Computational methodologies for hydrodynamics and other solution properties of rigid macromolecules

Summary:

Information on macromolecular size and shape can be obtained from measurements of the solution properties such as sedimentation coefficients, translational and rotational diffusion coefficients, relaxation times and intrinsic viscosities. For this purpose, models and computational methods which permit the calculation of properties from the macromolecular structure are required. This is particularly easy when the macromolecule can be represented by models of simple geometry (spheres, ellipsoids, cylinders). However, many biological macromolecules exhibit peculiar, specific shapes which are relevant to their physiological function and cannot be modelled so simply. For such cases, which include a variety of proteins, DNA and nucleoprotein complexes, we have developed theoretical treatments and numerical methods that allow the calculation of hydrodynamic properties for structures of arbitrary shape. These advances are implemented in public-domain computer programs that can be used easily by non-specialists.

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