HETEROGENEITY OF PACKING - STRUCTURAL APPROACH

Analysis of the heterogeneity of packing in proteins showed that diffe rent groups of the protein preferentially contribute to low-or high-de nsity regions. Statistical distribution reveals the two preferable val ues for packing density in the form of two peaks. One peak occurs in t he range of densities 0.55-0.65, the other occurs in the range 0.75-0. 8. The high-density peak is originated primarily by high packing insid e the hydrogen bonded backbone and to some extent by side chains. Pola r/charged and apolar side chains both contribute to the low-density pe ak. The average packing density values of individual atomic groups sig nificantly vary for backbone atoms as well as for side chain atoms. Th e carbonyl oxygen atoms of protein backbone and the end groups of side chains show lower packing density than the rest of the protein. The s ide-chain atomic groups of a secondary structure element when packed a gainst the neighboring secondary structure element form stronger conta cts with the side chains of this element than with its backbone. Analy sis of the low-density regions around each buried peptide group was do ne for the set of proteins with different types of packing, including alpha-alpha, alpha-beta, and beta beta packing. It was shown that cavi ties are regularly situated in the groove of secondary structure eleme nt packed against neighboring elements for all types of packing. Low d ensity in the regions surrounding the peptide groups and the end group s of side chains can be explained by their positioning next to a cavit y formed upon the association of secondary structure elements. The mod el proposed can be applied to the analysis of protein internal motions , mechanisms of cellular signal transduction, diffusion through protei n matrix, and other events.