Figure 4.

Changes in DNA looping associated with large-scale opening of the Lac repressor. (a) Molecular images of 92-bp loops anchored in the dominant antiparallel and parallel orientations with the change in the opening angle Δα set to values that minimize the DNA elastic energy. Note the rearrangement of DNA on opened versus closed repressors (Figure 3a); (b) Distribution of the opening angle w (Δα) of Lac repressor proteins anchoring DNA loops subjected to energy minimization and collected in Monte Carlo (MC) sampling. The differences in repressor opening found with the two approaches reflect the different treatments of protein, i.e., precisely imposed routes of conformational change versus spatial forms indirectly captured in the course of DNA loop closure.