Table 2.
Comparative cost of nucleosomal deformation of generic DNA basepair steps with knowledge-based functions based on different subsets of observed protein-bound DNA conformations
| Score | Olson et al. (11) | A+B+AB | B+AB | B | B+AB+TA | B+TA |
|---|---|---|---|---|---|---|
| 〈E〉 | 7.8 | 9.1 | 9.3 | 9.2 | 9.2 | 9.1 |
| E0 | 0.9 | 0.9 | 0.9 | 1.0 | 0.9 | 0.9 |
| E | 24.3 | 25.2 | 26.3 | 27.6 | 26.5 | 27.7 |
| SH0 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 | 0.1 |
| SH† | −2.0 | −1.5 | −1.5 | −1.5 | −1.5 | −1.5 |
Knowledge-based scores (average cost 〈E〉 over the central 60 basepair steps of the best-resolved nucleosome core particle structure (2) and the least and most costly values, E0 and E) derived from the basepair step parameters of DNA dimers of different conformational types in high-resolution protein-DNA structures. Locations SH0 and SH† of the least and most costly steps are expressed in terms of superhelical position, i.e., number of helical turns with respect to the structural dyad. See text and legend to Table 1.