TABLE 2.
Biotinylated proteinsa
| Protein ID | Protein description | WT MA-BirA* (%) | ΔMA-BirA* (%) | Ratio | Reference(s) |
|---|---|---|---|---|---|
| ATX2L_HUMAN | Ataxin-2-like protein | 21.2 | 0 | UD | 50 |
| CD2AP_HUMAN | CD2-associated protein | 12.6 | 0 | UD | None |
| CDV3_HUMAN | Protein CDV3 homolog | 10.6 | 0 | UD | None |
| DDX3X_HUMAN | ATP-dependent RNA helicase DDX3X | 8.1 | 0 | UD | 22, 36, 50, 67, 68 |
| E41L2_HUMAN | Band 4.1-like protein 2 | 12.6 | 0 | UD | None |
| GEMI5_HUMAN | Gem-associated protein 5 | 14.4 | 0 | UD | None |
| H12_HUMAN | Histone H1.2 | 9.1 | 0 | UD | 36, 50, 69 |
| HAP28_HUMAN | 28-kDa heat- and acid-stable phosphoprotein | 7.6 | 0 | UD | None |
| IF4G1_HUMAN | Eukaryotic translation initiation factor 4 gamma 1 | 12.1 | 0 | UD | 50, 69 |
| IF5_HUMAN | Eukaryotic translation initiation factor 5 | 9.6 | 0 | UD | 70 |
| KI67_HUMAN | Antigen KI-67 | 9.3 | 0 | UD | 67, 69 |
| LARP1_HUMAN | La-related protein 1 | 15.2 | 0 | UD | 50 |
| NUFP2_HUMAN | Nuclear fragile X mental retardation-interacting protein 2 | 12.6 | 0 | UD | 50 |
| PKP1_HUMAN | Plakophilin-1 | 7.6 | 0 | UD | None |
| PRC2A_HUMAN | Protein PRRC2A | 21.0 | 0 | UD | None |
| PRC2C_HUMAN | Protein PRRC2C | 27.5 | 0 | UD | None |
| RBM2 6_HUMAN | RNA-binding protein 26 | 7.4 | 0 | UD | None |
| RL40_HUMAN | Ubiquitin-60S ribosomal protein L40 | 11.7 | 0 | UD | 35, 69, 71 |
| SEMG1_HUMAN | Semenogelin-1 | 10.3 | 0 | UD | 72 |
| SEMG2_HUMAN | Semenogelin-2 | 12.4 | 0 | UD | 72 |
| SYEP_HUMAN | Bifunctional glutamate/proline-tRNA ligase | 9.9 | 0 | UD | 50, 69 |
| TOX4_HUMAN | TOX high-mobility-group box family member 4 | 16.5 | 0 | UD | None |
| UBAP2_HUMAN | Ubiquitin-associated protein 2 | 16.3 | 0 | UD | None |
| VIGLN_HUMAN | Vigilin | 12.2 | 0 | UD | None |
| XRN1_HUMAN | 5′–3′ exoribonuclease 1 | 12.6 | 0 | UD | 73 |
| UBP2L_HUMAN | Ubiquitin-associated protein 2-like | 28.9 | 1.1 | 27.4 | None |
| MAP4_HUMAN | Microtubule-associated protein 4 | 38.7 | 1.6 | 24.5 | 50, 67, 74–76 |
| IRS4_HUMAN | Insulin receptor substrate 4 | 16.7 | 1.1 | 15.8 | None |
| PERQ2_HUMAN | PERQ amino acid-rich with GYF domain-containing protein 2 | 22.7 | 1.6 | 14.4 | 50 |
| AFAD_HUMAN | Afadin | 13.6 | 1.1 | 13.0 | 69 |
| IF4B_HUMAN | Eukaryotic translation initiation factor 4B | 19.5 | 1.6 | 12.4 | None |
| FLNA_HUMAN | Filamin-A | 426.5 | 44.2 | 9.6 | 35, 67, 69, 77 |
| PAIRB_HUMAN | Plasminogen activator inhibitor 1 RNA-binding protein | 19.4 | 2.1 | 9.2 | None |
| 41_HUMAN | Protein 4.1 | 24.1 | 2.6 | 9.2 | 72 |
| DSG2_HUMAN | Desmoglein-2 | 18.7 | 2.6 | 7.1 | None |
| SRC8_HUMAN | Src substrate cortactin | 14.8 | 2.1 | 7.0 | 72 |
| HORN_HUMAN | Hornerin | 18.2 | 2.6 | 6.9 | None |
| E41L3_HUMAN | Band 4.1-like protein 3 | 17.4 | 2.6 | 6.6 | None |
