Local Structure Prediction of Proteins

Abstract

Protein architecture represents a complex and multilayered hierarchy (Fig. 7.1; Crippen, 1978; Rose, 1979). It starts from a linear chain of amino acid residues (primary structure) that arrange themselves in space to form local structures (secondary structure and supersecondary structure) and extends up to the globular threedimensional structure of a fully functional folded protein (tertiary and quaternary structure). This chapter focuses on how the physicochemical properties of the primary structure enable the prediction of the local structural features of a protein, in particular how the secondary (Section 7.2) and supersecondary structure (Section 7.3) of a protein can be predicted from sequence and how disordered regions (Section 7.4) and sequence repeats (Section 7.5) can be detected. In addition, the application of the prediction of these local structures in other fields such as multiple sequence alignment (MSA) (Section 7.6) and tertiary structure prediction (Section 7.7) is discussed. In Section 7.8, a number of currently available software packages that perform these tasks are presented and described in detail. Section 7.9 presents a collection of resources for protein local structure prediction, including online software and databases, with pointers to where they can be used or downloaded.1 Section 7.10 gives a summary of the chapter’s most important points.