Mimicry by asx- and ST-turns of the four main types of beta-turn in proteins

Abstract

Hydrogen-bonded beta-turns in proteins occur in four categories: type I (the most common), type II, type II', and type I'. Asx-turns resemble beta-turns, in that both have an NH. . .OC hydrogen bond forming a ring of 10 atoms. Serine and threonine side chains also commonly form hydrogen-bonded turns, here called ST-turns. Asx-turns and ST-turns can be categorized into four classes, based on side chain rotamers and the conformation of the central turn residue, which are geometrically equivalent to the four types of beta-turns. We propose asx- and ST-turns be named using the type I, II, I', and II' beta-turn nomenclature. Using this, the frequency of occurrence of both asx- and ST-turns is: type II' > type I > type II > type I', whereas for beta-turns it is type I > type II > type I' > type II'. Almost all type II asx-turns occur as a recently described three residue feature named an asx-nest.

Figure 1.

Distributions of torsion angles of asx- and ST-turns. (A–C) Diagrams of the β-turn, asx-turn (with aspartate side chain), and ST-turn (with serine side chain), respectively.φ_e, ψ_e, and ω_e are the angles equivalent to φ, ψ, and ω of β-turns; they are also defined in B and C. Residue positions are indicated, and it should be noted that position i + 1 of an asx- or ST-turn is equivalent to i + 2 of a β-turn. ψ_e, φ_e, and ω_e have a fixed approximate relationship to ψ, χ₁, and χ₂: ψ_e ≈ψ+ 120°; φ_e ≈χ₁ - 120°; ω_e ≈χ₂ + 180°. (D–E) Turns of different types are represented by data points of different colors, as indicated by the legend. D and E show asx-turn angles whereas F and G show ST-turn angles. D and F plot the asx- or ST-turn angles φ_e vs. ψ_e, equivalent to φ and ψ of residue i + 1 of a β-turn; E and G plot φ against ψ for asx- or ST-turn residue i + 1, equivalent to residue i + 2 of a β-turn.