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 ((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(CαHα), (1)J(CαCβ), (1)J(CαC'), (1)J(C'N'), (1)J(N'Cα), (1)J(N') (HN), (2)J(CαN'), (2)J(HNCα), (2)J(C'HN), and (2)J(HαC'). Comparison with (1)J and (2)J data from reference proteins and pattern analysis on a per-residue basis permitted main-chain ϕ,ψ 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 β turns at progressively shorter sequence intervals, in agreement with the crystal structure.
School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom. j.m.schmidt@kent.ac.uk
Jürgen M
JM
Schmidt
Shen
S
Zhou
Michelle L
ML
Rowe
Mark J
MJ
Howard
Richard A
RA
Williamson
Frank
F
Löhr
D000595:Amino Acid Sequence; D003198:Computer Simulation; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011490:Protein Disulfide Reductase (Glutathione) / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011993:Recombinant Fusion Proteins
D011993:Recombinant Fusion Proteins; D011490:Protein Disulfide Reductase (Glutathione); C477009:TXNDC12 protein, human