Calculation of hydrodynamic properties of globular proteins from their atomic-level structure

The solution properties, including hydrodynamic quantities and the radius o f gyration, of globular proteins are calculated from their detailed, atomic -level structure, using bead-modeling methodologies described in our previo us article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76,3044-3057 ). We review how this goal has been pursued by other authors in the past. O ur procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overla pping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 protei ns. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 Angstrom, with deviat ions that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be exp lained in terms of protein hydration. A computational shortcut makes the pr ocedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer progra m.