Bridging of partially negative atoms by hydrogen bonds from main-chain NH groups in proteins: The crown motif.

Abstract

The backbone NH groups of proteins can form N1N3-bridges to δ-ve or anionic acceptor atoms when the tripeptide in which they occur orients them appropriately, as in the RL and LR nest motifs, which have dihedral angles 1,2-αR αL and 1,2-αL αR , respectively. We searched a protein database for structures with backbone N1N3-bridging to anionic atoms of the polypeptide chain and found that RL and LR nests together accounted for 92% of examples found (88% RL nests, 4% LR nests). Almost all the remaining 8% of N1N3-bridges were found within a third tripeptide motif which has not been described previously. We term this a "crown," because of the disposition of the tripeptide CO groups relative to the three NH groups and the acceptor oxygen anion, and the crown together with its bridged anion we term a "crown bridge." At position 2 of these structures the dihedral angles have a tight αR distribution, but at position 1 they have a wider distribution, with ϕ and ψ values generally being lower than those at position 1. Over half of crown bridges involve the backbone CO group three residues N-terminal to the tripeptide, the remainder being to other main-chain or side-chain carbonyl groups. As with nests, bridging of crowns to oxygen atoms within ligands was observed, as was bridging to the sulfur atom of an iron-sulfur cluster. This latter property may be of significance for protein evolution.