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

NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

740
When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
740
Atomic Nuclei: Types of Nuclear Relaxation01:28

Atomic Nuclei: Types of Nuclear Relaxation

334
Nuclear relaxation restores the equilibrium population imbalance and can occur via spin–lattice or spin–spin mechanisms, which are first-order exponential decay processes.
In spin–lattice or longitudinal relaxation, the excited spins exchange energy with the surrounding lattice as they return to the lower energy level. Among several mechanisms that contribute to spin–lattice relaxation, magnetic dipolar interactions are significant. Here, the excited nucleus transfers...
334
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

888
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
888
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.1K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.1K
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.1K
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...
1.1K
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

1.4K
A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to...
1.4K

You might also read

Related Articles

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

Sort by
Same author

Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of GAAG and GCAA tetraloops.

RNA (New York, N.Y.)·2026
Same author

Effects of residue substitutions on the cellular abundance of proteins.

eLife·2026
Same author

StruCloze: A Unified Framework for Backmapping and Inpainting Biomolecule Structures.

Journal of chemical theory and computation·2026
Same author

A Stickiness Scale for Disordered Proteins.

The journal of physical chemistry. B·2026
Same author

Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.

Nature communications·2026
Same author

Correction to "Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates".

Journal of chemical theory and computation·2026
Same journal

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame.

Journal of chemical theory and computation·2026
Same journal

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.

Journal of chemical theory and computation·2026
Same journal

Generalizable Protein Folding Pathway Exploration with DA2-GRASP: Extending Beyond Miniproteins.

Journal of chemical theory and computation·2026
Same journal

Improving PCM in Protic Media: Markov State Models for TD-DFT Calculations.

Journal of chemical theory and computation·2026
Same journal

Efficient Coupled-Cluster Python Frameworks for Next-Generation GPUs: A Comparative Study of CuPy and PyTorch on the Hopper and Grace Hopper Architecture.

Journal of chemical theory and computation·2026
Same journal

Extending the MARTINI 3 Coarse-Grained Force Field to Polypeptoids.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Jul 27, 2025

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.0K

Fitting Force Field Parameters to NMR Relaxation Data.

Felix Kümmerer1, Simone Orioli1,2, Kresten Lindorff-Larsen1

  • 1Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.

Journal of Chemical Theory and Computation
|June 5, 2023
PubMed
Summary
This summary is machine-generated.

Optimizing protein force fields with NMR relaxation data improves simulations. Modified parameters enhance agreement with experimental data and better represent protein dynamics in solution.

More Related Videos

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

5.3K
Measuring the Spin-Lattice Relaxation Magnetic Field Dependence of Hyperpolarized [1-13C]pyruvate
11:57

Measuring the Spin-Lattice Relaxation Magnetic Field Dependence of Hyperpolarized [1-13C]pyruvate

Published on: September 13, 2019

6.6K

Related Experiment Videos

Last Updated: Jul 27, 2025

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.0K
15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
08:09

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

5.3K
Measuring the Spin-Lattice Relaxation Magnetic Field Dependence of Hyperpolarized [1-13C]pyruvate
11:57

Measuring the Spin-Lattice Relaxation Magnetic Field Dependence of Hyperpolarized [1-13C]pyruvate

Published on: September 13, 2019

6.6K

Area of Science:

  • Computational chemistry and biophysics
  • Structural biology
  • Nuclear Magnetic Resonance (NMR) spectroscopy

Background:

  • Accurate molecular dynamics (MD) simulations are crucial for understanding protein dynamics.
  • Force field parameters significantly influence the accuracy of MD simulations.
  • NMR relaxation experiments provide time-dependent data sensitive to molecular motion.

Purpose of the Study:

  • To develop and validate a method for optimizing protein force field parameters using NMR relaxation data.
  • To improve the accuracy of MD simulations for protein dynamics.
  • To enable more direct comparison between simulation results and experimental NMR data.

Main Methods:

  • Scanning dihedral angle potential energy terms for methyl group rotation in proteins.
  • Calculating NMR relaxation rates from MD simulations with modified force fields.
  • Comparing simulated rates with experimental deuterium relaxation measurements of T4 lysozyme.
  • Validating the optimized force field using simulations of CI2 and ubiquitin.

Main Results:

  • A minor adjustment to Cγ methyl group parameters significantly improved agreement with experimental NMR relaxation data.
  • The optimized force field demonstrated improved accuracy for both the training protein (T4 lysozyme) and validation proteins (CI2, ubiquitin).
  • Enhanced force field parameters facilitated more effective a posteriori reweighting of MD trajectories.

Conclusions:

  • Optimized force fields enable more direct comparisons between MD simulations and side-chain NMR relaxation data.
  • The refined force field allows for the construction of more accurate ensembles representing protein dynamics in solution.
  • This approach enhances the predictive power of computational methods in structural biology.