Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.
Protein Sci. 2022 Jan;31(1):63-74. doi: 10.1002/pro.4181. Epub 2021 Sep 22.
Nuclear magnetic resonance (NMR) provides site specific information on local environments through chemical shifts. NMR is widely used in the study of proteins, ranging from determination of three-dimensional (3D) structures to characterizing dynamics and binding of small molecules and other proteins or ligands. Assigned chemical shift data for the atoms within proteins is a treasure trove of information that can facilitate a broad range of biochemical and biophysical studies. The Biological Magnetic Resonance Data Bank (BMRB) is a publicly accessible database that contains a large number of assigned chemical shifts; however, translating this wealth of knowledge into a practical application is not straightforward. Herein we present nightshift: a Python command line utility and library for plotting simulated two-dimensional (2D) and 3D NMR spectra from assigned chemical shifts in the BMRB. This tool allows users to simulate routinely collected amide and methyl fingerprint spectra, backbone triple-resonance assignment spectra, and user-defined custom correlations, including ones that do not necessarily correspond to published experiments. This tool enables experienced NMR spectroscopists, those learning the craft, and interested scientists seeking to utilize NMR the ability to preview or examine a wide range of spectra for proteins whose assignments are deposited in the BMRB, irrespective of whether those experiments have been executed or reported. The tool applies equally to folded and intrinsically disordered proteins, limited only by the existence of a BMRB deposition. The features of nightshift are described along with applications that illustrate the ease with which complicated correlation spectra and binding events can be simulated.
核磁共振（NMR）通过化学位移提供有关局部环境的特定位置信息。NMR 在蛋白质研究中得到广泛应用，范围从确定三维（3D）结构到表征小分子和其他蛋白质或配体的动力学和结合。分配给蛋白质中原子的化学位移数据是一个信息宝库，可以促进广泛的生化和生物物理研究。生物磁共振数据银行（BMRB）是一个公开可访问的数据库，其中包含大量分配的化学位移；然而，将这些知识转化为实际应用并不简单。在此，我们介绍 nightshift：一个用于从 BMRB 中分配的化学位移绘制模拟二维（2D）和 3D NMR 谱的 Python 命令行实用程序和库。该工具允许用户模拟常规采集的酰胺和甲基指纹谱、骨架三共振分配谱以及用户定义的自定义相关谱，包括不一定对应于已发表实验的相关谱。该工具使有经验的 NMR 光谱学家、学习该技术的人员以及有兴趣利用 NMR 的科学家能够预览或检查 BMRB 中分配的蛋白质的各种光谱，而不论这些实验是否已经执行或报告。该工具同样适用于折叠和固有无序的蛋白质，仅受 BMRB 沉积存在的限制。描述了 nightshift 的功能，并举例说明了如何轻松模拟复杂的相关谱和结合事件。
