Relaxation Matrix Analysis of Spin Diffusion for the NMR Structure Calculation with eNOEs
Relaxation Matrix Analysis of Spin Diffusion for the NMR Structure Calculation with eNOEs
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DOI：
10.1021/ct3002249
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发表时间：
2012-10-01
影响因子：
5.5
通讯作者：
Riek, Roland
中科院分区：
文献类型：
--
作者：
Orts, Julien;Voegeli, Beat;Riek, Roland
NMR 结构测定通常基于从 NOESY 谱中的交叉峰体积或强度半定量提取的距离限制。 Vogeli 等人最近引入了精确 NOE (eNOE)。为基于 eNOE 衍生的定量距离限制的蛋白质整体结构测定开辟了一条途径。我们提出了一种从累积曲线强度中提取 eNOE 的方法。对于 eNOE 的测定，自旋扩散是误差的主要来源。使用完整弛豫矩阵分析来计算自旋扩散对每个感兴趣的单独自旋对的 NOESY 交叉峰的贡献。编写了一个软件程序，需要输入各种 NOESY 光谱的峰强度以及蛋白质的 3D 结构。该结构可以是X射线结构或用常规方法确定的NMR结构。该程序的输出是 eNOE 速率、自动松弛速率以及来自各个 NOE 建立曲线的图表和品质因数，用于对导出速率进行半自动分析。该协议很简单，并且该程序很好地集成到当前的结构计算工作流程中。
NMR structure determination is usually based on distance restraints extracted semiquantitatively from cross peak volumes or intensities in NOESY spectra. The recent introduction of exact NOEs (eNOE) by Vogeli et al. opens an avenue for the ensemble-based structure determination of proteins on the basis of eNOE-derived quantitative distance restraints. We present an approach to extract eNOE from build-up curve intensities. For the determination of eNOEs, spin diffusion is a major source of errors. A full relaxation matrix analysis is used to calculate the spin diffusion contribution to the NOESY cross peaks of each individual spin pair of interest. A software program is written, which requires as input the peak intensities from the various NOESY spectra as well as a 3D structure of the protein. This structure can be either an X-ray structure or an NMR structure determined with the conventional approach. The outputs of the program are the eNOE rates, the autorelaxation rates, as well as graphs and quality factors from the individual NOE build-up curves for semiautomated analysis of the derived rates. The protocol is straightforward, and the program integrates well into the current structure calculation workflow.