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Biophys J, February 2000, p. 719-730, Vol. 78, No. 2
Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30071 Murcia, Spain
The solution properties, including hydrodynamic
quantities and the radius of gyration, of globular proteins are
calculated from their detailed, atomic-level structure, using
bead-modeling methodologies described in our previous 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. Our 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 overlapping 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 proteins.
For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 Å, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A
computational shortcut makes the procedure feasible, even in personal
computers. All of the model-building and calculations are carried out
with a HYDROPRO public-domain computer program.
Biophys J, February 2000, p. 719-730, Vol. 78, No. 2
© 2000 by the Biophysical Society 0006-3495/00/02/719/12 $2.00
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C. J. Ackerman, M. M. Harnett, W. Harnett, S. M. Kelly, D. I. Svergun, and O. Byron 19 A Solution Structure of the Filarial Nematode Immunomodulatory Protein, ES-62 Biophys. J., January 1, 2003; 84(1): 489 - 500. [Abstract] [Full Text] [PDF]
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