The radius of gyration of L-arabinose-binding protein decreases upon binding of ligand.

The technique of small angle x-ray scattering has been employed to study the effect of sugars on the radius of gyration of the L-arabinose-binding protein, a component of the high affinity L-arabinose transport system in Escherichia coli. We find that the binding of L-arabinose to the "sugar-free" protein in solution causes a 0.94 +/- 0.33 A decrease in the radius of gyration while D-glucose, a nonbinder, produces no such effect. The radius of gyration calculated from the complete atomic co-ordinates of the crystal structure of L-arabinose-binding protein (solved with bound L-arabinose) corresponds to the experimentally determined value for the radius of gyration in the presence of L-arabinose. This reduction in radius of gyration can be best accounted for in terms of a substrate-induced cleft closure in which one lobe rotates relative to the other lobe. A compute modeling study indicates that a rotation of 18 degrees about a hinge deep in the base of the sugar-binding cleft between the two domains would produce the observed decrease in the radius of gyration. The findings (Newcomer, M. E., Gilliland, G. L., and Quiocho, F. A. (1981) J. Biol. Chem. 256, 13213-13222) that the L-arabinose molecule embedded in the cleft between two domains is completely inaccessible to the solvent is consistent with a closing of the cleft between the two lobes.