Table 1.
Sequences and binding affinities of peptides BIV-5 and R-01 to R-28 to RRE, as determined in EMSA.[a]
| Mimetic | 1 | 2 | 3 | 4 | 5 | Position | 8 | 9 | 10 | 11 | 12 | Kd | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 6 | 7 | [μm] | |||||||||||
| BIV-5 | R | R | G | T | R | G | K | R | R | I | G | R | 0.3 |
| R-01 | W | R | R | R | A | T | DR | Q | R | N | R | R | 1 |
| R-02 | W | R | R | R | A | P | DR | Q | R | N | R | R | 1 |
| R-03 | W | R | R | R | G | P | DR | Q | R | N | R | R | 0.5 |
| R-04 | W | R | R | R | V | P | DR | Q | R | N | R | R | 1 |
| R-05 | W | R | R | R | A | G | DR | Q | R | N | R | R | 0.4 |
| R-06 | W | R | R | R | A | G | K | Q | R | N | R | R | 0.3 |
| R-07 | W | R | R | R | A | T | DR | G | R | N | R | R | 0.3 |
| R-08 | W | R | R | R | A | P | DR | G | R | N | R | R | 0.5 |
| R-09 | W | R | R | R | G | P | DR | G | R | N | R | R | 0.5 |
| R-10 | W | R | R | R | G | T | DR | Q | R | N | R | R | 0.7 |
| R-11 | W | R | R | R | V | G | DR | Q | R | N | R | R | 0.5 |
| R-12 | W | R | R | R | A | S | DR | Q | R | N | R | R | 0.4 |
| R-13 | W | R | R | R | A | K | G | Q | R | N | R | R | 0.2 |
| R-14 | W | R | L | R | A | K | G | Q | R | N | R | R | nd |
| R-15 | W | R | Q | R | A | K | G | Q | R | N | R | R | nd |
| R-16 | W | R | R | R | A | K | G | Q | R | N | R | V | 0.5 |
| R-17 | W | R | L | R | A | DR | G | Q | R | N | R | R | 0.4 |
| R-18 | W | R | L | R | A | K | K | Q | R | N | R | R | 0.3 |
| R-19 | W | R | K | R | A | G | K | Q | R | N | R | R | 0.4 |
| R-20 | W | R | K | R | A | K | G | Q | R | N | R | R | 0.2 |
| R-21 | W | R | R | R | A | DR | G | Q | R | N | R | R | 0.5 |
| R-22 | W | R | L | R | A | DR | G | K | R | N | R | R | 0.25 |
| R-23 | W | R | R | R | A | G | R | Q | R | N | R | R | 0.15 |
| R-24 | R | R | L | R | A | DR | G | Q | R | N | R | R | 0.1 |
| R-25 | R | R | L | R | A | K | G | Q | R | N | R | R | 0.1 |
| R-26 | R | V | R | R | A | K | G | Q | R | N | R | R | 0.3 |
| R-27 | R | C | R | R | A | K | G | Q | R | R | C | R | 0.1 |
| R-28 | K | R | Q | R | T | K | G | R | R | L | O | R | 0.1 |
a
Positions 1–12 refer to residues 1–12 as mounted on the D-Pro-L-Pro template (Figure 2, left). The dissociation constants (Kd) were determined in the presence of a large excess (280 μgmL–1) of E. coli tRNA that was used as a control for nonspecific binding. Binding reactions were conducted in Tris-HCl buffer (50 mM, pH 8.0), KCl (50 mM), 1,4-dithiothreitol (DTT; 200 mM) and Triton X-100 (0.05%). nd = no binding detected.