Identification of Essential Residues from Protein Secondary Structure Prediction and Applications

Proteins can perform functions when they fold into proper three-dimensional structures. However, since determining the structure of a protein through wet-lab experiments can be time-consuming and laborintensive, computational approaches are preferable. To characterize the structural topology of proteins, Linderstrøm-Lang proposed the concept of a protein structure hierarchy with four levels: primary, secondary, tertiary, and quaternary. In the hierarchy, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures, since it represents the local conformation of amino acids into regular structures. There are three basic secondary structure elements (SSEs): α-helices (H), β-strands (E), and coils (C). Many researchers employ PSS as a feature to predict the tertiary structure (Fischer et al., 2001, Gong & Rose, 2005, Meiler & Baker, 2003, Rost, 2001), function (Aydin et al., 2006, Eisner et al., 2005, Ferre & King, 2006, Laskowski et al., 2005), or subcellular localization (Nair & Rost, 2003, Nair & Rost, 2005, Su et al., 2007) of proteins. It is noteworthy that, among the various features used to predict protein function, such as amino acid composition, disorder patterns, and signal peptides, PSS makes the largest contribution (Lobley et al., 2007). Moreover it has been suggested that secondary structure alone may be sufficient for accurate prediction of a protein’s tertiary structure (Przytycka et al., 1999).