Table 2. Examples of non-histone proteins detected by MS in the supernatants of Dox-treated, Dox + PYR-41 co-treated and control samples.
| Protein function | Increased fraction | Examples | Fold change (Dox) | Fold change (Dox + PYR-41) |
|---|---|---|---|---|
| Chromatin architecture | 9/9 | Isoform 2 of Nucleosome assembly protein 1-like 1 | 6.70 | 2.81 |
| Regulator of chromosome condensation 2, isoform CRA_a | 4.42 | 3.79 | ||
| Isoform 2 of Histone deacetylase 2 | 1.68 | 0.79 | ||
| Histone acetyltransferase type B catalytic subunit | 6.10 | 4.52 | ||
| Lamina-associated polypeptide 2, isoforms beta/gamma | 2.80 | 2.60 | ||
| Transcription / RNP / Splicing | 32/34 | U5 small nuclear ribonucleoprotein 200 kDa | 3.32 | 0.54 |
| Heterogeneous nuclear ribonucleoprotein K, isoform CRA_d | 2.39 | 1.87 | ||
| Pre-mRNA-processing factor 19 | 5.96 | 3.39 | ||
| RNA transcription, translation and transport factor protein | 2.01 | 1.27 | ||
| Isoform 3 of 60 kDa SS-A/Ro ribonucleoprotein | 2.36 | 2.08 | ||
| Replication / Repair | 20/20 | RuvB-like helicase (Fragment) | 3.11 | 1.23 |
| DNA helicase | 2.28 | 2.42 | ||
| Poly [ADP-ribose] polymerase 1 | 2.70 | 2.07 | ||
| DNA-dependent protein kinase catalytic subunit | 2.83 | 1.41 | ||
| DNA replication licensing factor MCM6 | 2.72 | 2.84 | ||
| Nuclear Import / Export | 8/8 | Importin-7 | 2.78 | 0.52 |
| GTP-binding nuclear protein Ran | 2.98 | 2.46 | ||
| Importin-5 | 2.35 | 2.24 | ||
| Importin subunit beta-1 OS | 3.19 | 3.55 | ||
| Exportin-1 | 1.36 | 1.12 | ||
| Ubiquitination / Proteasome / SUMOylation | 32/34 | Proteasome subunit alpha type | 2.72 | 0.63 |
| SUMO-activating enzyme subunit 2 | 2.52 | 2.40 | ||
| SUMO-activating enzyme subunit 1 | 1.60 | 2.26 | ||
| Polyubiquitin-B (Fragment) | 3.54 | 4.25 | ||
| Proteasome activator complex subunit 2 | 2.00 | 2.11 | ||
| Heat Shock Proteins | 4/5 | Heat shock 60kDa protein 1 (Chaperonin), isoform CRA_a | 2.25 | 2.53 |
| Heat shock protein HSP 90-beta | 2.51 | 2.58 | ||
| Heat shock 70 kDa protein 4 | 2.71 | 2.71 | ||
| Isoform Beta of Heat shock protein 105 kDa | 2.34 | 2.16 |
Fold change was calculated as in Table 1. Increased fraction in the functional categories designates the ratio of the number of different proteins with elevated levels in the supernatant (fold change (Dox) > 1) and the total number of identified proteins in that functional group. Proteins exhibiting reversal of the Dox-effect by PYR-41 are shown in italics.