|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 22.1, pp. 535-536
|
The detail provided by these surfaces will depend on the radius of the probe used for their construction.
One may argue that the behaviour of the rolling probe sphere does not accurately model real hydrogen-bonded water. Instead, its `rolling' more closely mimics the behaviour of a nonpolar solvent. An attempt has been made to incorporate more realistic hydrogen-bonding behavior into the probe sphere, allowing for the definition of a hydration surface more closely linked to the behaviour of real water (Gerstein & Lynden-Bell, 1993c![[link]](/graphics/greenarr.gif)
).
The definitions of accessible surface and molecular surface can be related back to the Voronoi construction. The molecular surface is similar to `time-averaging' the surface formed from the faces of Voronoi polyhedra (the Voronoi surface) over many water configurations, and the accessible surface is similar to averaging the Delaunay triangulation of the first layer of water molecules over many configurations.
There are a number of other definitions of protein surfaces that are unrelated to either the probe-sphere method or Voronoi polyhedra and provide complementary information (Kuhn et al., 1992; Leicester et al., 1988; Pattabiraman et al., 1995).
References
Gerstein, M. & Lynden-Bell, R. M. (1993c). What is the natural boundary for a protein in solution? J. Mol. Biol. 230, 641–650.Google Scholar
Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228, 13–22.Google Scholar
Leicester, S. E., Finney, J. L. & Bywater, R. P. (1988). Description of molecular surface shape using Fourier descriptors. J. Mol. Graphics, 6, 104–108.Google Scholar
Pattabiraman, N., Ward, K. B. & Fleming, P. J. (1995). Occluded molecular surface: analysis of protein packing. J. Mol. Recognit. 8, 334–344.Google Scholar
