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Decoding protein structural characteristics and formation is essential to the understanding of its function. Despite the diversity and enormity of protein universe, the dissection of known protein structures has identified regular secondary structure elements (SSEs), namely, α-helix and β-strand, that constitute the basic structural elements of protein universe (Levitt and Chothia, 1976). As a remarkable characteristics of the overall topology of a polypeptide, the specific spatial arrangement of these SSEs is a hallmark of the protein tertiary conformation (Murzin et al., 1995). Unraveling the rules that govern the specific packing of the SSEs is critical to understanding the folding and formation of the tertiary structure of a protein and thus its function. Previously , numerous studies have attempted to identify the factors that determine the stability and specificity of SSE associations through analysis of super-secondary structure model systems like β-sheets and coiled-coils. Using designed β-hairpins or other β-sheet model systems, researchers have identified many factors that can significantly change the folding rate, stability or strand registry of β-sheets, such as charge interactions (Smith and Regan, 1995), beta propensity (Phillips et al., 2005) and β-sheet surface complementarity (Liang et al., 2008). The coiled-coil motif is another model system for understanding of molecular mechanisms that govern the super-secondary structure formation. Through NMR study of mutated GCN4p (Matousek et al., 2007) and design of stable and specific coiled-coils (Woolfson, 2005; Oakley and Kim, 1998), researchers have suggested the importance of elec-trostatic and polar interactions in determining the coiled-coil packing stability and specificity. In addition, Kennan and Ryan showed that changing the length of residue side chains could dramatically influence the stability of coiled-coils (Ryan and Kennan, 2007). Despite the extensive attention on the factors that determine the specific packing of SSEs in certain forms, most of the above discoveries were made in simple soluble model systems but not natural proteins. Thus so far a global view of the effect of these factors on the protein topology still remains unclear. In this study, we would like to provide an evolutionary perspective into the roles of physiochemical properties in spatial arrangement of SSEs in protein universe. Based on a large ortholog group dataset, we systematically analyzed the coevolution signals of a variety of physiochemical properties for association of SSEs in protein evolution. To analyze the extent of coevolution of two SSEs with regard to different physiochemical properties during protein evolution, we designed an analysis framework, …

Coevolution signals capture the specific packing of secondary structures in protein architecture