Packing of α-Helices onto β-Pleated sheets and the anatomy of [formula omitted] proteins

Abstract

We propose a model for the packing of α-helices on β-sheets in α β proteins. It involves the association of two smooth surfaces with complementary twists: the surface of a regular β-sheet with a right-handed twist, and the helix face formed by two rows of residues i, i + 4, i + 8, etc. and i + 1, i + 5, i + 9, etc. The model requires the helix axis to be parallel to the β-strands, and the contacts to be limited to the residues just mentioned. It follows from the model that, when two helices pack against each other as well as on the β-sheet, their axes should be at an angle of about −40 ° compatible with only one class of helix-helix interaction. We examine helix-sheet and helix-helix contacts in eight proteins of known three-dimensional structure in order to substantiate our model. The angular geometry and the patterns formed by contact residues are in agreement with the model, the few exceptions being often due to distortions in the β-sheet. The contact regions have atypical amino acid compositions, especially in the β-sheets, that are very rich in valine and isoleucine, two types of residues that contribute to the formation of a smooth surface. Thus, the requirement of helix-sheet packing sets severe restrictions on the configuration and on the amino acid composition of the secondary structures in α β proteins.