Reducing the measurement time of exact NOEs by non-uniform sampling.
Reducing the measurement time of exact NOEs by non-uniform sampling.
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DOI：
10.1007/s10858-020-00344-8
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发表时间：
2020-12
影响因子：
2.7
通讯作者：
Vogeli, Beat
中科院分区：
文献类型：
--
作者：
Nichols, Parker J.;Born, Alexandra;Henen, Morkos A.;Strotz, Dean;Jones, David N.;Delaglio, Frank;Vogeli, Beat
我们之前曾报道过精确核奥弗豪泽效应（eNOEs）的测量，与传统核奥弗豪泽效应相比，它能提供大量额外信息。我们已将这些eNOEs用于多种应用，包括计算蛋白质和RNA分子的高分辨率结构。然而，eNOEs的采集具有挑战性，因为需要在一次测量中测量一个由通常四个具有不同混合时间的核奥弗豪泽效应光谱（NOESY）组成的核奥弗豪泽效应建立系列。虽然二维版本可以在几天内完成，但一个完全采样的三维核奥弗豪泽效应建立系列可能需要10天或更长时间来获取。这可能既昂贵，对于在如此长时间内不稳定的样品来说也是个问题。一种显著减少eNOEs所需测量时间的潜在方法是使用非均匀采样（NUS）来减少间接维度上测量的点数。NUS对从eNOEs中提取的极严格距离约束的影响可能非常显著。因此，我们研究了在不断降低的NUS密度下从三个测试案例中测量的eNOEs的准确性：18.4 kDa的人类Pin1蛋白、Pin1的4.1 kDa WW结构域（两者均为三维）以及一个4.6 kDa的14聚体RNA UUCG四环（二维）。我们的结果表明，对于所有三个案例，从高质量数据得出的eNOE距离在低至10%的采样率下，NUS产生的误差可忽略不计，但eNOE的产率有明显下降，这取决于样品潜在的稀疏性，进而取决于其复杂性。对于Pin1，这种转变大约发生在40%的采样率，而对于WW结构域和UUCG四环，分别发生在较低的NUS密度20%和10%。我们通过在各种条件下的重建模拟对这些数值进行了合理的解释。这种损失的程度取决于所进行的扫描次数以及要重建的峰的数量。基于这些发现，我们制定了根据二维或三维核奥弗豪泽效应光谱最密集区域中需要重建的峰的数量来选择最佳NUS密度的指南。
We have previously reported on the measurement of exact NOEs (eNOEs), which yield a wealth of additional information in comparison to conventional NOEs. We have used these eNOEs in a variety of applications, including calculating high-resolution structures of proteins and RNA molecules. The collection of eNOEs is challenging, however, due to the need to measure a NOESY buildup series consisting of typically four NOESY spectra with varying mixing times in a single measurement session. While the 2D version can be completed in a few days, a fully sampled 3D-NOESY buildup series can take 10 days or more to acquire. This can be both expensive as well as problematic in the case of samples that are not stable over such a long period of time. One potential method to significantly decrease the required measurement time of eNOEs is to use non-uniform sampling (NUS) to decrease the number of points measured in the indirect dimensions. The effect of NUS on the extremely tight distance restraints extracted from eNOEs may be very pronounced. Therefore, we investigated the fidelity of eNOEs measured from three test cases at decreasing NUS densities: the 18.4 kDa protein human Pin1, the 4.1 kDa WW domain of Pin1 (both in 3D), and a 4.6 kDa 14mer RNA UUCG tetraloop (2D). Our results show that NUS imparted negligible error on the eNOE distances derived from good quality data down to 10% sampling for all three cases, but there is a noticeable decrease in the eNOE yield that is dependent upon the underlying sparsity, and thus complexity, of the sample. For Pin1, this transition occurred at roughly 40% while for the WW domain and the UUCG tetraloop it occurred at lower NUS densities of 20% and 10%, respectively. We rationalized these numbers through reconstruction simulations under various conditions. The extent of this loss depends upon the number of scans taken as well as the number of peaks to be reconstructed. Based on these findings, we have created guidelines for choosing an optimal NUS density depending on the number of peaks needed to be reconstructed in the densest region of a 2D or 3D NOESY spectrum.
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影响因子：
15
作者：
Hyberts, Sven G.;Takeuchi, Koh;Wagner, Gerhard
通讯作者：
Wagner, Gerhard
影响因子：
15
作者：
BRUSCHWEILER, R;ROUX, B;ERNST, RR
通讯作者：
ERNST, RR
影响因子：
0.9
作者：
Born, Alexandra;Nichols, Parker J.;Henen, Morkos A.;Chi, Celestine N.;Strotz, Dean;Bayer, Peter;Tate, Shin-Ichi;Peng, Jeffrey W.;Vogeli, Beat
通讯作者：
Vogeli, Beat
影响因子：
2.7
作者：
Hyberts SG;Frueh DP;Arthanari H;Wagner G
通讯作者：
Wagner G
影响因子：
2.7
作者：
Chi, Celestine N.;Strotz, Dean;Voegeli, Beat
通讯作者：
Voegeli, Beat