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Hydrogen‐Bond Detection, Configuration Assignment and Rotamer Correction of Side‐Chain Amides in Large Proteins by NMR Spectroscopy through Protium/Deuterium Isotope Effects
Author(s) -
Liu Aizhuo,
Wang Jifeng,
Lu Zhenwei,
Yao Lishan,
Li Yue,
Yan Honggao
Publication year - 2008
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.200800467
Subject(s) - deuterium , chemistry , side chain , nuclear magnetic resonance spectroscopy , deuterium nmr , conformational isomerism , hydrogen bond , kinetic isotope effect , isotope , computational chemistry , mass spectrometry , stereochemistry , organic chemistry , molecule , physics , nuclear physics , chromatography , polymer
The configuration and hydrogen‐bonding network of side‐chain amides in a 35 kDa protein were determined by measuring differential and trans‐hydrogen‐bond H/D isotope effects by using the isotopomer‐selective (IS)‐TROSY technique, which leads to a reliable recognition and correction of erroneous rotamers that are frequently found in protein structures. First, the differential two‐bond isotope effects on carbonyl 13 C′ shifts, which are defined as Δ 2 Δ 13 C′(ND)= 2 Δ 13 C′(ND E )‐ 2 Δ 13 C′(ND Z ), provide a reliable means for the configuration assignment for side‐chain amides, because environmental effects (hydrogen bonds and charges, etc.) are greatly attenuated over the two bonds that separate the carbon and hydrogen atoms, and the isotope effects fall into a narrow range of positive values. Second and more importantly, the significant variations in the differential one‐bond isotope effects on 15 N chemical shifts, which are defined as Δ 1 Δ 15 N(D)= 1 Δ 15 N(D E )‐ 1 Δ 15 N(D Z ) can be correlated with hydrogen‐bonding interactions, particularly those involving charged acceptors. The differential one‐bond isotope effects are additive, with major contributions from intrinsic differential conjugative interactions between the E and Z configurations, H‐bonding interactions, and charge effects. Furthermore, the pattern of trans‐H‐bond H/D isotope effects can be mapped onto more complicated hydrogen‐bonding networks that involve bifurcated hydrogen‐bonds. Third, the correlations between Δ 1 Δ 15 N(D) and hydrogen‐bonding interactions afford an effective means for the correction of erroneous rotamer assignments of side‐chain amides. Rotamer correction by differential isotope effects is not only robust, but also simple and can be applied to large proteins.