Table 1. Proteins and peptides with modulated phosphorylation in HuH7 cells expressing HCV core protein.
| Ratio cT/ WT | ||||||||
|---|---|---|---|---|---|---|---|---|
| Gene Names | Accession number | Protein Names | Modified sequence | Probabilities of phosphorylation on STY | Phosphorylated position | S1 | S2 | S3 |
| BCKDHA | F5H5P2 | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | IGHHS(ph)T(ph)SDDSSAYRSVDEVNYWDKQDHPISR | S(0.424)T(0.424) | S371/T372 | 2.58 | _ | _ |
| IGHHS(ph)TSDDSSAY(ph)RSVDEVNYWDK | S(0.748)Y(0.283) | S371/Y379 | _ | 2.36 | 1.54 | |||
| SNTB1 | Q13884 | Beta-1-syntrophin | LVHSGPGKGS(ph)PQAGVDLSFATR | S(1) | S389 | 3.8 | 1.67 | 1.83 |
| SH3KBP1 | Q96B97 | SH3 domain-containing kinase-binding protein 1 | S(ph)IEVENDFLPVEK | S(1) | S230 | 2.05 | _ | 2.08 |
| RPS6KA3;RPS6KA6 | P51812 | Ribosomal protein S6 kinase alpha-3 | KAYS(ph)FCGTVEYMAPEVVNRR | S(0.987) | S227 | _ | 2.57 | _ |
| TPKDS(ph)PGIPPSANAHQLFR | S(0.998) | S369 | 1.5 | 3.98 | 1.77 | |||
| SDAD1 | Q9NVU7 | Protein SDA1 homolog | YIEIDS(ph)DEEPRGELLSLR | S(1) | S585 | 2.11 | 1.7 | 1.5 |
| FAM122A | Q96E09 | Protein FAM122A | RIDFIPVS(ph)PAPS(ph)PTR | S(1)S(0.99) | S143/S147 | _ | 2.03 | 1.59 |
| EIF4EBP1 | Q13541 | Eukaryotic translation initiation factor 4E-binding protein 1 | RVVLGDGVQLPPGDYSTT(ph)PGGTLFSTT(ph)PGGTR | T(0.968)T(0.493) | T37/T46 | 1.15 | 2.95 | 2.23 |
| EIF4EBP2 | Q13542 | Eukaryotic translation initiation factor 4E-binding protein 2 | TVAISDAAQLPHDYCTT(ph)PGGTLFSTT(ph)PGGTR | T(0.5)T(0.469) | T37/T46 | _ | 1.96 | 1.81 |
| SRP72 | O76094 | Signal recognition particle 72 kDa protein | TVSSPPTS(ph)PRPGS(ph)AATVSASTSNIIPPR | S(0.31)S(0.354) | S625/S630 | _ | 2.03 | 1.81 |
| EHBP1 | Q8NDI1 | EH domain-binding protein 1 | DLSTS(ph)PKPSPIPS(ph)PVLGR | S(0.739)S(0.998) | S428/S436 | 1.67 | _ | 2 |
| DLSTS(ph)PKPS(ph)PIPS(ph)PVLGR | S(0.401)S(1)S(1) | S428/S432/S436 | 1.52 | 2.29 | 2 | |||
| TMPO | P42167 | Lamina-associated polypeptide 2, isoforms beta/gamma | GPPDFS(ph)S(ph)DEEREPT(ph)PVLGSGAAAAGR | S(1)S(1)T(0.987) | S66/S67/T74 | _ | 2.08 | 1.52 |
| SEC16A | J3KNL6 | Protein transport protein Sec16A | GSVSQPS(ph)T(ph)PS(ph)PPKPTGIFQTSANSSFEPVK | S(0.715)T(0.715)S(0.81) | S592/T593/S595 | _ | 2.97 | 1.88 |
| TPI1 | P60174 | Triosephosphate isomerase | KQS(ph)LGELIGTLNAAK | S(1) | S58 | 1.63 | 2.41 | 2.79 |
| NUCKS1 | Q9H1E3 | Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 | KVVDYS(ph)QFQESDDADEDYGRDSGPPTK | S(0.526) | S14 | _ | 2.2 | 1.79 |
| VVDYSQFQES(ph)DDADEDYGRDSGPPTK | S(0.992) | S19 | _ | 2.07 | 1.82 | |||
| FAM21A;FAM21B | Q641Q2 | WASH complex subunit FAM21A;WASH complex subunit FAM21B | ASALLFS(ph)S(ph)DEEDQWNIPASQTHLASDSR | S(0.999)S(1) | S619/S620 | _ | 1.51 | 2.69 |
