Results of metadynamics simulations.

<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the outermost blue contour in (C). (B) Network diagram of clusters from metadynamics simulation. Each cluster represents conformations whose backbone is within a 3.0 Å RMSD, and connected clusters are whose backbones are within 3.8 Å RMSD. Purple clusters represent those in which pTyr657 faces inward toward Arg649 and Arg625. In all these clusters, Arg664 faces into the active site (more than 50% of the conformations in that cluster feature Arg664:Cζ within 8 Å of ATP:Pγ), while Leu665 and Pro666 face outward without blocking the active site (the average distance between the center of mass of the side chain carbon atoms and the Cα atom of the catalytic base Asp626 is greater than 8 Å). Blue clusters represent those in which Arg664 faces inward and Leu665 and Pro666 face outward, even though pTyr657 does not face inward. All other clusters are black. (C) Contour map indicating the density of conformations in the black, blue and purple clusters, projected onto the same axes as in (A). Each contour represents an increase in density of 0.005. (D) Representative conformation in cluster 15, the most highly populated cluster in which pTyr657 faces inward.