Prediction of Hydrodynamic Parameters of Biopolymers from Small-Angle Scattering Data

Abstract

For correlating a number of structural and hydrodynamic parameters, biopolymers were modeled as prolate or oblate ellipsoids of revolution or as spheres (whole-body approaches). Axial ratios were estimated by combining the radius of gyration with either the hydrated volume or the surface-to-volume ratio. From these axial ratios and other parameters (volume, molar mass, partial specific volume), various hydrodynamic quantities were derived: frictional ratios, sedimentation and diffusion coefficients, Simha factors and intrinsic viscosities. In addition, the radii of several kinds of equivalent spheres (related to experimental volume and experimental or calculated values of diffusion coefficients and intrinsic viscosities) were computed and compared with each other and with the corresponding radii of gyration. Finally, the validity of simple empirical equations relating radius of gyration and diffusion coefficient or viscosity radius, sedimentation coefficient and molar mass was tested. As examples, the structural and hydrodynamic properties of a variety of globular biopolymers (such as proteins, viruses and ribonucleic acids) of different molar mass and shape were considered. Far-reaching conformity between observed and predicted values provided by the different techniques and approaches was achieved; for certain cases (e.g. hollow or inhomogeneous particles), however, more sophisticated procedures had to be applied. Predictive approaches were also used for hydrodynamic modeling of ligand-induced shape changes of enzymes. A representative example was elaborated in detail, including a critical assessment of errors.