7 - COMMON POLYPEPTIDE SECONDARY STRUCTURES

Abstract

This chapter discusses common polypeptide secondary structures. The polypeptides may be considered as sequences of planar trans-peptide linkages connected through α-carbon atoms. The most stable configuration of these planes occurs when the carbonyl groups of adjacent planes are either aligned or opposed. For each of these possibilities, there are preferred ψ and φ torsion angles. If the carbonyls are aligned on one side of the chain, the N–H bonds are necessarily aligned on the opposite side of the chain. When these bonds are so aligned, the preferred torsional angles allow the polypeptide chain to coil on itself and form a helix. This conformation is stabilized by hydrogen bond formation between carbonyl oxygen atoms and the hydrogens of N–H bonds that are further along the polypeptide backbone. In the β-structure form, the carbonyls of adjacent planes point in opposite directions and the polypeptide chain conformation is an extended, pleated structure. Two or more chains with such conformations can form hydrogen bonds between chains. This can occur in two ways—with the chains going in the same direction or in opposite directions. All of these conformations can easily be constructed from these models by simply dialing the appropriate torsional angles typical of these structures while building the polypeptide backbone.