Variants of 3₁₀-helices in proteins

Abstract

An analysis of the shortest 3₁₀-helices, containing three helical residues and two flanking capping residues that participate in two consecutive i + 3 → i hydrogen bonds, shows that not all helices belong to the classic 3₁₀-helix, where the three central residues adopt the right-handed helical conformation (α_R). Three variants identified are: 3¹⁰_L-helix with all residues in the left-handed helical region (α_L), 3¹⁰_EL-helix where the first residue is in the extended region followed by two residues in the α_L conformation, and its mirror-image, the 3¹⁰_EL-helix. In the context of these helices, as well as the equivalent variants of α-helices, the length dependence of the handedness of secondary structures in protein structure is discussed. There are considerable differences in the amino acid preferences at different positions in the various types of 3₁₀-helices. Each type of 3₁₀-helix can be thought to be made up of an extension of a particular type of β-turn (made up of residues i to i + 3) such that the (i + 3)th residue assumes the same conformation as the preceding residue. Distinct residue preferences at i and i + 3 positions seem to decide whether a particular stretch of four residues will be a β-turn or a 3₁₀-helix in the folded structure.