Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation
Figure 2
Example of the Hierarchical Loop Prediction, Applied to Reconstructing the Phosphorylated Activation Loop of CDK2/Cyclin A
In this example, only the loop is predicted, and the remainder of the protein is held rigid in its crystallographic conformation.
(A) Backbone traces for the ten lowest-energy loops sampled in the initial build-up stage (left) and the third and final refinement stage (right) of the hierarchical loop prediction protocol (figures prepared with Chimera [72]).
(B) Energies as a function of backbone RMSD values of the 20 lowest-energy loops sampled in the four stages of the loop prediction protocol.
(C) Energies as a function of the error in the phosphorus atom position, relative to the crystal structure, for the 20 lowest-energy loops sampled in the four stages of the loop prediction protocol.