Volume occupation, environment and accessibility in proteins. The problem of the protein surface

Abstract

The volumes occupied by atoms or groups of atoms in ribonuclease S are calculated, using a new treatment of the surface, and considering buried and exposed atoms separately. The volumes occupied by particular atom types fall within a narrow range, with standard deviations between 10% and 15% of the mean. Summation of volumes over main and side-chain groups removes inaccuracies in the single atom data, and results in even narrower distributions. Comparison of the volume spreads with those found in model glasses suggests that the remaining variation is unlikely to be much reduced by improving further either the space-subdivision method or the surface treatment. These improved volume distributions might be used as more stringent criteria against which to test trial tertiary structures. The computer program used produces additional information that could be used to investigate quantitatively the possible freedom of movement in different parts of the molecule. It also provides complementary data on environment and surface exposure.