Figure 3.

Allosteric coupling in designed network structures. (A and a) For both designed networks, the initial structure and the final structure with the ligand bound to the allosteric pocket are shown. Elastic connections between network beads are shown as thin transparent lines and pocket beads are colored blue (allosteric pocket) and red (regulated pocket), respectively. In both designed networks the initial and respective final structure is very similar (see text), but the large-amplitude motions of pocket beads evidencing intrastructure allosteric communication are apparent. In the network with symmetric cooperativity, ligand-induced closing of the allosteric pocket triggers allosteric closing of the regulated pocket, whereas, in the network with asymmetric cooperativity, the allosteric response consisted of opening of the regulated site. (B and b) Given here are traces showing changes in the size of both pockets upon binding of the ligand bead to the allosteric pockets (blue color for allosteric the pocket, red for the regulated pocket). To see this figure in color, go online.