Conformational and sequence signatures in β helix proteins

Abstract

β helix proteins are characterized by a repetitive fold, in which the repeating unit is a β-helical coil formed by three strand segments linked by three loop segments. Using a data set of left- and right-handed β helix proteins, we have examined conformational features at equivalent positions in successive coils. This has provided insights into the conformational rules that the proteins employ to fold into β helices. Left-handed β helices attain their equilateral prism fold by incorporating "corners" with the conformational sequence P_II-P_II-α_L-P_II, which imposes sequence restrictions, resulting in the first and third P_II residues often being G and a small, uncharged residue (V, A, S, T, C), respectively. Right-handed β helices feature mid-sized loops (4, 5, or 6 residues) of conserved conformation, but not of conserved sequence; they also display an α-helical residue at the C-terminal end of L2 loops. Backbone conformational parameters (Φ,Ψ) that permit the formation of continuous, loopless β helices (Perutz nanotubes) have also been investigated.