14–18) |
| Q9HB71 Calcyclin-binding protein Length: 228 AA | CACYBP | Known UniProt isoform Q9HB71-3; N-terminal truncation of 43 AA. | Partial loss of region for interaction with SIAH1 (AA 2–80) |
| Q14444 Caprin-1 Length: 709 AA | CAPRIN1 | High-confident N-terminal proteoform; N-terminal truncation of 116 AA | Loss of the coiled-coil domain (60–94) |
| P20810 Calpastatin Length: 708 | CAST | The identified N-terminal peptide cannot differentiate which proteoform was identified: known UniProt isoforms P20810-4 (missing AA 9-30 and AA 44–62) or P20810-8 only missing AA 9–30. | — |
| Q9Y281 Cofilin-2 Length: 166 AA | CFL2 | Known UniProt isoform Q9Y281-3; N-terminal truncation of 17 AA | Partial loss of the region for interaction with CSRP3 (AA 2–55) and partial loss of the ADF-H domain (AA 4–153). |
| O75535 Cold shock domain–containing protein E1 Length: 798 AA | CSDE1 | High-confident N-terminal proteoform; N-terminal truncation of 176 AA | Loss of the CDS1 domain (AA 26–87) and loss of most of the CSD2 domain (AA 136–179) |
| P60842 Eukaryotic initiation factor 4A-I Length: 406 | EIF4A1 | High-confident N-terminal proteoform; N-terminal truncation of 211 AA | Partial loss of the helicase ATP-binding domain (63–234), loss of a Q motif (AA 32–60), and loss of a DEAD box motif (AA 182–185) |
| P49354 Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha Length: 379 AA | FNTA | High-confident N-terminal proteoform; N-terminal truncation of 38 AA | Loss of a Pro-rich region (AA 22–31) |
| Q7Z434 Mitochondrial antiviral-signaling protein Length: 540 AA | MAVS | Known UniProt isoform Q7Z434-4; N-terminal truncation of 141 AA | Loss of the CARD domain (AA 10–77), loss of the region for interaction with NLRX1 (AA 10–77), partial loss of the Pro-rich region (AA 103–153), and the region for TRAF2 interaction becomes outer N-terminal |
| Q9H074 Polyadenylate-binding protein–interacting protein 1 Length: 479 AA | PAIP1 | Known UniProt isoform Q9H074-3; N-terminal truncation of 112 AA | Loss of the Gly-rich region (AA 10–36), loss of the Pro-rich region (AA 45–98), and PABPC interaction motif 2 becomes N-terminal (AA 116–143) |
| Q14558 Phosphoribosyl pyrophosphate synthase–associated protein 1 Length: 356 AA | PRPSAP1 | Known UniProt isoform Q14558-2; N-terminal extension of 29 AA | Gain of 11 linear motifs according to ELM |
| Q86TP1 Exopolyphosphatase PRUNE Length: 453 AA | PRUNE | The identified N-terminal peptide cannot differentiate which proteoform was identified: known UniProt isoforms Q86TP1-3 (missing AA 1–182) and Q86TP1-5 (missing AA 1–182 and AA 259–311) | Loss of a DHH motif (AA 106–108) |
| P49023 Paxillin Length: 591 | PXN | Known UniProt isoform P49023-4; N-terminal truncation of 133 AA and also missing AA 278–311 | Loss of a LD motif (AA 3–15) and loss of the Pro-rich region (AA 46–53) |
| P54136 Arginine-tRNA ligase, cytoplasmic Length: 660 AA | RARS | Known UniProt Isoform P54136-2; N-terminal truncation of 72 AA | Loss of a region that could be involved in the assembly of the multisynthetase complex (AA 1–72) |
| Q9UBP0 Spastin Length: 616 AA | SPAST | The identified N-terminal peptide cannot differentiate which proteoform was identified: known UniProt isoforms Q9UBP0-3 (missing AA 1–86) or Q9UBP0-4 (missing AA 1–86 and AA 197–228) | Loss of the region for interaction with ATL1 (AA 1–80), loss of the region needed for nuclear localization (AA 1–50), loss of the region for interaction with SSNA1 and microtubules (AA 50–87), loss of NLS (AA 4–11), loss of nuclear export signal (AA 59–67), partial loss of the region for interaction with RTN1 (AA 1–300), and partial loss of the region for midbody localization (AA 1–194) |
| Q99576 TSC22 domain family protein 3 Length: 134 AA | TSC22D3 | High-confident N-terminal proteoform; N-terminal truncation of 57 AA. | Almost complete loss of the AP1-binding region |
| Q9BSL1 Ubiquitin-associated domain–containing protein 1 Length: 405 AA | UBAC1 | High-confident N-terminal proteoform; N-terminal truncation of 102 AA | Loss of the ubiquitin-like domain (AA 14–98) |
| P61081 NEDD8-conjugating enzyme Ubc12 Length: 183 AA | UBE2M | High-confident N-terminal proteoform; N-terminal extension of 42 AA. | Gain of a caspase cleavage motif (AA 14–18), gain of a glycosaminoglycan attachment site (AA 13–16 and 35–38), gain of a IAP-binding motif (AA 1–4 and 17–21), and gain of a TRAF2-binding site (AA 3–6) |
| Q9BZV1 UBX domain–containing protein 6 Length: 441 AA | UBXN6 | Known UniProt isoform Q9BZV1-2; N-terminal truncation of 53 AA | Loss of the region for interaction with LMAN1 (AA 1–10) and a VCP/p97-interacting motif (VIM) becomes N-terminal, with 2 AA removed (AA 51–63) |
| P09936 Ubiquitin carboxyl-terminal hydrolase isozyme L1 Length: 223 AA | UCHL1 | Two high-confident N-terminal proteoforms: N-terminal truncations of 5 or 11 AA | Proteoform 1: ubiquitin interaction domain (AA 5–11) becomes outer N-terminal Proteoform 2: loss of the ubiquitin interaction domain (AA 5–11) |
| Q8TCF1 AN1-type zinc finger protein 1 Length: 268 | ZFAND1 | Known UniProt isoform Q8TCF1-2; N-terminal truncation of 107 AA | Loss of the AN1-type 1 zinc finger domain (7–58) and loss of most of the AN1-type 2 zinc finger domain (AA 61-110) |
| ENST00000403258 ACTB pseudogene 8 Length: 146 AA | NTR protein | High-confident N-terminal proteoform; N-terminal truncation of 11 AA | ELM predicts several motifs and domains for this protein. |
For each protein, information about the canonical protein is provided (UniProt protein accession and gene name), and about the N-terminal proteoform(s) concerning the length of the truncation or extension. In the last column, differences between the canonical proteins and the N-terminal proteoforms with regard to domains, motifs, or ELMs are listed.