Accommodating sequence changes in beta-hairpins in proteins.

A systematic study of homologous beta-hairpins in proteins of known structure reveals how insertions and deletions (herein known as indels) in the sequence are accommodated. The study was made for 12 protein families comprising 50 different structures, in which there were 49 independent hairpins. Each hairpin was classified according to its loop length and hydrogen bonding pattern. Most indels were found to occur in the loops and their frequency decreases rapidly with the size of the indel and approximately halves for each extra residue inserted. In very short loops, critical glycines are the primary determinants of loop structure and conversions between the two classic two-residue hairpin loops (with type I' and II' beta-turns) are quite common. Longer insertions are often accommodated by extending the beta-ladder and forming extra hydrogen bonds. There are also several indels that are not accommodated in the loop, but by forming a beta-bulge in one of the strands. This study should provide a useful aid to modelling hairpins in homologous structures.