The use of sedimentation coefficients to distinguish between models for protein oligomers.
The sedimentation coefficients of proteins are dependent on their sizes, shapes and densities and on the density and viscosity of the solvent. However, when the sedimentation coefficients of an oligomeric protein and its protomer are measured under the same experimental conditions, the ratio of the two coefficients depends only on the protomer shape and the mode of aggregation. This property, which we shall call the sedimentation ratio, therefore provides a way of distinguishing between models for oligomeric proteins. To allow examination of the behaviour of the sedimentation ratio, sedimentation coefficients are calculated for a comprehensive range of protomer shapes and modes of aggregation in hexameric systems using equations derived by Kirkwood. As illustrations of the method the resulting sedimentation ratios are compared with experimental values for insulin and arthroped hemocyanin, which eliminates many of the possible structures for these proteins. When experimental estimates of degree of hydration and molecular dimensions are also considered, all but a group of virtually identical structures are eliminated for the insulin hexamer and a single most likely structure remains for arthropod hemocyanin. The insulin structure is in good agreement with that determined by X-ray crystallography while the hemocyanin hexameric structure is a hexagonal prism formed by the cyclic aggregation of prolate ellipsoids of axial ratio about 2.5 : 1.
D001665:Binding Sites; D006433:Hemocyanins; D007328:Insulin; D046911:Macromolecular Substances; D008433:Mathematics; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins; D014461:Ultracentrifugation; D014961:X-Ray Diffraction
D007328:Insulin; D046911:Macromolecular Substances; D011506:Proteins; D006433:Hemocyanins