Globular proteins supersecondary structures

Globular proteins are constructed by combining secondary structural elements (a-helices, 3-sheets, nonrepetitive sequences). These form primarily the core region—that is, the interior of the molecule. They are connected by loop regions (for example, 3-bends) at the surface of the protein. Supersecondary structures are usually pro duced by packing side chains from adjacent secondary structural elements close to each other. Thus, for example, a-helices and 3-sheets that are adjacent in the amino acid sequence are also usu ally (but not always) adjacent in the final, folded protein. Some of the more common motifs are illustrated in Figure 2.8. 

Godzik, A., and Skolnick, J. (1992). Sequence-structure matching in globular proteins application to supersecondary and tertiary structure determination. Proc. Natl. Acad. Sci. U.S.A. 89, 12098-12102. 

The complex structures of globular proteins can be analyzed by examining stable substructures called supersecondary structures,... 

The association of secondary structures can give rise to so-caUed supersecondary structures, often referred to as folds, which frequently constitute compactly folded domains in globular proteins. They are presented in Figure 3.12... 

Many globular proteins contain combinations of a-helix and /Tpleated sheet secondary structures (Figure 5.20). These patterns are called supersecondary structures. In the /la/1 unit, two parallel /Tpleated sheets are connected by an a-helix segment. In the fi-meander pattern, two antiparallel /1-sheets are connected by polar amino acids and glycines to effect an abrupt change in direction of the polypeptide chain called reverse or fi-turns. In aa-units, two successive a-helices separated by a loop or nonhelical segment become enmeshed because of compatible side chains. Several j8-barrel arrangements are formed when various... 

Certain groupings of secondary structure elements, including the segments of polypeptide chain that connect these structural elements, occur in many globular proteins and are termed motifs or supersecondary stmctures (Figure 5.7). The motifs are a higher level of organization that preserves the structure hierarchy. These are ... 

F. 2.9. Main structural motifs in globular proteins. (A) ordered structures (1) a-helix from Cozey and Pauling (1956) (2) segment of extended structure, parallel and anti parallel P sheets from Corey and Pauling (1956) (3) P turns type I and II from Lewis et al. (1971). (B) Supersecondary structures. (C) Diagrammatic protein structures left, chymotrypsin with two P barrels right, triose phosphate isomerase (altemance of helices and P barrels) (from Schulz and Schirmer, 1979) (courtesy of Schulz). 

There are different levels of substructure in proteins. The folding units or supersecondary structures which are an assembly of secondary structures have been considered. The term domain defines larger assemblies having the characteristics of complete globular protein, i.e., compactness and stability (see Rossmann and Argos, 1980). 

Theoretical studies associated with the crystallographic data might allow one to determine some rules for the association of structured fragments (i.e., for the formation of substructures such as supersecondary structures, and the assembly of these building blocks to form domains, and then the association of domains to form the globular compact structure of a protein). 

---