A novel main chain motif in proteins bridged by cationic groups: the niche.

We have surveyed the bridging of pairs of main chain carbonyl oxygens by cations or by delta(+) hydrogens within hydrogen bonding groups. A three to four residue motif, which we call the niche, with characteristic phi,psi angles, is by far the commonest feature with this property. The niche accommodates atoms or groups that offer delta(+) charges, including water molecules or metal ions, as well as amines, guanidines, and other NH(2) groups. Seven percent of all residues in an average soluble protein belong to a niche; another 7% have the niche conformation but no obvious bridging delta(+) group. Fifty-five percent of niches occur either following a type 1 beta-turn or at the C-termini of alpha-helices, and niches turn out to be the most common C-terminal features of alpha-helices: 39% of alpha-helical C-termini are niches, whereas 34% are Schellman loops. 3(10) helices also frequently terminate in niches. Niches that bind K(+), Na(+) or Ca(2+) occur in some functional contexts: in the cyclic peptides valinomycin and antamanide; in several enzymes that are allosterically activated by Na(+) or K(+); and in the calcium pump, where a niche is integrally involved in the ion transport.

TOPS: an enhanced database of protein structural topology.

The TOPS database holds topological descriptions of protein structures. These compact and highly abstract descriptions reduce the protein fold to a sequence of Secondary Structure Elements (SSEs) and three sets of pairwise relationships between them, hydrogen bonds relating parallel and anti- parallel beta strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in betaalphabeta units and between parallel alpha helices. The database is used as a resource for visualizing folding topologies, fast topological pattern searching and structure comparison. Here, significant enhancements to the TOPS database are described. The topological description has been enhanced to include packing relationships between helices, which significantly improves the description of protein folds with little beta strand content. Further, the topological description has been annotated with sequence information. The query interfaces to the database have been improved and the new version can be found at http://www.tops.leeds.ac.uk/.