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

Potential Energy00:52

Potential Energy

42.7K
The energy stored by a structure and location of matter in space is called potential energy. For instance, raising a kettlebell changes its spatial location and increases its potential energy. Similarly, a stretched rubber band contains potential energy which, under certain conditions, can be converted into other forms of energy, such as kinetic energy.
Chemical bonds that form attractive forces between atoms also contain potential energy, called chemical energy. When a chemical reaction...
42.7K
Potential Energy01:09

Potential Energy

1.0K
A conservative force, such as a gravitational or elastic force, gives the body the capacity to do work. This capacity, measured as the potential energy, depends on the body's location or “position” relative to a fixed reference position or datum. The gravitational potential energy is considered zero at the reference point. Suppose a body is located at some vertical distance above a fixed horizontal reference or datum. In that case, the weight of the body has positive gravitational potential...
1.0K
Cell Potential and Free Energy02:58

Cell Potential and Free Energy

46.6K
Thermodynamics of a Redox Reaction
Thermodynamics is the branch of physics dealing with the relationship between heat and other forms of energy. In an electrochemical cell, chemical energy is converted into electrical energy.
Thus, a link can be predicted between cell potential, free energy change, and the equilibrium constant for the reaction. Cell potential can also be measured as the oxidant or the reducing strength, and similar acid-base strength measures are reflected in equilibrium...
46.6K
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

8.8K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.8K
Conformity01:20

Conformity

48.2K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
48.2K
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

21.0K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
21.0K

You might also read

Related Articles

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

Sort by
Same author

Streamlined Postprocessing of NMR Structures with the Molecular Restrainer: A Universal Tool for High-Quality Protein-Ligand Models and Non-Standard Amino Acid Residues.

International journal of molecular sciences·2025
Same author

ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.

Journal of computer-aided molecular design·2019
Same author

Controlled-advancement rigid-body optimization of nanosystems.

Journal of computational chemistry·2019
Same author

Incremental solver for orbital-free density functional theory.

Journal of computational chemistry·2019
Same author

Incremental update of electrostatic interactions in adaptively restrained particle simulations.

Journal of computational chemistry·2018
Same author

ART-RRT: As-Rigid-As-Possible exploration of ligand unbinding pathways.

Journal of computational chemistry·2018

Related Experiment Video

Updated: Feb 7, 2026

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

1.5K

Generating conformational transition paths with low potential-energy barriers for proteins.

Minh Khoa Nguyen1, Léonard Jaillet2, Stéphane Redon1

  • 1Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP (Institute of Engineering Univ. Grenoble Alpes), LJK, 38000, Grenoble, France.

Journal of Computer-Aided Molecular Design
|August 3, 2018
PubMed
Summary

A new method generates protein conformational transition paths with low energy barriers. Combining As-Rigid-As-Possible (ARAP) interpolation with energy minimization significantly reduces potential energy for protein mechanism studies.

Keywords:
As-Rigid-As-PossibleLow-energy pathNudged elastic bandProtein conformational transition

More Related Videos

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells
08:31

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Published on: September 16, 2014

12.5K
High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.2K

Related Experiment Videos

Last Updated: Feb 7, 2026

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers
09:33

Monitoring Conformational Dynamics of Single Unmodified Proteins using Plasmonic Nanotweezers

Published on: March 21, 2025

1.5K
Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells
08:31

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Published on: September 16, 2014

12.5K
High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States
04:37

High-Pressure NMR Experiments for Detecting Protein Low-Lying Conformational States

Published on: June 29, 2021

3.2K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Understanding protein conformational changes is crucial for elucidating biological mechanisms.
  • The As-Rigid-As-Possible (ARAP) method generates protein transition paths but ignores atomic interactions, potentially creating unrealistic pathways.
  • Geometry-based path generation can lead to inconsistencies due to unconsidered atom interactions.

Purpose of the Study:

  • To introduce a novel method for generating protein conformational transition paths with minimized potential energy barriers.
  • To improve the realism and energetic favorability of protein conformational pathways.
  • To provide a computationally efficient approach for exploring protein dynamics.

Main Methods:

  • A three-stage process combining As-Rigid-As-Possible (ARAP) interpolation, a clash remover, and Nudged Elastic Band (NEB) optimization.
  • Initial path generation using ARAP interpolation to maintain conformational rigidity.
  • Post-processing with a clash remover to resolve steric hindrances.
  • Final path refinement using NEB to minimize potential energy.

Main Results:

  • The combined method yields significant reductions in potential energy compared to ARAP interpolation alone.
  • Generated paths exhibit lower energy barriers, facilitating more biologically plausible conformational transitions.
  • ARAP interpolation proved effective as an initial step, outperforming other common methods in generating low-energy paths.

Conclusions:

  • The novel three-stage method effectively generates low-energy conformational transition paths for proteins.
  • Integrating geometric interpolation with energy minimization enhances the accuracy and biological relevance of protein pathway modeling.
  • This approach offers a valuable tool for studying protein mechanisms and dynamics.