Related Experiment Video
Updated: Oct 20, 2025
09:25
Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
Published on: November 1, 2024
2.2K
nightshift: A Python program for plotting simulated NMR spectra from assigned chemical shifts from the Biological
1Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.
Protein Science : a Publication of the Protein Society
|September 13, 2021
Summary
Nightshift is a Python tool that simulates NMR spectra from BMRB chemical shifts. This enables visualization of protein structures and binding events, aiding biochemical and biophysical studies.
Area of Science:
- Biochemistry
- Biophysics
- Structural Biology
Background:
- Nuclear magnetic resonance (NMR) spectroscopy provides crucial site-specific data on protein local environments via chemical shifts.
- Assigned chemical shift data, stored in the Biological Magnetic Resonance Data Bank (BMRB), offers extensive information for biochemical and biophysical research.
- Utilizing BMRB data for practical applications, such as spectrum simulation, presents challenges.
Purpose of the Study:
- To introduce nightshift, a Python utility for simulating 2D and 3D NMR spectra.
- To enable users to generate various NMR spectra from BMRB-assigned chemical shifts.
- To facilitate the preview and examination of NMR spectra for proteins in the BMRB.
Main Methods:
- Development of a Python command-line utility and library named nightshift.
- Implementation of functions to simulate amide and methyl fingerprint spectra, backbone triple-resonance assignment spectra, and custom correlations.
- Utilizing assigned chemical shift data from the BMRB as input.
Main Results:
- Nightshift successfully simulates a range of NMR spectra, including standard and custom correlations.
- The tool can preview spectra for proteins with BMRB depositions, regardless of whether experiments were previously performed.
- Applications demonstrate the simulation of complex correlation spectra and binding events.
Conclusions:
- Nightshift provides a valuable tool for NMR spectroscopists and scientists to explore protein chemical shift data.
- The utility simplifies the visualization and analysis of NMR spectra, aiding in structural and binding studies.
- It supports both folded and intrinsically disordered proteins, expanding its applicability in structural biology.
Keywords:
2D spectra3D spectraBMRBPythonchemical shiftnuclear magnetic resonancespectral visualizationMore Related Videos
07:24Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
Published on: September 23, 2021
1.9K
10:28Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy NMR and Microscale Thermophoresis MST
Published on: November 2, 2018
12.3K
Related Concept Videos
01:15NMR Spectroscopy: Chemical Shift Overview
2.0K
The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
For instance, the proton...
For instance, the proton...
2.0K
01:02¹H NMR: Interpreting Distorted and Overlapping Signals
1.2K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
1.2K
01:17NMR Spectrometers: Radiofrequency Pulses and Pulse Sequences
1.0K
A pulse is a short burst of radio waves distributed over a range of frequencies that simultaneously excites all the nuclei in the sample. Upon passing a radio frequency pulse along the x-axis, the nuclei absorb energy corresponding to their Larmor frequencies and achieve resonance. This shifts the net magnetization vector from the z-axis toward the transverse plane. This angle of rotation of the magnetization vector, or the flip angle, is proportional to the duration and intensity of the pulse.
1.0K
01:19NMR Spectroscopy Of Amines
9.7K
In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is...
9.7K
01:12Two-Dimensional (2D) NMR: Overview
998
The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
998
01:14NMR Spectroscopy of Aromatic Compounds
5.3K
Aromatic compounds can be identified or analyzed using proton NMR and carbon‐13 NMR. Typically, aromatic hydrogens or hydrogens directly bonded to the aromatic rings are strongly deshielded by the aromatic ring current. Therefore, they absorb in the range of 6.5–8.0 ppm in proton NMR spectra. For instance, aromatic hydrogens directly bonded to the benzene ring absorb at 7.3 ppm. However, aromatic hydrogens of larger rings absorb farther upfield or downfield than the ideal range.
5.3K