Prediction of Secondary Structure from the Amino Acid Sequence

Abstract

To a rough approximation the secondary structure of a chain segment is a function of the constituent amino acids alone. A glimpse at Dayhoff’s Atlas of Protein Sequence and Structure (20) shows that the number of known amino acid sequences far exceeds the number of known three-dimensional structures. Since the amino acid sequence contains the complete structural information (section 1.2 and Ref. 177), it should be possible to derive the spatial structure from the sequence alone without X-ray analysis. The first step in this direction should be to try to bridge the gap between the two lowest levels of structural organization in proteins (Figure 5–1), between sequence and secondary structure. This organization is approximately hierarchic. But the hierarchy is not strict so that the formation of secondary structure in a given segment of the polypeptide chain does not depend on the sequence in this segment alone. Other segments at a distance along the chain also exert an influence, the functional dependence between the two lowest levels being of a rather nonlocal nature.¹