Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins

Afzal, A. M., Al-Shubailly, F., Leader, D. P., and Milner-White, E. J. (2014) Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins. Proteins: Structure Function and Bioinformatics, 82(11), pp. 3023-3031. (doi:10.1002/prot.24663)

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Abstract

The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αRαL (RL nests) or 1,2-αLαR (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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Leader, Dr David and Milner-White, Professor E
Authors: Afzal, A. M., Al-Shubailly, F., Leader, D. P., and Milner-White, E. J.
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
College of Medical Veterinary and Life Sciences > School of Life Sciences
Journal Name:Proteins: Structure Function and Bioinformatics
Publisher:Wiley Periodicals, Inc.
ISSN:0887-3585
ISSN (Online):1097-0134

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