Logical analysis of the mechanism of protein folding: IV. Super-secondary structures

Abstract

Super-secondary structures are typical building blocks of proteins, such as mononucleotide binding folds, β -rich structures and helix-rich structures. Among them, a β -strand- α -helix- β -strand unit ( βαβ -unit), which is a substructure of a mononucleotide binding fold, is noticed to have a preference for a right-handed sense and is analyzed on the basis of statistical predictabilities. In order to represent the mode of interactions quantitatively and schematically, helical ( α -) and β -structural ( β -) strength orders are introduced by a pair of numbers, such as 21 3 , to show the ranking of the potential at a region both over a whole range of the polypeptide chain by the upper number and over the whole range of 36 representative proteins by the lower number. The strength orders are written in Figure 2 on the schematical representations of structures of typical proteins having a right-handed βαβ -unit (group I) and a large antiparallel β -sheet (group II). A βαβ -unit or a β c β -unit can be classified into several typical cases, and the strength orders are calculated and listed in Table 1. It is suggested that one of the requirements for an adjacent βαβ -unit is a well-balanced and fairly strong potential of the respective β, α and β -segments. The right-handed preference of a βαβ -unit can be explained by the twisted helix- β -candidate interaction, as shown in Figure 3, as a time average as well as by Chothia's rule about the right-hand twist of a β -sheet. It seems to be supported by the rather concentrated distribution of dihedral angles of the residues of β -sheets in the mononucleotide binding folds or their modifications as shown in Figure 4(a). The present analysis suggests many aspects of competitive protein folding.