Protein packing: Dependence on protein size, secondary structure and aminoacid composition

We have used the occluded surface algorithm to estimate the packing of both buried and exposed amino acid residues in protein structures. This method works equally well for buried residues and solvent-exposed residues in cont rast to the commonly used Voronoi method that works directly only on buried residues. The atomic packing of individual globular proteins may vary sign ificantly from the average packing of a large data set of globular proteins . Here, we demonstrate that these variations in protein packing are due to a complex combination of protein size, secondary structure composition and amino acid composition. Differences in protein packing are conserved in pro tein families of similar structure despite significant sequence differences . This conclusion indicates that quality assessments of packing in protein structures should include a consideration of various parameters including t he packing of known homologous proteins. Also, modeling of protein structur es based on homologous templates should take into account the packing of th e template protein structure. (C) 2000 Academic Press.