Figure 1.

Examples of conformational heterogeneity in the T4 lysozyme and a schematic of how PopShift accounts for this heterogeneity. These renders show the multiple conformations even the L99A pocket bound to toluene is capable of accessing under crystallographic study. The top section shows the room temperature structure (PDB 7L39) and a cryogenic structure from the same study (PDB 7L3A). All residues with alternative locations in the F-helix, and also toluene, are shown in sticks. Extensive alternative locations are present in both, even though this protein is reckoned to be rigid and to bind simple, largely rigid, fragments. Note that the two alternative locations for the ligand are nearly identical at both temperatures. Nearly every residue in the critical F-helix shows heterogeneity, centered on valine 111, which extends down toward the toluene. The lower panel shows a schematic of the PopShift method, showing MSM populations from a ligand free ensemble being biased by varying degrees of ligand affinity to those states to approximate the ligand-bound ensemble. The sea-blue pac-man represents the protein, with three states in equilibrium, green circle sizes indicating abundance, and the shape cut out of the pac-man representing varying degrees of pocket accessibility to the ligand, which is schematically represented by a star.