The influence of short-range interactions on protein onformation. II. A model for predicting the alpha-helical regions of proteins.

On the basis of earlier energy computations, the various single peptide units in proteins were designated as helix-making or helix-breaking.(1) With the use of these designations, empirical rules for distinguishing between alpha-helical and non-alpha-helical regions of proteins have been formulated. These rules include conditions for initiation and termination of a helical segment which, when combined with changes in the designation of three peptide units, correctly identify the helical or nonhelical character of over three fourths of the individual peptide units in four proteins of known amino acid sequence and structure: myoglobin, lysozyme, tosyl-alpha-chymotrypsin, and ribonuclease-A. The model is discussed, some of its predictions are checked, and further predictions about the structure of various proteins are made.