| TCPQ_HUMAN | T-complex protein 1 subunit theta | 52.1 | 7.9 | 6.6 | None |
| AHNK_HUMAN | Neuroblast differentiation-associated protein AHNAK | 70.1 | 11.1 | 6.3 | 35 |
| TPR_HUMAN | Nucleoprotein TPR | 84.1 | 13.7 | 6.1 | 42, 69, 72 |
| FAS_HUMAN | Fatty acid synthase | 75.8 | 13.2 | 5.8 | 22, 36, 50, 69 |
| HNRPM_HUMAN | Heterogeneous nuclear ribonucleoprotein M | 8.9 | 1.6 | 5.7 | 22, 36, 50, 69 |
| AAAT_HUMAN | Neutral amino acid transporter B(0) | 8.8 | 1.6 | 5.6 | None |
| CSDE1_HUMAN | Cold shock domain-containing protein E1 | 19.8 | 3.7 | 5.4 | 50, 69, 71 |
| AT1A1_HUMAN | Sodium/potassium-transporting ATPase subunit alpha-1 | 12.5 | 2.6 | 4.8 | 22, 35, 67, 69 |
| FLNB_HUMAN | Filamin-B | 7.0 | 1.6 | 4.4 | 68, 69 |
| EF1A1_HUMAN | Elongation factor 1-alpha 1 | 46.9 | 15.8 | 3.0 | 50, 69, 71, 78 |
| LYRIC_HUMAN | Protein Lyric | 7.8 | 2.6 | 3.0 | 50, 69, 79 |
| POL | HIV-1 Pol | 7.8 | 3.2 | 2.5 | NA |
| GAG | HIV-1 Gag | 136.9 | 56.8 | 2.4 | NA |
| ZCCHV_HUMAN | Zinc finger CCCH-type antiviral protein 1 | 57.7 | 35.3 | 1.6 | 50, 69, 80 |
| PRKDC_HUMAN | DNA-dependent protein kinase catalytic subunit | 8.3 | 5.3 | 1.6 | 22, 50, 67, 69, 71 |
| BIRA* | E. coli bifunctional ligase/repressor BirA* | 100 | 100 | 1 | NA |
| 4F2_HUMAN | 4F2 cell surface antigen heavy chain | 8.3 | 8.4 | 1.0 | 35, 67, 69 |
| LAP2B_HUMAN | Lamina-associated polypeptide 2, isoforms beta/gamma | 15.5 | 16.3 | 0.9 | 50, 69 |
| ENV | HIV-1 Env | 0 | 10.5 | 0 | NA |
Proteins specifically biotinylated in transfected cell samples were determined as described in Materials and Methods. The left two columns give protein UniProt ID names and descriptions. The third and fourth columns give MS signals in WT MA-BirA*-transfected and ΔMA-BirA*-transfected cells, respectively: these values are percentages of the BirA* protein signals in the respective transfected cell samples. The list is ordered based on the values in the ratio column, which lists the percent WT BirA*/percent ΔMA BirA* ratios, where UD means “undefined.” The rightmost column indicates references to publications of research exploring whether a protein has or has not been previously implicated as an effector of HIV-1 replication, as an HIV-1 binding protein, or as present in HIV-1 virus particles. Numbers in this column refer to cited reference numbers. The HIV-1 Env peptides identified in the ΔMA-BirA* sample all mapped to the TM CT and represented the following env codons: 724 to 738, 746 to 759, 760 to 768, 769 to 778, 779 to 785, 817 to 826, and 827 to 836. Note that these represent sequenced peptides from the biotinylated TM protein but do not necessarily represent the specifically biotinylated peptides. None, no previous references; NA, not applicable.