| CDS2 | O95674 | Phosphatidate cytidylyltransferase 2 | VAHEPVAPPEDKES(ph)ESEAKVDGET(ph)ASDSESR | S(0.714)T(0.537) | S21/T31 | _ | 1.59 | 2.39 |
| MAP4 | E7EVA0 | Microtubule-associated protein 4 | DMES(ph)PTKLDVTLAK | S(0.995) | S297 | _ | 2.27 | 2.2 |
| EIF4B | E7EX17 | Eukaryotic translation initiation factor 4B | SLENETLNKEEDCHSPT(ph)SKPPKPDQPLK | T(0.917) | T466 | _ | 1.63 | 3.39 |
| SYAP1 | Q96A49 | Synapse-associated protein 1 | EQDLPLAEAVRPKT(ph)PPVVIK | T(1) | T248 | _ | 2.37 | 1.52 |
| HMGCS1 | Q01581 | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | RPTPNDDTLDEGVGLVHSNIATEHIPS(ph)PAK | S(0.999) | S495 | 1.52 | _ | 3.82 |
| EPB41L2 | O43491 | Band 4.1-like protein 2 | EVRS(ph)PTKAPHLQLIEGK | S(1) | S598 | _ | 1.77 | 2.16 |
| EPPK1 | P58107 | Epiplakin | RQVS(ph)ASELHTSGILGPETLR | S(0.918) | S2716 | 1.71 | 2 | _ |
| ABCF1 | Q8NE71 | ATP-binding cassette sub-family F member 1 | KLS(ph)VPT(ph)S(ph)DEEDEVPAPKPR | S(1)T(1)S(1) | S105/T108/S109 | 2.69 | 2.12 | _ |
| HSPB1 | P04792 | Heat shock protein beta-1 | GPS(ph)WDPFRDWYPHSR | S(1) | S15 | 4.21 | 3.02 | 2.99 |
| TJP1 | G3V1L9 | Tight junction protein ZO-1 | VQIPVSRPDPEPVS(ph)DNEEDSY(ph)DEEIHDPR | S(0.963)Y(0.783) | S125/Y132 | 0.54 | 0.55 | _ |
| HNF1B | P35680 | Hepatocyte nuclear factor 1-beta | GRLS(ph)GDEGS(ph)EDGDDYDTPPILK | S(1)S(1) | S75/S80 | 0.39 | 0.38 | _ |
| EPS8L3 | Q8TE67-3 | Epidermal growth factor receptor kinase substrate 8-like protein 3 | RS(ph)SS(ph)PEDPERDEEVLNHVLR | S(0.667)S(0.667) | S229/S231 | 0.46 | 0.4 | _ |
| LRP2 | P98164 | Low-density lipoprotein receptor-related protein 2 | ES(ph)VAATPPPS(ph)PSLPAKPKPPSR | S(0.942)S(0.958) | S4608/S4616 | 0.2 | 0.26 | _ |
| RAB11FIP1 | Q6WKZ4 | Rab11 family-interacting protein 1 | HLFSS(ph)TENLAAGSWKEPAEGGGLSSDR | S(0.805) | S357 | 0.31 | 0.46 | _ |
| KRT18 | P05783 | Keratin, type I cytoskeletal 18 | STSFRGGMGS(ph)GGLATGIAGGLAGMGGIQNEK | S(0.776) | S60 | _ | 0.32 | 0.55 |
| SQSTM1 | Q13501 | Sequestosome-1 | KIALESEGRPEEQMES(ph)DNCS(ph)GGDDDWTHLSSK | S(0.997)S(0.998) | S328/S332 | _ | 0.54 | 0.41 |
The table encompasses the genes, protein names and their accession numbers according to the UniProt-SwissProt database. In the peptide sequences, (ph) after S/T/Y residue indicates the phosphorylated status. The probability for the site of phosphorylation was calculated by MaxQuant. The study was performed in biological triplicate (S1/S2/S3) and Phosphorylated peptides were considered to be significantly regulated when exhibiting an abundance ratio core/WT exceeding mean + 1.96 standard deviation in at least two replicates.