One-bond and two-bond J couplings help annotate protein secondary-structure motifs: J-coupling indexing applied to human endoplasmic reticulum protein ERp18

Schmidt, Jürgen M. and Zhou, Shen and Rowe, Michelle L. and Howard, Mark J. and Williamson, Richard A. and Löhr, Frank (2011) One-bond and two-bond J couplings help annotate protein secondary-structure motifs: J-coupling indexing applied to human endoplasmic reticulum protein ERp18. Proteins: Structure, Function, and Bioinformatics, 79 (2). pp. 428-443. ISSN 0887-3585. (The full text of this publication is not available from this repository)

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Official URL
http://dx.doi.org/10.1002/prot.22893

Abstract

NMR coupling constants, both direct one-bond (1J) and geminal two-bond (2J), are employed to analyze the protein secondary structure of human oxidized ERp18. Coupling constants collected and evaluated for the 18-kDa protein comprise 1268 values of 1JCaHa, 1JCaCb, 1JCaC', 1JC'N', 1JN'Ca, 1JN'HN, 2JCaN', 2JHNCa, 2JC'HN, and 2JHaC'. Comparison with 1J and 2J data from reference proteins and pattern analysis on a per-residue basis permitted main-chain f,y torsion-angle combinations of many of the 149 amino-acid residues in ERp18 to be narrowed to particular secondary-structure motifs. J-coupling indexing is here being developed on statistical criteria and used to devise a ternary grid for interpreting patterns of relative values of J. To account for the influence of the varying substituent pattern in different amino-acid sidechains, a table of residue-type specific threshold values was compiled for discriminating small, medium and large categories of J. For the 15-residue insertion that distinguishes the ERp18 fold from that of thioredoxin, the J-coupling data hint at a succession of five isolated type-I b turns at progressively shorter sequence intervals, in agreement with the crystal structure.

Item Type: Article
Subjects: Q Science
Q Science > QD Chemistry
Q Science > QC Physics
Divisions: Faculties > Science Technology and Medical Studies > School of Biosciences
Faculties > Science Technology and Medical Studies > School of Biosciences > Protein Science Group
Depositing User: Jurgen M Schmidt
Date Deposited: 19 Jan 2011 15:17
Last Modified: 30 Apr 2014 15:15
Resource URI: http://kar.kent.ac.uk/id/eprint/26247 (The current URI for this page, for reference purposes)
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