Table II.
Proteins specifically interacting with the MCP21 antibody: proteins known to belong to or to be related to the UPP
Proteins listed in the table were purified as described under “Experimental Procedures,” separated by SDS-PAGE, and identified by nano-LC-ESI-LTQ-Orbitrap MS/MS analysis and database searching in the Swiss-Prot TrEMBL database. Nonspecific interactions could be eliminated by performing a differential analysis with proteins purified with the OX8 antibody and similarly identified. Criteria for acceptance of protein identification are described under “Experimental Procedures.” For proteins identified in several repeats, the best results in terms of protein recovery are reported. N, “normal,” i.e. without formaldehyde cross-linking; F, “formaldehyde,” i.e. with formaldehyde cross-linking.
| Name | Accession no.a | No. of unique peptides
|
Sequence coverage
|
MS/MS counting (n = 2)
|
Ref.c | |||
|---|---|---|---|---|---|---|---|---|
| N | F | N | F | Averaged ratio F/Nb | S.D. | |||
| % | ||||||||
| Ubiquitind | P62988 | 6 | 6 | 68 | 68 | 1.8 | 0.3 | 32 |
| Deubiquitinating enzymes | ||||||||
| USP14d | P54578 | 11 | 25 | 23 | 55 | 3.8 | 0.5 | 32 |
| UCH37d | Q9Y5K5 | 8 | 10 | 26 | 37 | 1.3 | — | 32 |
| USP7 | Q93009 | 28 | 0 | 25 | 0 | — | — | |
| E3 ligases | ||||||||
| F-box protein7e | Q5TGC3 | 14 | 10 | 25 | 19 | 0.4 | 0.1 | 25 |
| SKP1e | P63208 | 18 | 14 | 85 | 64 | 0.5 | 0.1 | 25 |
| Cullin-1e | Q13616 | 49 | 0 | 65 | 0 | — | — | 25 |
| Ring-box protein 1f | P62877 | 1 | 0 | 26 | 0 | — | — | |
| Ubiquitin-protein ligase E3Cd,f | Q15386 | 19 | 0 | 21 | 0 | — | — | 32 |
| Cullin-associated NEDD8-dissociated protein 1f | Q86VP6 | 0 | 7 | 0 | 9 | — | — | |
| Multiubiquitin chain-binding proteins | ||||||||
| hHR23Bd | P54727 | 0 | 3 | 0 | 7 | — | — | 32 |
| DDI1 homolog 2e,f | Q5TDH0 | 0 | 3 | 0 | 9.5 | — | — | 55 |
| eEF1α1d | P68104 | 0 | 5 | 0 | 16 | — | — | 32 |
| PACs | ||||||||
| PAC1 | Q6FHD3 | 8 | 9 | 31 | 37 | 1.3 | 0.4 | 52, 53 |
| PAC2 | Q969U7 | 8 | 13 | 28 | 38 | 2.3 | — | 52, 53 |
| PAC3 | A4D216 | 0 | 3 | 0 | 26 | — | — | 52, 53 |
| Chaperones | ||||||||
| HSP70 1d | P08107 | 12 | 2 | 27 | 4 | 0.5 | — | 32 |
| Heat shock cognate 71d | P11142 | 28 | 10 | 46 | 17 | 0.3 | — | 32 |
| HSP90-βd | P08238 | 0 | 5 | 0 | 14 | — | — | 32 |
| HSPA5 | Q2KHP4 | 0 | 3 | 0 | 8 | — | — | |
| Valosin-containing proteind | Q0V924 | 7 | 20 | 12 | 31 | 3.6 | 0.1 | 74 |
| TCP-1γd,f | P49368 | 2 | 0 | 4 | 0 | — | — | 21, 32 |
| TCP-1ηd,f | Q99832 | 2 | 0 | 6 | 0 | — | — | 21, 32 |
For greater clarity, the reported member of the protein group is the one that we considered as the most significant according to the functional description given in the UniProt Knowledgebase.
MS/MS counting ratios (F/N) were calculated when a significant number of MS/MS scans (>50) was performed at least for one experiment (without or with formaldehyde cross-linking). Statistical data were obtained from two independent replicates. When no averaged ratio is indicated, it means that the total MS/MS number for the protein did not reach 50. If no standard deviation is provided, the MS/MS threshold of 50 was reached only with one of the experiments. Dashes indicate that no value could be obtained for the reasons explained above.
Selected references reporting this protein as a PIP by affinity purification strategies or other biochemical approaches.
Reported human PIPs.
Reported PIPs only in other species.
Identified in one experiment only.