FIGURE 4.

Views of open and closed Taq polymerase complexes, focused on DNA segments at the exit from the protein. Arrows (a, b in open, a′, b′ in closed) show the designation of the segment vectors between adjacent C_5′ atoms and the direction of the applied force f (parallel to axis of the ds DNA helix). Other DNA segments than these two schematized here do not change significantly in going from their open to close states. Portions of the protein (blue) within 10 Å of the segments a or a′ are shown; the atoms in this part of the protein are the main contributors to the restriction of orientations available to the DNA segments. The explicit solvent and ions included in the simulation are omitted.