title: Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins.
abstract: The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2β-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond.
authors.affiliation: College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
authors.forename: Avid M
authors.initials: AM
authors.lastname: Afzal
authors.forename: Fawzia
authors.initials: F
authors.lastname: Al-Shubailly
authors.forename: David P
authors.initials: DP
authors.lastname: Leader
authors.forename: E James
authors.initials: EJ
authors.lastname: Milner-White
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000838:Anions / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D000838:Anions
keywords: ST-motif; Schellman loop; asx-motif; asx-turn; hydrogen bond; molecular mimicry; nest; β-bulge; β-turn