Local interactions as a structure determinant for protein molecules: III

Investigation of the known protein structures has led to the generalization that the native folding permits each sidechain to select those nearest-neighbors which maximize stabilization from van der Waals interactions. With regard to secondary structure: 1. Helical and beta regions exhibit characteristic patterns of short-range contacts (residue numbers k and k + t with [t] less than or equal to 4) due to the geometries of these secondary structures. However, these are not strictly obligatory, and preferred short-range contacts which would result in unfavorable van der Waals interactions are replaced by favorable long-range contacts. 2. The generalization mentioned at the outset holds for individual proteins, both for short-range and long-range contacts, and without regard for the type or amount of secondary structure present. 3. These observations imply that van der Waals interactions arising from short-range contacts partially determine secondary structure, and this is demonstrated by tests based upon assignment of regions of secondary structure in the known proteins. The principle of optimizing van der Waals stabilization from long-range contacts is applied to predict the structure of the complex formed by the S-peptide and S-protein of ribonuclease-S. The formation of favorable pairs is found to be more important than the total number of intermolecular contacts, and 40 to 50% of this stabilization is contributed by two residues of the S-peptide, Phe-8 and Met-13.