6626 Nucleic Acids Research, 2005, Vol. 33, No. 20 Figure 2. (A) Positive supercoil relaxation, snapshots from the molecular dynamics results for system 1 in Table 1. Colors and perspective as in Figure 1A, except that nose-cone helices and linker domain are in darker green. Direction of downstream DNA rotation is counterclockwise. The two-sided red arrow points at the increasing separation of the lips. Notice that, in this case, the hinge does not stretch (see also inset). Distances in both figures measured between corresponding Ca atoms. Also note that in both cases in (A) and (B). DNA is still in the grip of the protein. (B) Negative supercoil relaxation: structural details from simulation (system 2 in Table 1). All details same as in panel A of this figure, except that direction of downstream DNA rotation is clockwise. Snapshots are at 90 intervals. Relative stretching of the hinge shown with two-sided blue arrows. Inset shows distances His367 to Ala499 (corresponding to distal clamp), Gly365 to Ser534 (proximal clamp), and Leu429 to Lys436 (hinge).