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One‐bond and two‐bond j couplings help annotate protein secondary‐structure motifs: J ‐coupling indexing applied to human endoplasmic reticulum protein ERp18
Author(s) -
Schmidt Jürgen M.,
Zhou Shen,
Rowe Michelle L.,
Howard Mark J.,
Williamson Richard A.,
Löhr Frank
Publication year - 2011
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22893
Subject(s) - chemistry , crystallography , substituent , protein secondary structure , stereochemistry , coupling constant , crystal structure , physics , biochemistry , quantum mechanics
Abstract 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. Proteins 2011. © 2010 Wiley‐Liss, Inc.