Volume occupation, environment, and accessibility in proteins. Environment and molecular area of RNase-S

Abstract

Using the same Voronoi polyhedron approach as has been used successfully to examine the internal volume occupation and packing efficiency in proteins (Richards, 1974; Finney, 1975), data on the molecular area and internal environment of protein molecules can be obtained. With small modifications, contact areas, surface roughness and solvent accessibility can be estimated, thus providing a single procedure for quantifying many related aspects of protein structure. Data for RNase-S are presented and discussed, in particular the nature and extent of internal and surface interactions. Although energy estimates have suggested that hydrogen-bonded polar groups within the protein can be treated as “hydrophobic units”, problems associated with the concept at the molecular level are discussed. Within the limitations of the X-ray co-ordinates, significant interactions between polar and apolar groups are implied, presumably of a dipoleinduced dipole nature. Comparison with simple clathrate hydrates suggests these interactions are stronger than those expected in proposed prototype structures thought to be associated with the hydrophobic interaction.