Figure 9.

The interdye distances and bend angles of free AdMLP_14ds probes and bound to cTBP and yTBP, at 20 °C. (A) To calculate the P(R) distance distribution, it is required to obtain the lifetime of the single and double-labeled probe as free and bound complexes with TBP proteins. The Xr*AdMLP_14ds*Fl and Ta*AdMLP_14ds*Fl probes were straight but after complex formation with yTBP or cTBP, the DNA is bent, which shortens the interdye R resulting in more energy transfer from Fl donor toward the acceptor (Ta or Xr). (B) The P(R) distance distribution is described by the mean distance $\overline{R}$ and the spread σ of the unbound probes and the respective complexes formed with yTBP and cTBP. (C) The bend angle (α) of the TATA distortion for the canonical AdMLP is calculated according to Equation (25), requiring the $\overline{R}$-value and where L2 was 20.4 Å. The bend angle produced by each protein was independent of the probe used since the values overlapped in error for the Xr*AdMLP_14ds*Fl and Ta*AdML_P14ds*Fl complexes formed with yTBP and cTBP, respectively. The bend angles caused by cTBP for both probes were larger than those observed by yTBP since the latter has an N-terminal domain that regulated the binding and shifts the equilibrium to the left, or towards the reactants [40].