Tracking conformational states in allosteric transitions of phosphorylase

An intrinsic molecular property of a protein domain can be determined by calculating its principal axes from the inertia tensor matrix. The mass-weighted principal axes can be used to calculate an ellipsoid representing the shape of the protein domain, providing an easy means of visualizing domain movements. Most importantly, the mass-weighted principal axes provide an intuitive means of characterizing domain relationships within a protein, as well as the disposition of domains in different protein conformers. Thus, this method provides a simple, quantitative description of differences of domain positions within various protein structures