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. 538-539
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Measuring the packing efficiency inside the protein core provides a good reference point for comparison, and a number of other studies have looked at this in comparison with other parts of the protein. The most obvious thing to compare with the protein inside is the protein outside, or surface. This is particularly interesting from a packing perspective, since the protein surface is covered by water, and water is packed much less tightly than protein and in a distinctly different fashion. (The tetrahedral packing geometry of water molecules gives a packing efficiency of less than half that of hexagonal close-packed solids.)
Calculations based on crystal structures and simulations have shown that the protein surface has intermediate packing, being packed less tightly than the core but not as loosely as liquid water (Gerstein & Chothia, 1996; Gerstein et al., 1995). One can understand the looser packing at the surface than in the core in terms of a simple trade-off between hydrogen bonding and close packing, and this can be explicitly visualized in simulations of the packing in simple toy systems (Gerstein & Lynden-Bell, 1993a,b).
References
Gerstein, M. & Chothia, C. (1996). Packing at the protein–water interface. Proc. Natl Acad. Sci. USA, 93, 10167–10172.Google ScholarGerstein, M. & Lynden-Bell, R. M. (1993a). Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure. J. Phys. Chem. 97, 2982–2991.Google Scholar
Gerstein, M. & Lynden-Bell, R. M. (1993b). Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding. J. Phys. Chem. 97, 2991–2999.Google Scholar
Gerstein, M., Tsai, J. & Levitt, M. (1995). The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249, 955–966.Google Scholar