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Related Concept Videos

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

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

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.
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

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Related Experiment Video

Updated: Jun 15, 2026

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

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.

Cameron F Abrams1, Eric Vanden-Eijnden

  • 1Department of Chemical and Biological Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA. cfa22@drexel.edu

Proceedings of the National Academy of Sciences of the United States of America
|March 3, 2010
PubMed
Summary

Temperature-accelerated molecular dynamics (TAMD) efficiently samples protein conformational changes. This method accurately predicts key structural transitions in proteins like GroEL and HIV-1 gp120, aiding in drug development.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Multidomain proteins exhibit complex conformational dynamics crucial for function.
  • All-atom molecular dynamics simulations are computationally intensive for exploring large-scale protein motions.

Purpose of the Study:

  • To demonstrate the application of temperature-accelerated molecular dynamics (TAMD) for enhanced conformational sampling of multidomain proteins.
  • To validate TAMD's ability to predict functionally relevant protein conformations using all-atom simulations.

Main Methods:

  • Utilized temperature-accelerated molecular dynamics (TAMD) with collective variables based on subdomain Cartesian coordinates.
  • Applied TAMD to simulate the GroEL subunit and HIV-1 gp120 in explicit solvent.
  • Employed a fictitious high temperature to accelerate exploration of the free-energy surface.

Main Results:

  • TAMD successfully recapitulated the GroEL t --> r transition, showing significant domain displacement and reduced RMSD.
  • For HIV-1 gp120, TAMD predicted domain counterrotation and bridging sheet disruption, deviating from known conformations.
  • Generated plausible models for the unliganded HIV-1 gp120 conformation and estimated free-energy barriers.

Conclusions:

  • TAMD is an effective method for sampling conformational landscapes of multidomain proteins in all-atom simulations.
  • The method shows high predictive capability for functionally relevant conformational changes.
  • TAMD-generated models of unliganded HIV-1 gp120 can aid in the design of inhibitors and immunogens.