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

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.