Differences between the crystal structures and the ensembles are mapped on to the three-dimensional structures of CheY, the αL I-domain, and Ras. Orange colored sticks indicate residues that make a state dependent contact (or have a state dependent side chain angle). Blue colored sticks reflect a contact (side chain) that differs between the two structures, but are not state dependent.

Schematic energy profile plotted as a function of the number of residues that change between states on a one-dimensional energy landscape. (A) All-or-nothing model in which all residues switch together and the conformational change between states happens in a concerted manner. (B) Domino model in which one residue interacts with its neighbor and so on as the conformational change between states proceeds along a specific propagation pathway. (C) Block model in which groups of tightly coupled interactions switch together and each block is loosely coupled to other blocks such that conformational change between states happens through interacting blocks. All of these models would appear as two-state transitions experimentally, however, the domino and block models transition through multiple intermediate states.

Left panel shows a two-dimensional map of the energy landscape showing the Cα-rmsd to the starting and alternative crystal conformations (locations are indicated by black dots on the axes). Each point represents a single low-energy model on the landscape colored by energy from low (blue) to high (red). The central panel shows a hierarchical clustering of the association (ϕ coefficient) between pairwise interactions. The white to black coloring reflects the association between residue pairs, where white represents no association (ϕ = 0) and black represents a strong association (ϕ = 1). A colored square has been added around strongly associated clusters of pairwise interactions. The right panel maps the residue pairs with the strongest associations onto the three-dimensional protein structure. Residues are colored based on the hierarchical clustering.

The Rosetta all-atom energy is plotted against Cα-rmsd for models generated by simulations starting from the native conformation in the bound state with the allosteric effector removed from the crystal structure. Left panel shows the rmsd comparison to the alternative crystal structure when all loops have been remodeled, the center panel, the rmsd comparison to the alternative crystal structure with remodeling of loop or secondary structure regions that differ between the states. Arrows indicate the locations of the starting structure (gray) and lowest-energy model from the cluster with the largest number of structures (cyan). Right panel shows the superposition of the lowest-energy model taken from the largest cluster in the center panel (cyan) to the starting (gray) and alternative (magenta) crystal structures. The allosteric effector and protein binding site are indicated by * and ** respectively. The bright regions indicate regions that differ the most between the two crystal structures and were remodeled, while remaining regions are faded. Black arrows indicate the regions in the lowest-energy model that have moved toward the alternative state.