Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase

The plastic network model (PNM) is used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. In this model, the energy basins corresponding to known conformers are connected at their lowest common energies. The results are used to evaluate and analyze the minimal energy pathways between these basins. The open to closed transition analysis provides an identification of hinges that is in agreement with the existing definitions based on the available X-ray structures. The elastic energy distribution and the Cα pseudo-dihedral variation provide similar information on these hinges. The ensemble of the 45 published structures for this protein and closely related proteins is shown to always be within 3.0 Å of the pathway, which corresponds to a conformational change between two end structures that differ by a Cα-atom root-mean-squared deviation of 7.1 Å.