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. We show the utility of this method by characterizing the quaternary and tertiary differences as observed in eight structures of phosphorylated or dephosphorylated glycogen phosphorylase with different effectors bound. This analysis revealed domain movements which were characteristic of the activated phosphorylase structures. The monomers of the phosphorylase dimer were found to move apart by a 2.5-A translation and to rotate apart, in three orthogonal directions, by a minimum of 3.2 degrees. Analysis of the three domains within the phosphorylase monomer showed that both simple and complex domain movements occur and that multiple domain configurations are energetically stable. We suggest that the C-terminal domain of phosphorylase moves along a simple path in the transition from an inactive to active conformation. The direction of translation and rotation is consistent, but the magnitude is variable. In contrast, this analysis showed that the activation domain did not behave as a rigid body, and therefore, the motion of this domain is not as easily characterized.