Hydrodynamic bead modeling of biological macromolecules

This chapter discusses the hydrodynamic bead modeling of biological macromolecules. Hydrodynamic bead modeling is the representation of a macromolecule, with an assembly of spheres, for which a profile of measurable hydrodynamic parameters is computed. As a modeling method, it is complemented by whole-body modeling approaches: the use of ellipsoids of revolution or general triaxial ellipsoids to represent macromolecules, whose shape can reasonably be approximated to such a generalized geometrical topology and for which a wide range of shape functions can be calculated and compared with hydrodynamic measurements and the use of other more complex whole-body geometries, for which small-angle scattering curves can be simulated. Hydrodynamic bead modeling is closely related to Debye sphere modeling, with which the scattering curves acquired in small-angle X-ray, neutron (and in some instances, light) scattering studies can be interpreted. Proteins can also embody one or more points of segmental flexibility and the computation of the hydrodynamic properties in such cases is the subject of intensive study