Table I. A list of proteins that can bind to aptamer Sgc-3b or Sgc-4e identified using the SILAC method.
| Refseq protein accession | Gene symbol | Description | Unique peptides | Sequence coverage (%) | PEPa | Protein abundance ratio (Sgc-3b/Sgc-4e)b |
|---|---|---|---|---|---|---|
| Specific binding proteins toward aptamer Sgc-3b or Sgc-4e | ||||||
| NP_000646 | SELL | Selectin L precursor | 4 | 11.7 | 4.75E-47 | 13.00 ± 3.61 |
| NP_006280 | TLN1 | Talin-1 | 4 | 1.9 | 1.97E-19 | 0.15 ± 0.07 |
| NP_000876 | ITGA4 | Integrin α-4 precursor | 13 | 14.5 | 1.69E-77 | 0.07 ± 0.03 |
| NP_002202 | ITGB1 | Isoform β-1A of Integrin β-1 | 7 | 10.9 | 9.95E-25 | 0.07 ± 0.03 |
| Endogenously biotinylated proteins | ||||||
| NP_000402 | HLCS | Biotin-protein ligase | 6 | 7.9 | 1.47E-13 | 1.13 ± 0.14 |
| NP_000911 | PC | Pyruvate carboxylase | 42 | 43.5 | 0 | 1.08 ± 0.05 |
| NP_000273 | PCCA | Propionyl-Coenzyme A carboxylase, α polypeptide isoform a precursor | 32 | 48.6 | 0 | 1.04 ± 0.05 |
| NP_071415 | MCCC2 | Isoform 1 of Methylcrotonoyl-CoA carboxylase β chain | 12 | 28.6 | 3.30E-84 | 1.02 ± 0.08 |
| NP_064551 | MCCC1 | Methylcrotonoyl-CoA carboxylase subunit α | 19 | 35.2 | 6.91E-214 | 0.99 ± 0.06 |
| NP_000523 | PCCB | Propionyl coenzyme A carboxylase, β polypeptide, isoform CRA_c | 19 | 43.6 | 0 | 0.97 ± 0.11 |
| NP_942131 | ACACA | Isoform 4 of Acetyl-CoA carboxylase 1 | 64 | 28.2 | 0 | 0.93 ± 0.07 |
| Proteins with similar binding affinities toward aptamers Sgc-3b and Sgc-4e | ||||||
| NP_001460 | XRCC6 | X-ray repair cross-complementing protein 6 | 33 | 49.3 | 1.34E-251 | 1.58 ± 0.76 |
| NP_066964 | XRCC5 | ATP-dependent DNA helicase 2 | 25 | 34.7 | 2.90E-191 | 1.57 ± 0.81 |
| NP_006089 | GNB2L1 | Guanine nucleotide-binding protein subunit β-2-like 1 | 4 | 13.2 | 1.3904E-09 | 1.42 ± 0.52 |
| NP_031381 | HSP90AB1 | Heat shock protein HSP 90-β | 5 | 14.8 | 4.14E-66 | 1.15 ± 0.40 |
| NP_003134 | SSBP1 | Single-stranded DNA-binding protein | 4 | 33.1 | 4.71E-123 | 1.11 ± 0.92 |
| NP_001949 | EEF1A2 | Elongation factor 1-α2 | 3 | 6.3 | 2.03E-11 | 1.11 ± 0.51 |
| NP_006588 | HSPA8 | Isoform 1 of heat shock cognate 71 kDa protein | 6 | 10.7 | 2.67E-51 | 1.09 ± 0.39 |
| NP_003312 | TUFM | Tu translation elongation factor | 3 | 9.5 | 8.85E-18 | 1.00 ± 0.13 |
| NP_002147 | HSPD1 | 60 kDa heat shock protein | 15 | 29.3 | 1.54E-79 | 0.94 ± 0.08 |
| NP_004125 | HSPA9 | Stress-70 protein | 6 | 9.6 | 4.12E-36 | 0.92 ± 0.16 |
a PEP, the posterior error probability. This value essentially operates as a p value, where smaller is better.
b The data represent the mean and standard deviation of results from independent forward and reverse pull-down experiments.