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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.4K
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...
1.4K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.8K
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.
1.8K

You might also read

Related Articles

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

Sort by
Same author

Benchtop High-MAS NMR for Paramagnetic Materials.

Molecules (Basel, Switzerland)·2026
Same author

Extending molecular dynamics with dipolar NMR tensors as constraints to chiral phosphorus compounds.

Physical chemistry chemical physics : PCCP·2024
Same author

Development of in situ high resolution NMR: Proof-of-principle for a new (spinning) cylindrical mini-pellet approach applied to a Lithium ion battery.

Solid state nuclear magnetic resonance·2023
Same author

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations.

Magnetic resonance in chemistry : MRC·2023
Same author

Residual dipolar couplings as a tool for structural analysis of ionic liquids.

Chemical communications (Cambridge, England)·2023
Same author

Structures Controlled by Entropy: The Flexibility of Strychnine as Example.

Molecules (Basel, Switzerland)·2022

Related Experiment Video

Updated: Apr 4, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.9K

Molecular dynamics simulations on PGLa using NMR orientational constraints.

Ulrich Sternberg1, Raiker Witter2,3

  • 1Technomedicum, Tallinn University of Technology, Ehitajate tee 5, 19086, Tallinn, Estonia. ulrich.sternberg@partner.kit.edu.

Journal of Biomolecular NMR
|September 12, 2015
PubMed
Summary

Solid-state Nuclear Magnetic Resonance (NMR) data provides orientational constraints for molecular dynamics simulations. This approach accurately determines the structure and dynamics of peptides like PGLa within membranes.

Keywords:
2H NMRCell penetrating peptideForce field calculationsMDOCMolecular dynamics simulationsOrder parametersOrientational NMR constraintsOriented samplesPGLa peptide

More Related Videos

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.1K
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.5K

Related Experiment Videos

Last Updated: Apr 4, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
05:56

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

1.9K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.1K
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.5K

Area of Science:

  • Biophysics
  • Computational Chemistry
  • Structural Biology

Background:

  • Understanding peptide structure and dynamics in membrane environments is crucial for biological function.
  • Solid-state Nuclear Magnetic Resonance (NMR) provides valuable orientational information from anisotropic samples.
  • Traditional molecular dynamics simulations often struggle to incorporate experimental NMR data effectively.

Purpose of the Study:

  • To develop and apply a novel computational method integrating solid-state NMR data into molecular dynamics simulations.
  • To determine the structure and dynamics of the antimicrobial peptide PGLa within a membrane environment.
  • To validate the new method by comparing simulation results with experimental NMR parameters.

Main Methods:

  • Utilized the recently developed Molecular Dynamics with Orientational Constraints (MDOC) technique.
  • Introduced orientation-dependent pseudo-forces into the COSMOS-NMR force field to guide simulations.
  • Applied MDOC to the PGLa peptide and a related dimer model, using solid-state NMR data as constraints.

Main Results:

  • MDOC simulations successfully reproduced experimental NMR parameters within error bounds for PGLa and its dimer.
  • Directly derived alignment, conformation, and order parameters of membrane-bound PGLa and its dimer.
  • Obtained novel insights into segmental orientation distributions and order parameter tensors for dimer systems.

Conclusions:

  • The MDOC method effectively integrates experimental NMR data to accurately model peptide structure and dynamics in membranes.
  • The study confirms a membrane-spanning orientation for PGLa at a specific peptide-to-lipid ratio.
  • MDOC offers a powerful, versatile approach for studying flexible molecules and their interactions within complex environments.