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Identification and characterization of two classes of G1 ?-bulge.

ABSTRACT: In standard ?-bulges, a residue in one strand of a ?-sheet forms hydrogen bonds to two successive residues (`1' and `2') of a second strand. Two categories, `classic' and `G1' ?-bulges, are distinguished by their dihedral angles: 1,2-?R?R (classic) or 1,2-?L?R (G1). It had previously been observed that G1 ?-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 ?-bulges, G1? and G1?, may be distinguished by their conformation (?R or ?R) at residue `0' of the second strand. ?-Bulges that are constituents of the composite structure named the ?-bulge loop are of the G1? type, whereas those that are constituents of the composite structure named ?-link here are of the G1? type. A small proportion of G1? ?-bulges, but not G1? ?-bulges, occur in other contexts. There are distinctive differences in amino-acid composition and sequence pattern between these two types of G1 ?-bulge which may have practical application in protein design.

SUBMITTER: Leader DP 

PROVIDER: S-EPMC7869896 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Identification and characterization of two classes of G1 β-bulge.

Leader David P DP   Milner-White E James EJ  

Acta crystallographica. Section D, Structural biology 20210126 Pt 2

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<sub>R</sub>β<sub>R</sub> (classic) or 1,2-α<sub>L</sub>β<sub>R</sub> (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 exi  ...[more]

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