Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins
Figure 2
Rigid-body partitioning and quaternary network in phosphofructokinase (PFK).
(A) The active state structure (4PFK) colored by identified rigid bodies, except red, which marks flexible segments. (B) Quaternary network representation of the quaternary nodes (rigid bodies and flexible segments) shown in (A). Circular nodes represent rigid bodies and hexagonal nodes represent flexible segments. Areas of protein nodes correspond to their physical sizes in number of residues, and their colors correspond to the colors of the rigid bodies in (A). Each rigid body is labeled by the chains and domains it contains, e.g. the rigid body labeled “A1+B1” contains the largest portion of chain A and the largest portion of chain B, the rigid body labeled “D2” contains the second-largest portion of chain D, etc. Each flexible segment is labeled by its chain identifier followed by its range of residue numbers. Substrate and effector “sites” are shown as rectangles and diamonds, respectively. Each substrate (effector) site represents all the substrate (effector) molecules from a given chain in either the inactive or the active state. An edge indicates a quaternary interface, that is, two or more atomic (4.0 Å) contacts between a pair of quaternary nodes, or two or more atomic contacts between a quaternary node and a ligand. An edge between two rigid bodies is labeled by the rotation in degrees (see methods for rotation calculations), provided the smaller rigid body is ten residues or larger. A grey dashed line marks the boundary of the main allosteric unit of the graph. Graphs drawn by yEd graph editor (http://www.yworks.com).