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Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations
The Journal of Physical Chemistry B ( IF 3.3 ) Pub Date : 2018-03-02 00:00:00 , DOI: 10.1021/acs.jpcb.8b00853
Jodi Kraus 1, 2 , Rupal Gupta 1 , Jenna Yehl 1 , Manman Lu 1, 2 , David A. Case 3 , Angela M. Gronenborn 2, 4 , Mikael Akke 5 , Tatyana Polenova 1, 2
Affiliation  

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15NH. Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13Cα, while larger scatter is observed for 15NH chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

中文翻译:

Galectin-3的碳水化合物结合域的化学位移从魔角旋转NMR和混合量子力学/分子力学计算

魔角旋转NMR光谱法特别适用于以原子分辨率探测不溶性蛋白质和蛋白质装配体的结构和动力学,其NMR化学位移包含有关生物分子结构的丰富信息。但是,由于蛋白质的化学位移的精确量子力学计算仍然具有挑战性,尤其是对于15 N H而言,获取此信息是有问题的。在这里,我们报告了微晶galectin-3的碳水化合物识别域的各向同性化学位移预测,该预测是通过使用混合量子力学/分子力学(QM / MM)计算,使用自动片段化方法以及极高的分辨率(0.86Å)获得的乳糖结合和1.25 Apo形式的X射线晶体结构。用作AF-NMR程序输入的X射线晶体结构的分辨率在很大程度上不会影响化学位移计算的准确性。对于得到的实验和计算的位移之间极好的一致性13 Ç α,而较大的散射为观察到15 Ñ ħ 化学位移,在更大程度上受静电相互作用,氢键和溶剂化的影响。
更新日期:2018-03-02
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