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

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

1.1K
When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
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
Double Resonance Techniques: Overview01:12

Double Resonance Techniques: Overview

260
Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by...
260
Molecular Spectroscopy: Absorption and Emission01:14

Molecular Spectroscopy: Absorption and Emission

2.4K
Molecules possess discrete energy levels called quantum states. Unlike atoms, which have simpler energy levels, molecules possess additional rotational and vibrational energy levels.  Each energy level is separated by an energy gap, with the gaps between adjacent electronic, vibrational, and rotational levels varying significantly. The three types of energy levels in a diatomic molecule are shown in Figure 1.
2.4K
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

749
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...
749
Nuclear Overhauser Enhancement (NOE)01:07

Nuclear Overhauser Enhancement (NOE)

777
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...
777

You might also read

Related Articles

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

Sort by
Same author

Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.

Journal of chemical theory and computation·2026
Same author

Highly Atypical 2025 Influenza A Season in Brazil.

Influenza and other respiratory viruses·2026
Same author

Mortality trends for diabetes mellitus, hypertension and cardiovascular disease among people living with and without HIV in Brazil during the COVID-19 pandemic, 2020-2022.

HIV medicine·2026
Same author

Beyond MIDAS: An <i>In Silico</i> Study of a Putative Noncanonical C16 Binding Site in αvβ3 Integrin.

ACS omega·2026
Same author

Leveraging probabilistic forecasts for dengue preparedness and control: The 2024 Dengue Forecasting Sprint in Brazil.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Peptide-based covalent inhibitor of tubulin detyrosination promotes mesenchymal-to-epithelial transition in lung cancer cells.

Proceedings of the National Academy of Sciences of the United States of America·2025

Related Experiment Video

Updated: Aug 14, 2025

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.3K

MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from

Mauricio G S Costa1,2, Paulo R Batista1, Antoniel Gomes3

  • 1Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil.

Journal of Chemical Theory and Computation
|January 9, 2023
PubMed
Summary

Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring protein conformational changes. The new MDexciteR tool integrates MDeNM with GPU-accelerated simulations, improving protein dynamics exploration.

More Related Videos

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization
08:22

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization

Published on: August 6, 2018

6.9K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K

Related Experiment Videos

Last Updated: Aug 14, 2025

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.3K
Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization
08:22

Measurement of Ultrafast Vibrational Coherences in Polyatomic Radical Cations with Strong-Field Adiabatic Ionization

Published on: August 6, 2018

6.9K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K

Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Enhanced sampling methods are crucial for exploring protein conformational dynamics.
  • Molecular dynamics with excited normal modes (MDeNM) offers a low-bias approach to study protein motions.
  • Existing MDeNM implementations require significant user expertise and lack broad accessibility.

Purpose of the Study:

  • To develop and validate an automated, open-source implementation of MDeNM.
  • To generalize MDeNM for incorporating experimental data via principal components.
  • To assess the utility of coarse-grained normal modes in MDeNM simulations.

Main Methods:

  • Development of MDexciteR, an automated MDeNM implementation compatible with GPU-accelerated molecular dynamics engines.
  • Generalization of MDeNM to utilize principal components derived from experimental ensembles.
  • Evaluation of coarse-grained normal modes from elastic network models for MDeNM.
  • Testing the method on globular proteins and a protein-membrane system.

Main Results:

  • MDexciteR successfully integrates MDeNM with GPU-enabled simulation packages.
  • The generalized MDeNM approach accurately captures conformational changes using experimental data.
  • Coarse-grained normal modes provide a computationally efficient alternative without significant loss of accuracy.
  • Performance and limitations were characterized across diverse protein systems.

Conclusions:

  • MDexciteR enhances the accessibility and applicability of MDeNM for protein dynamics studies.
  • The generalized MDeNM approach facilitates the integration of experimental and simulation data.
  • Coarse-grained MDeNM offers a viable strategy for large-scale conformational sampling.
  • The study provides insights into the strengths and weaknesses of these advanced MDeNM techniques.