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)

1.0K
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...
1.0K

You might also read

Related Articles

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

Sort by
Same author

First order approximation of polyatomic ion and neutral diffusion in neutral gases under arbitrary fields.

The Journal of chemical physics·2026
Same author

Ion Mobility Suite (IMoS) 2: A General Computational Framework for Solving the Generalized Boltzmann Equation with Rotational Transport for Polyatomic Ions in Arbitrary Fields.

Analytical chemistry·2026
Same author

Structural promiscuity in the human circulatory IgA1 clonal repertoire.

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

Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction.

bioRxiv : the preprint server for biology·2026
Same author

Optimization of Electric Field Traveling Waves in SLIM Platforms for Improved Resolution via Analytical Solutions of the Nernst-Planck Equation.

Journal of the American Society for Mass Spectrometry·2026
Same author

Characterization of Gas-Phase Native(-like) Proteins Using Structures for Lossless Ion Manipulations.

Analytical chemistry·2025

Related Experiment Video

Updated: Jun 9, 2025

Direct Imaging of Laser-driven Ultrafast Molecular Rotation
10:52

Direct Imaging of Laser-driven Ultrafast Molecular Rotation

Published on: February 4, 2017

9.7K

Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods.

Viraj D Gandhi1,2, Leyan Hua1,2, Morgan Lawrenz3

  • 1Department of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States.

Journal of Chemical Theory and Computation
|October 23, 2024
PubMed
Summary

Accurate gas-phase protein structure determination is challenging. Enhanced sampling methods in Molecular Dynamics simulations improved Collision Cross-Section (CCS) predictions, aligning simulated and experimental values within 4%.

More Related Videos

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.2K
In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx
09:49

In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx

Published on: May 13, 2020

4.0K

Related Experiment Videos

Last Updated: Jun 9, 2025

Direct Imaging of Laser-driven Ultrafast Molecular Rotation
10:52

Direct Imaging of Laser-driven Ultrafast Molecular Rotation

Published on: February 4, 2017

9.7K
Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.2K
In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx
09:49

In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx

Published on: May 13, 2020

4.0K

Area of Science:

  • Computational chemistry
  • Biophysics
  • Structural biology

Background:

  • Accurate characterization of gas-phase protein structures is crucial but challenging.
  • Discrepancies exist between initial Molecular Dynamics (MD) simulations and experimental Collision Cross-Section (CCS) values obtained via Ion Mobility-Mass Spectrometry (IMS-MS).

Purpose of the Study:

  • To improve the accuracy of gas-phase protein structure characterization.
  • To reconcile discrepancies between simulated and experimental Collision Cross-Section (CCS) values.

Main Methods:

  • Utilized Molecular Dynamics (MD) simulations combined with enhanced sampling techniques.
  • Employed Harmonic Biasing Potential and Adaptive Biasing Force methods, using radius of gyration as a guiding parameter.
  • Applied guiding forces to overcome energy barriers, allowing proteins to reach compact conformations.

Main Results:

  • Enhanced sampling methods significantly improved the alignment between simulated and experimental CCS values.
  • Achieved close agreement (within approximately 4%) between calculated and experimentally measured CCS.
  • Validated the efficacy of Harmonic Biasing Potential and Adaptive Biasing Force in predicting gas-phase protein structures.

Conclusions:

  • Enhanced sampling techniques are effective for accurate gas-phase protein structure prediction.
  • This study provides a foundation for optimizing biasing methods for improved structural characterization.
  • Future work will focus on expanding collective variables for more precise predictions.