首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >Inadequacies of the Point-Dipole Approximation for Describing Electron-Nuclear Interactions in Paramagnetic Proteins: Hybrid Density Functional Calculations and the Analysis of NMR Relaxation of High-Spin Iron (Ⅲ) Rubredoxin
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Inadequacies of the Point-Dipole Approximation for Describing Electron-Nuclear Interactions in Paramagnetic Proteins: Hybrid Density Functional Calculations and the Analysis of NMR Relaxation of High-Spin Iron (Ⅲ) Rubredoxin

机译:描述顺磁性蛋白质中电子-核相互作用的点-偶极近似的不足:混合密度泛函计算和高自旋铁(Ⅲ)Rubredoxin的NMR弛豫分析

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摘要

High-level, all-electron, density functional calculations have been used, in conjunction with high-resolution X-ray structural data, to predict, and to compare with experiment, the contribution of unpaired electrons to the relaxation times for ↑(15)N nuclei in oxidized Clostridium pasteurianum rubredoxin. Published X-ray structures for the iron (Ⅲ) rubredoxin from C. pasteurianum were employed to construct a 104-atom model for the iron center that included all atoms shown to have strong electronic interactions with the unpaired iron electrons. The remainder of the amide nitrogen resonances in the protein, which show no apparent Fermi contact contribution to the chemical shift, are represented in the model by ghost atoms (atoms with no charge or basis functions). This model served as a starting point for quantum mechanical calculations at the B3LYP/ 6-311G↑(**) level, which, in turn, yielded calculated values for eigenvalues of the spin-differential field gradient tensor, which finally yielded expectation values for effective distances between nuclei and the delocalized spin-density. We report here that using effective distances, which are calculated from the spin-differential field gradient tensor, in the Solomon-Bloembergen equation in place of distances measured from the crystal structures greatly improves the correlation for a plot of experimental relaxation rates versus r↑(-6) for ↑(15)N resonances in C. pasteurianum iron(Ⅲ) rubredoxin. With increases in the speed of computers and algorithms, iterative quantum chemical optimization of paramagnetic center geometries based on NMR-derived distance and angular constraints from paramagnetic interactions should lead to significant improvements in the determination of the structures of paramagnetic centers in proteins by NMR spectroscopy.
机译:结合高分辨率X射线结构数据,使用了高级全电子密度函数计算来预测未配对电子对↑(15)的弛豫时间的贡献,并与实验进行比较。氧化巴氏杆菌红氧化还原酶中的N核。利用已发布的巴氏梭菌铁(Ⅲ)氧化还原酶的X射线结构,为铁中心构建了104个原子的模型,其中包括与未成对的铁电子具有强电子相互作用的所有原子。在模型中,剩余的酰胺氮共振没有显示费米接触对化学位移的明显贡献,在模型中由虚原子(无电荷或基本功能的原子)表示。该模型用作B3LYP / 6-311G↑(**)级别的量子力学计算的起点,进而产生了自旋微分场梯度张量的特征值的计算值,最终得出了原子核与离域自旋密度之间的有效距离。我们在此报告,在Solomon-Bloembergen方程中使用从自旋微分场梯度张量计算的有效距离代替从晶体结构测得的距离,极大地改善了实验弛豫率与r↑( -6)为巴氏梭菌铁(Ⅲ)氧化还原酶中的↑(15)N共振。随着计算机和算法速度的提高,基于NMR衍生的距离和顺磁性相互作用的角度约束,对顺磁性中心几何结构进行迭代量子化学优化,应该会导致通过NMR光谱法测定蛋白质中顺磁性中心结构的显着改善。

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