Electrostatic interactions and secondary structures in proteins.

In an attempt to understand the occurrences of secondary forms in proteins, we have calculated approximate free energies for a large set of regular secondary regions and have compared several methods for choosing a single molecular conformation. Approximate conformational free energies have been obtained by directly calculating electrostatic energies and approximating the nonelectrostatic energies in a simple manner, with parameters being related to the actual fractions of conformations occurring within the protein. Indirect evidence for the importance of electrostatic energies in determining secondary structures was offered by the success of the prediction method of Ptitsyn and Finkelstein and more directly by the observation of the occurrences of favorable side-chain charged pairs in ..cap alpha..-helices.