Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule01:10

Interpreting ¹H NMR Signal Splitting: The (n + 1) Rule

3.2K
In the AX proton spin system, proton A can sense the two spin states of a coupled proton X, resulting in a doublet NMR signal with two peaks of equal (1:1) intensity. When proton A is coupled to two equivalent protons (AX2 spin system), the spin states of each X can be aligned with or against the external field, creating three possible scenarios. This results in a 1:2:1  triplet signal, where the central peak corresponds to the chemical shift of A and is twice as large or intense as the...
3.2K
Nuclear Localization Signals and Import01:46

Nuclear Localization Signals and Import

8.5K
Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
8.5K
Applications Of NMR In Biology01:25

Applications Of NMR In Biology

4.8K
Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics  for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
4.8K
Nuclear Overhauser Enhancement (NOE)01:06

Nuclear Overhauser Enhancement (NOE)

1.7K
Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. This phenomenon, called the nuclear Overhauser enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active...
1.7K
¹H NMR: Pople Notation01:09

¹H NMR: Pople Notation

2.9K
The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
2.9K
Other Nuclides: 31P, 19F, 15N NMR01:16

Other Nuclides: 31P, 19F, 15N NMR

915
Many organic, inorganic, and biological molecules contain spin-half nuclei such as nitrogen-15, fluorine-19, and phosphorus-31. As a result, NMR studies of these nuclei have found extensive applications in chemical and biological research.
While fluorine-19 and phosphorous-31 have high natural abundances (100%) and positive gyromagnetic ratios, nitrogen-15 has a low natural abundance and a negative gyromagnetic ratio. However, nitrogen-15 is still preferred over nitrogen-14 (which has a...
915

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Methodology for the Pediatric Dose Optimization for Seizures in Emergency Medical Services (PediDOSE) study.

Trials·2025
Same author

<i>CCK</i> * (Convex Closure <i>K</i> *): A Suite of Algorithms for the De Novo Design of L- and D-peptide Binders.

bioRxiv : the preprint server for biology·2025
Same author

Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.

Proteins·2025
Same author

Predicting pose distribution of protein domains connected by flexible linkers is an unsolved problem.

bioRxiv : the preprint server for biology·2025
Same author

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.

PLoS computational biology·2025
Same author

Has AlphaFold 3 Solved the Protein Folding Problem for D-Peptides?

bioRxiv : the preprint server for biology·2025
Same journal

Relative Suffix Trees.

The computer journal·2018
Same journal

Developing a smartphone software package for predicting atmospheric pollutant concentrations at mobile locations.

The computer journal·2015
See all related articles

Related Experiment Video

Updated: Apr 18, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

16.2K

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

Mehmet Serkan Apaydin1, Bülent Çatay1, Nicholas Patrick2

  • 1Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı Tuzla, 34956 ıstanbul, Turkey.

The Computer Journal
|January 13, 2015
PubMed
Summary
This summary is machine-generated.

This study presents a new method for protein structure determination using Nuclear Magnetic Resonance (NMR) spectroscopy. The approach improves the assignment of NMR peaks, crucial for understanding protein structure and interactions.

Keywords:
automated NMR assignmentsbinary integer programmingstructural bioinformatics

More Related Videos

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

723
NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

4.0K

Related Experiment Videos

Last Updated: Apr 18, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

16.2K
Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance
10:07

Exploring Protein-Glycan Interactions: Advances in Nuclear Magnetic Resonance

Published on: August 26, 2025

723
NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

4.0K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is vital for studying protein structure and dynamics.
  • A key challenge in NMR is assigning spectral peaks to specific nuclei.
  • Structure-based assignment (SBA) uses homologous template proteins to aid this process.

Purpose of the Study:

  • To develop an improved method for structure-based assignment (SBA) in NMR spectroscopy.
  • To enhance the accuracy and flexibility of automated NMR peak assignment.
  • To enable analysis of different data types for protein structure determination.

Main Methods:

  • Formulated SBA as a linear assignment problem incorporating Nuclear Overhauser Effect (NOE) constraints.
  • Utilized the Nuclear Vector Replacement (NVR) framework's scoring functions and data types.
  • Extended NVR by allowing the use of CH and NH Residual Dipolar Couplings (RDCs) alongside NH RDCs.

Main Results:

  • Achieved assignment accuracy comparable to NVR on existing datasets.
  • Demonstrated higher assignment accuracy on four novel proteins compared to NVR.
  • Successfully implemented partial assignments and identified optimal/near-optimal solutions.

Conclusions:

  • The developed SBA method offers a robust and flexible approach to NMR peak assignment.
  • The method's ability to incorporate diverse RDC data improves accuracy, especially for novel proteins.
  • The framework is extensible for incorporating new data types, advancing protein structure analysis.