Solvent accessibility studies of β-bends and application to cyclic hexapeptides

Abstract

The solvent-accessible surface areas (ASAs), of the atoms in tripeptides around the minimum-energy conformations of the β-bend types I, I', II, and II' have been computed as a first step in the systematic solvent accessibiity study of secondary structures. The side chains chosen at the two middle positions of the bend are L-Ala, D-Ala, and Gly. The ASAs of the hydrogen atoms are reported here and are found useful in determining the type of β-bends in six examples of cyclic hexapeptides whose crystal structures are known. Comparison with observation showed that all the β-bends in these cyclic hexapeptides were correctly identified by the present method. This points to a possible use of the method in identifying β-bend types in solution.