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

Leader, D. P. and Milner-White, J. (2015) Bridging of partially negative atoms by hydrogen bonds from main-chain NH groups in proteins: the crown motif. Proteins: Structure Function and Bioinformatics, 83(11), pp. 2067-2076. (doi: 10.1002/prot.24923) (PMID:26358948)

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-αRαL and 1,2-αLαR, 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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Leader, Dr David
• Authors: Leader, D. P., and Milner-White, J.
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: Proteins: Structure Function and Bioinformatics
• Publisher: Wiley
• ISSN: 0887-3585
• ISSN (Online): 1097-0134