Packing at the protein-water interface.
We have determined the packing efficiency at the protein-water interface by calculating the volumes of atoms on the protein surface and nearby water molecules in 22 crystal structures. We find that an atom on the protein surface occupies, on average, a volume approximately 7% larger than an atom of equivalent chemical type in the protein core. In these calculations, larger volumes result from voids between atoms and thus imply a looser or less efficient packing. We further find that the volumes of individual atoms are not related to their chemical type but rather to their structural location. More exposed atoms have larger volumes. Moreover, the packing around atoms in locally concave, grooved regions of protein surfaces is looser than that around atoms in locally convex, ridge regions. This as a direct manifestation of surface curvature-dependent hydration. The net volume increase for atoms on the protein surface is compensated by volume decreases in water molecules near the surface. These waters occupy volumes smaller than those in the bulk solvent by up to 20%; the precise amount of this decrease is directly related to the extent of contact with the protein.
Gerstein
M
M
Department of Structural Biology, Stanford University, CA 94305, USA.
Chothia
C
C
D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004798:Enzymes / Q000737:chemistry*; D006860:Hydrogen Bonding; D008961:Models, Structural; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013499:Surface Properties; D014867:Water
D004798:Enzymes; D011506:Proteins; D014867:Water