Stranded in isolation: structural role of isolated extended strands in proteins

Abstract

Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of β -sheets. However E-strands, not part of β-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated E-strands. Using a dataset of 250 largely non-homologous and high-resolution (<2 Å) crystal structures of proteins, we have identified 518 isolated E-strands from 187 proteins. The two most distinguishing features of isolated E-strands from β-strands in β-sheets are the high preponderance of prolyl residues occuring in isolated E-strands and their high exposure to the surroundings. Removal of regions with polyproline conformation from the dataset did not significantly reduce the propensity of prolyl residues to occur in isolated E-strands. Isolated E-strands are often characterized by their main-chain amide and carbonyl groups involved in hydrogen bonding with polar side chains or water. They are often flanked by irregular loop structures and are less well conserved, than β-sheet forming β-strands, among homologous protein structures. It is suggested that isolated β-strands have many characteristics of loop segments but with repetitive (φ,ψ) values falling within the β-region of the Ramachandran map.