Identification and characterization of two classes of G1 β-bulge

In standard β-bulges, a residue in one strand of a β-sheet forms hydrogen bonds to two successive residues (‘1’ and ‘2’) of a second strand. Two categories, ‘classic’ and ‘G1’ β-bulges, are distinguished by their dihedral angles: 1,2-α(R)β(R) (classic) or 1,2-α(L)β(R) (G1). It had previously been observed that G1 β-bulges are most often found as components of two quite distinct composite structures, suggesting that a basis for further differentiation might exist. Here, it is shown that two subtypes of G1 β-bulges, G1α and G1β, may be distinguished by their conformation (α(R) or β(R)) at residue ‘0’ of the second strand. β-Bulges that are constituents of the composite structure named the β-bulge loop are of the G1α type, whereas those that are constituents of the composite structure named β-link here are of the G1β type. A small proportion of G1β β-bulges, but not G1α β-bulges, occur in other contexts. There are distinctive differences in amino-acid composition and sequence pattern between these two types of G1 β-bulge which may have practical application in protein design.