Prediction of super-secondary structure in proteins

Abstract

Various methods for the prediction of secondary structure from amino acid sequence can consistently achieve on average 60% accuracy when tested for several proteins^1–3. Improvement on this value has proved difficult, despite increasing the size of the data set and refining predictive techniques⁴. The difficulty almost certainly derives from the influence of long-range interactions and the restrictions required to attain favourable protein topologies. We describe here a novel approach to structure prediction from amino acid sequence based on the recognition of super-secondary structure. The structure we initially consider is the βαβ unit, which consists of two parallel β-strands connected by an α-helix. From an analysis of all known βαβ units, an ideal secondary structure sequence was derived. This was used as a template to locate probable βαβ sequences in a standard secondary structure prediction. The method correctly predicted the location of 70% of the βαβ units in 16 β/α type proteins. This led to a 7.5% average improvement over the original secondary structure prediction.