Table 2.
Contributions to base pair flexibility in protein-bound DNA dimers
| Step |
Vstep*, deg3Å3
|
±ΔTwist†, deg | ±ΔTilt†, deg | ±ΔRoll†, deg | ±ΔShift†, (Å) | ±ΔSlide†, (Å) | ±ΔRise†, Å | |
|---|---|---|---|---|---|---|---|---|
| P⋅DNA | B–DNA‡ | |||||||
| CG | 12.1 | 1.3 | 4.9 | 0 | −4.3 | 0 | −0.08 | 0.05 |
| CA | 9.8 | 1.8 | 6.2 | 1.0 | −3.1 | 0.03 | 0.52 | 0.03 |
| TA | 6.3 | 1.7 | 3.9 | 0 | −6.1 | 0 | 0.27 | 0.06 |
| AG | 2.1 | 0.3 | 4.4 | −0.4 | −1.1 | −0.28 | −0.02 | 0.04 |
| GG | 6.1 | — | 4.8 | 1.6 | −1.8 | 0.10 | 0.10 | 0.08 |
| AA | 2.9 | 0.7 | 2.8 | −0.4 | −5.2 | −0.08 | −0.12 | 0.02 |
| GA | 4.5 | 0.3 | 2.9 | 0.2 | −5.0 | −0.05 | 0.02 | 0.14 |
| AT | 1.6 | 0.4 | 3.8 | 0 | −4.3 | 0 | 0.01 | 0.06 |
| AC | 2.3 | — | 3.6 | 0 | −3.2 | 0.02 | 0.02 | 0.07 |
| GC | 4.0 | 3.6 | 3.8 | 0 | −3.7 | 0 | 0.29 | 0.05 |
| MN | 9.2 | — | 4.7 | 0 | −3.6 | 0 | 0.18 | 0.06 |
*
Volumes of conformation space within common energy contours given by the product of the eigenvalues of the stiffness matrix F.
†
Parametric changes that contribute to kBT/2 energy deformations along the longest principal axes obtained from the corresponding eigenvectors and eigenvalues. These deformations constitute the longest dimensions of the equi-potential surfaces.
‡
Volumes of B–DNA samples in Table 1. Steps with <25 examples are not considered.