Four classes of β-hairpins in proteins

Abstract

We show that beta-hairpins can be divided into four classes, each with a number of members. Hairpins from a single class are readily interconverted by loss or gain of hydrogen bonds, but interconversion between classes requires complete unzipping and reformation of the entire beta-hairpin. Sibanda & Thornton [(1985) Nature (London) 316, 170-174] have classified beta-hairpins as either two-residue, three-residue, four-residue etc., loops. We point out that their nomenclature, by itself, gives rise to ambiguities, but that, if the class (one of the four mentioned above) is also specified, the description of beta-hairpins becomes straightforward. A range of proteins of known three-dimensional structure has been examined; it provides examples of hairpins of each of the four classes and give some indication of their frequency of occurrence. The distribution observed is substantially different from that described by Sibanda & Thornton [(1985) Nature (London) 316, 170-174].

Structural Families in Loops of Homologous Proteins: Automatic Classification, Modelling and Application to Antibodies

“…In particular, Sibanda and Thornton (1985;Sibanda et al, 1989) recognised that short loops connecting strands of b-hairpins are constrained to a limited number of conformations. Together with the work of Milner-White and co-workers (Milner-White, 1986;Milner-White & Poet, 1986 a classification scheme for b-hairpins has been derived. Leszczynski & Rose (1986) defined a sub-set of loops that they termed V-loops with a characteristic shape while, more recently, Martin et al (1995) have performed an analysis of long loops in proteins and have defined two subsets of loops, which they term long-open and long-closed.…”

Local Protein Structures

“…They have been widely analyzed since they are widespread in globular proteins. Different classes have been identified resulting in the definition of structural families [169][170][171][172]. Interestingly, the short length hairpins are often characterized by a specific turn, i.e., a quick return of the protein backbone [173], like a β-turn [174].…”

Toward predicting protein topology: An approach to identifying β hairpins

“…Therefore, we developed a protocol to predict ␤ hairpins, which are simple SSS motifs formed by two adjacent, antiparallel, hydrogen-bonded ␤ strands (26)(27)(28). Their simplicity and ubiquity make them good targets for prediction (29)(30)(31)(32).…”