Hoogstraten C G, Markley J L
Department of Biochemistry, University of Wisconsin, Madison 53706, USA.
J Mol Biol. 1996 May 3;258(2):334-48. doi: 10.1006/jmbi.1996.0254.
New methods for collecting cross-relaxation data from proteins and nucleic acids make it possible to improve the accuracy and precision of interproton distance measurements used as input for NMR solution structure determinations. It thus is of interest to determine whether such experimentally achievable improvements in input distance constraints have significant effects on the precision and accuracy of the resulting structures. To answer this question, we have turned to a computational procedure involving the use of data simulated from a known structure, in order to allow unambiguous assessments of accuracy. The approach to improved distances evaluated here is that afforded by magnetization exchange network editing (MENE); MENE pulse sequences break the network of cross-relaxation interactions into regions that are manipulated so as to defeat certain spin-diffusion terms. A target structure was prepared from the X-ray structure of a small protein, turkey ovomucoid third domain (OMTKY3). A normal NOESY spectrum and two varieties of MENE spectra, BD-NOESY and CBD-NOESY, were simulated by means of complete relaxation matrix analysis. These results were used to create different input data sets with the same number of constraints (perfectly accurate distances derived from the target structure, more accurate distances derived from the MENE simulations, and less accurate distances derived from the NOESY simulation), and these, interpreted at different levels of precision, were used as input for solution structure calculations. The results showed that the use of more precise input data measurably improves the local precision and accuracy of calculated structures, but only if the more precise data include the actual target distance. Incorporation of the experimentally achievable, accurate distances with higher precision afforded by the MENE pulse sequences into the set of input distances was found to improve the accuracy of the resulting structures, particularly in terms of side-chain conformation.
从蛋白质和核酸中收集交叉弛豫数据的新方法，使得提高用于核磁共振溶液结构测定输入的质子间距离测量的准确性和精度成为可能。因此，确定输入距离约束在实验上可实现的这种改进是否会对所得结构的精度和准确性产生显著影响是很有意义的。为了回答这个问题，我们采用了一种计算程序，该程序涉及使用从已知结构模拟的数据，以便能够明确评估准确性。这里评估的改进距离的方法是由磁化交换网络编辑（MENE）提供的；MENE脉冲序列将交叉弛豫相互作用网络分解成可被操控的区域，从而消除某些自旋扩散项。一个目标结构是由一种小蛋白质——火鸡卵类粘蛋白第三结构域（OMTKY3）的X射线结构制备而来的。通过完整弛豫矩阵分析模拟了一个正常的NOESY谱以及两种MENE谱，即BD - NOESY和CBD - NOESY。这些结果被用于创建具有相同约束数量的不同输入数据集（从目标结构导出的完全准确的距离、从MENE模拟导出的更准确的距离以及从NOESY模拟导出的不太准确的距离），并且这些在不同精度水平下解释的数据被用作溶液结构计算的输入。结果表明，使用更精确的输入数据可显著提高计算结构的局部精度和准确性，但前提是更精确的数据包含实际目标距离。研究发现，将MENE脉冲序列提供的具有更高精度的实验上可实现的准确距离纳入输入距离集合中，可提高所得结构的准确性，特别是在侧链构象方面。
