Hydrophobic moments of protein structures: Spatially profiling the distribution

It is generally accepted that globular proteins fold with a hydrophobic cor e and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing t his distribution from the protein interior to exterior has been examined fo r 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys . A second-order hydrophobic moment has provided a simple measure of the sp atial variation. Shapes of the calculated spatial profiles of ail native st ructures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted p rotein structures and in discriminating between different protein-folding p athways. The spatial profiles of the 14 decoys are clearly distinguished fr om the profiles of their native structures.