Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures

Backbone mimicry by the formation of closed-loop C-7, C-10 and C-13 (mimics Of gamma-, beta- and alpha-turns) conformations through side chain-main ch ain hydrogen bonds by polar groups is a frequent observation in protein str uctures. A data set of 250 non-homologous and high-resolution protein cryst al structures was used to analyze these conformations for their characteris tic features. Seven out of the nine polar residues (Ser, Thr, Asn, Asp, Gin , Glu and His) have hydrogen bonding groups in their side chains which can participate in such mimicry and as many as 15% of all these polar residues engage in such conformations. The distributions of dihedral angles of these mimics indicate that only certain combinations of the dihedral angles invo lved aid the formation of these mimics. The observed examples were categori zed into various classes based on these combinations, resulting in well def ined motifs, Asn and Asp residues show a very high capability to perform su ch backbone secondary structural mimicry. The most highly mimicked backbone structure is of the C-10 conformation by the Asx residues. The mimics form ed by His, Ser, Thr and Glx residues are also discussed. The role of such c onformations in initiating the formation of regular secondary structures du ring the course of protein folding seems significant.