One-Bond And Two-Bond J Couplings Help Annotate Protein Secondary-Structure Motifs: J-Coupling Indexing Applied To Human Endoplasmic Reticulum Protein Erp 18

NMR coupling constants, both direct one-bond ((1)J) and geminal two-bond ((2)J), 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 (1)J(C alpha H alpha), (1)J(C alpha C beta), (1)J(C alpha C'), (1)J(C'N'), (1)J(N'C alpha), (1)J(N'HN), (2)J(C alpha N'), (2)J(HNC alpha), (2)J(C'HN), and (2)J(H alpha C'). Comparison with (1)J and (2)J data from reference proteins and pattern analysis on a per-residue basis permitted main-chain phi,psi 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 beta turns at progressively shorter sequence intervals, in agreement with the crystal structure. Proteins 2011; 79:428-443. (C) 2010 Wiley-Liss, Inc.