Domain interaction in rabbit muscle pyruvate kinase. II. Small angle neutron scattering and computer simulation

The effects of ligands on the structure of rabbit muscle pyruvate kinase were studied by small angle neutron scattering. The radius of gyration, R(G), decreases by about 1 Å in the presence of the substrate phosphoenolpyruvate, but increases by about the same magnitude in the presence of the allosteric inhibitor phenylalnine. With increasing pH or in the absence of Mg²⁺ and K⁺, the R(G) of pyruvate kinase increases. Hence, there is a 2-Å difference in R(G) between two alternative conformations. Length distribution analysis indicates that, under all experimental conditions which increase the radius of gyration, there is a pronounced increase observed in the probability for interatomic distance between 80 and 110 Å. These small angle neutron scattering results indicate a 'contraction' and 'expansion' of the enzyme when it transforms between its active and inactive forms. Using the α-carbon coordinates of crystalline cat muscle pyruvate kinase, a length distribution profile was calculated, and it matches the scattering profile of the inactive form. These observations are expected since the crystals were grown in the absence of divalent cations (Stuart, D. I., Levine, M., Muirhead, H., and Stammers, D. K. (1979) J. Mol. Biol. 134, 109-142). Hence, results from neutron scattering, x-ray crystallographic, and sedimentation studies (Oberfelder, R. W. Lee, L. L.-Y., and Lee J. C. (1984) Biochemistry 23, 3813-3821) are totally consistent with each other. With the acid of computer modeling, the crystal structure has been manipulated in order to effect changes that are consistent with the conformational change described by the solution scattering data. The structural manipulation involves the rotation of the B domain relative to the A domain, leading to the closure of the cleft between these domains. These manipulations resulted in the generation of new sets of atomic (C-α) coordinates, which were utilized in calculations, the result of which compared favorably with the solution data.