基于结构的全自动核磁共振甲基共振峰分配方法在大型蛋白质中的应用
Automatic structure-based NMR methyl resonance assignment in large proteins.
机构信息
Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
出版信息
Nat Commun. 2019 Oct 29;10(1):4922. doi: 10.1038/s41467-019-12837-8.
Isotopically labeled methyl groups provide NMR probes in large, otherwise deuterated proteins. However, the resonance assignment constitutes a bottleneck for broader applicability of methyl-based NMR. Here, we present the automated MethylFLYA method for the assignment of methyl groups that is based on methyl-methyl nuclear Overhauser effect spectroscopy (NOESY) peak lists. MethylFLYA is applied to five proteins (28-358 kDa) comprising a total of 708 isotope-labeled methyl groups, of which 612 contribute NOESY cross peaks. MethylFLYA confidently assigns 488 methyl groups, i.e. 80% of those with NOESY data. Of these, 459 agree with the reference, 6 were different, and 23 were without reference assignment. MethylFLYA assigns significantly more methyl groups than alternative algorithms, has an average error rate of 1%, modest runtimes of 0.4-1.2 h, and can handle arbitrary isotope labeling patterns and data from other types of NMR spectra.
同位素标记的甲基基团可作为 NMR 探针用于大型氘代蛋白质。然而，共振分配是甲基 NMR 更广泛应用的瓶颈。在这里，我们提出了一种基于甲基-甲基核 Overhauser 效应光谱（NOESY）峰列表的自动甲基 FLYA 分配方法。MethylFLYA 适用于五个包含总共 708 个同位素标记甲基基团的蛋白质（28-358 kDa），其中 612 个贡献了 NOESY 交叉峰。MethylFLYA 可以自信地分配 488 个甲基基团，占具有 NOESY 数据的甲基基团的 80%。其中，459 个与参考值一致，6 个不同，23 个没有参考分配。MethylFLYA 分配的甲基基团数量明显多于其他算法，平均错误率为 1%，运行时间为 0.4-1.2 小时，可处理任意同位素标记模式和来自其他类型 NMR 谱的数据。
Zotero 插件