Table 7.
Average of individual peptide intensities for proteins associating with PAB1 deletion derivatives
| Protein | PAB1 | PAB1-ΔRRM1 | PAB1-ΔRRM2 | PAB1-ΔRRM3 | PAB1-ΔRRM4 | PAB1-ΔP | PAB1-ΔC |
|---|---|---|---|---|---|---|---|
| eIF4G1 | 100 | 7.4 (4.7) | 3.9 (1.1) | 120 (29) | 110 (16) | 140 (28) | 160 (30) |
| eIF4G2 | 100 | 8.6 (4.7) | 25 (13) | 74 (26) | 210 (25) | 110 (50) | 72 (30) |
| NAB6 | 100 | 3.8 (3.7) | 23 (5.2) | 62 (9.0) | 130 (20) | 100 (20) | 94 (23) |
| PBP2 | 100 | 300 (160) | 150 (31) | 130 (9.0) | 260 (21) | 220 (60) | 0(0) |
| SSD1 | 100 | 110 (45) | 53 (20) | 22 (3.5) | 170 (42) | 180 (44) | 190 (90) |
| GBP2 | 100 | 0(0) | 42 (13) | 81 (28) | 65 (19) | 120 (18) | 94 (24) |
Mass spectrometric analysis was conducted as described in Table 6. The intensities for the peptides for each individual protein described in Table 6 were compared across the PAB1 deletion derivatives. Peptides that were represented in all or nearly all Flag-PAB1 deletion derivative pull-downs were considered “good” peptides for cross comparisons of peptide intensities. For several proteins no peptides were found in a particular Flag-PABl deletion derivative pull-down, but the peptide was retained in the “good” data set if this absence correlated with the domain that was suggested for interacting with the protein based on the results in Table 6. For eIF4G1, 14 peptides were identified as "good' peptides; for eIF4G2, there were 4 peptides; for NAB6, there were 4 peptides; for PBP2, there were 3 peptides; for SSD1, there were 4 peptides; and for GBP2, there were 3 peptides. One or no "good" peptides were identified for the other proteins listed in Table 6. The relative intensities were normalized to 100 for PAB1, wt, and the value given in the table is the average of these values for all of the peptides for each protein. Standard errors of the mean are given in parentheses where applicable. As additional controls, analysis of average intensities for “good” peptides for several proteins not listed in Table 6 but which were included in Table 4 as not associating with PAB1 through any particular domain demonstrated no differences in intensities across the various PAB1 deletion derivative pull-downs (RLR1, RRP5, yLR419w, and XRN1 were analyzed)