Usefulness of medium-angle X-ray scattering for structural characterization of flexible proteins studied by computer...

It is widely accepted that disordered regions in proteins, part of which takes predominantly α-helical conformation to a varying degree, play a critical role in biological function. Structural analysis of these flexible proteins is, however, not straightforward because existing methods to characterize the structural features of the disordered regions are not applicable to all the proteins with various sizes and physicochemical properties. In this study, to gain information on the helical propensity in the disordered regions as well as the overall three-dimensional structures of the proteins, usefulness of the combined small- and medium-angle X-ray scattering (SMAXS), which provides structural information at higher spatial resolution than commonly-used small-angle X-ray scattering, was investigated using computer simulations. For this purpose, various conformations of a protein that consists of two well-folded domains connected by a flexible linker were generated while the linker was modeled either to contain several α-helices or as random coils. The differences in the SMAXS scattering curves of these models were then evaluated. Analysis showed that the SMAXS curves allow to distinguish α-helices from random coils if at least ∼20% of all the residues in the proteins contributes to the helical formation in the disordered region, suggesting that structural analysis using SMAXS will be useful not only to obtain the three-dimensional domain organizations but also to gain information on the helical propensity in the disordered regions. This would lead to more accurate interpretation of reaction kinetics that the flexible proteins are involved in.