TABLE 2.
Agreement between observed and calculated intermolecular PREs for the specific Sox2·DNA complex
The position of Sox2 on the 29-bp specific Hoxb1 regulatory element is taken from the NMR structure of the Oct1·Sox2·Hoxb1-DNA ternary complex (23). The entire experimental PRE profiles are best fitted by simultaneously optimizing the positions of all three paramagnetic labels, each represented by a three-member ensemble, using simulated annealing (30).
| NaCl | Root mean square deviation between observed and calculated Γ2 rates |
PRE Q-factor |
||||
|---|---|---|---|---|---|---|
| Site 1 | Site 2 | Site 3 | Site 1 | Site 2 | Site 3 | |
| mm | s−1 | |||||
| 0 | 3.6 | 6.7 | 2.6 | 0.43 | 0.24 | 0.98 |
| 50 | 6.9 | 12.6 | 7.1 | 0.64 | 0.48 | 0.99 |
| 150 | 9.1 | 15.5 | 9.5 | 0.72 | 0.61 | 1.00 |