Table V. Identified nucleotide-binding proteins in capture experiments using 8-AHA-cAMP-CC (7c) in rat brain synaptosomal fractions (65–80 μg of total protein mixture as input).
All proteins were captured even in competition experiments when capturing was carried out in the presence of 2 mm 8-AHA-cAMP (4c). However, competition experiments were successful with other nucleotides (see column “Competition”). Proteins captured by scaffold 1 were disregarded except for DHE3, which showed binding to 1 although with a low number of identified peptides and assigned spectra. The identified unique peptides have a probability of ≥95% (sequences are reported in the supplemental material).
| No. | Protein name | UniProt/Swiss-Prot accession number | No. of identified peptides (runs 1–4) | No. of assigned spectra (runs 1–4) | Coverage | Competitiona | Molecular mass |
|---|---|---|---|---|---|---|---|
| % | kDa | ||||||
| 1 | DHE3, glutamate dehydrogenase 1, mitochondrial | P10860 | 14/27/22/14 | 17/47/36/20 | 28/44/35/32 | GTP, NADH | 61 |
| 2 | IMMT, inner membrane protein, mitochondrial | Q3KR86 | 13/14/4/8 | 15/16/5/8 | 27/30/8/19 | (ATP, GTP) | 67 |
| 3b | MPCP | P16036 | 3/5/9/6 | 3/8/19/9 | 8/15/19/21 | None | 39 |
| 4 | ATPB, ATP synthase subunitβ, mitochondrial | P10719 | 6/15/8/5 | 7/19/10/5 | 18/45/22/14 | (ATP, GTP) | 56 |
| 5 | EFTU, elongation factor Tu, mitochondrial | P85834 | 4/6/8/3 | 5/8/9/3 | 12/17/21/10 | (GTP, NADH) | 50 |
| 6 | ATAD3, ATPase family AAA domain-containing protein 3 | Q3KRE0 | 6/5/2/2 | 6/5/3/2 | 12/11/4/5 | (ATP) | 67 |
| 7 | ITPR1, inositol 1,4,5-trisphosphate receptor type 1 | P29994 | 2/7/6/10 | 2/7/6/10 | 1.1/3/1.9/6 | (GTP) | 313 |
| 8 | SEPT7, septin-7 | Q9WVC0 | 3/10/3/5 | 3/14/3/7 | 10/27/8/12 | NADH | 51 |
| 9 | GNAO, guanine nucleotide-binding protein Go subunit α | P59215 | 5/7/3/7 | 5/8/3/10 | 18/25/11/25 | (NADH) | 40 |
| 10 | STXB1, syntaxin-binding protein 1 | P61765 | 3/7/2/3 | 3/7/2/3 | 10/16/4/5 | (GTP) | 68 |
| 11 | AP3D1, adaptor-related protein complex 3, δ 1 subunit, isoform CRA_b | B5DFK6 | 3/4/4/6 | 3/5/5/6 | 4/5/5/7 | (NADH) | 136 |
| 12 | AT2B1, plasma membrane calcium-transporting ATPase 1 | P11505 | 3/4/2/7 | 3/4/2/7 | 3/4/2/7 | (NADH) | 139 |
| 13 | AT1A1, sodium/potassium-transporting ATPase subunit α -1 | P06685 | 4/4/1/9 | 4/4/1/12 | 6/5/1.8/11 | (GTP) | 113 |
| 14 | RAB3A, Ras-related protein Rab-3A | P63012 | 4/1/0/2 | 4/1/0/2 | 28/5/0/18 | GTP | 25 |
| 15 | SEPT8, septin-8 | B0BNF1 | 2/2/1/1 | 3/2/1/1 | 6/6/2/4 | NADH | 51 |
| 16 | GBRA1, γ-aminobutyric acid receptor subunit α -1 | P62813 | 2/5/1/0 | 2/5/1/0 | 5/13/2/0 | NADH, (ATP) | 52 |
| 17 | CN37, 2′,3′-cyclic-nucleotide 3′-phosphodiesterase | P13233 | 3/3/1/5 | 3/3/1/5 | 9/9/3/14 | ATP | 47 |
| 18 | SV2A, synaptic vesicle glycoprotein 2A | Q02563 | 2/1/2/3 | 2/1/3/3 | 11/1.5/3/5 | NADH | 83 |
a Nucleotides in parentheses did not give complete competition. Incomplete competition was defined to be the case when two or more assigned spectra but less than the half of those found in capture experiments were identified in the competition experiments.
b MPCP was captured in the presence of any of the three nucleotides used for competition (ATP, GTP, and NADH).