The use of molecular models in evaluating protein and peptide conformations

A new theoretical conformation of polypeptides and proteins designated as the “hexagonal con‐formation,” which was developed through the use of molecular models, is discussed. The term “hexagonal” applies to the arrangement of the peptide chain O‐atoms since the placement of the polymer backbone used in this conformation re‐sults in a planar hexagonal assignment of these atoms. For a cyclic hexapeptide, one hexagon of O‐atoms results; for a cyclic decapeptide, two hexagons result; and a protein subunit (e.g., cytochrome C) can form an extensive honeycomb network of hexagons. The coincidence of this network with a similar “second neighbor” oxygen network in water is discussed in relation to the importance of water in biological processes. Several models of complete peptide sequences assembled in the hexagonal conformation are evaluated in detail. It is suggested that in some instances the “reactivity” of these peptides may reside in an ability to disturb resonance patterns of the surrounding water in a precise manner at specific locations. Finally, the foreseeable prob‐lems involved in a uniform application of the “hexagonal concept” are discussed along with the extension of the hexagonal conformation of pro‐teins to cell membrane structures with their lipid bilayers.