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Related Concept Videos

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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Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

An approximate method in using molecular mechanics simulations to study slow protein conformational changes.

Lijiang Yang1, Yi Qin Gao

  • 1Department of Chemistry, Texas A and M University, College Station, Texas 77843, USA.

The Journal of Physical Chemistry. B
|February 27, 2007
PubMed
Summary

This study introduces an approximate molecular dynamics (MD) simulation method with a larger time step to efficiently study large protein conformational changes. The method successfully simulated the open-to-closed transition of Calmodulin, revealing intermediate structures.

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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Published on: October 15, 2018

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Last Updated: Jul 16, 2026

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
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Published on: September 1, 2023

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

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein dynamics are crucial for function but challenging to simulate.
  • Large-scale conformational changes in proteins are difficult to capture with standard molecular dynamics (MD) simulations due to computational cost.

Purpose of the Study:

  • To develop and validate an approximate MD method for studying slow, large-scale protein motions.
  • To efficiently simulate conformational transitions in complex biological systems.

Main Methods:

  • Utilized standard MD simulations with a significantly larger integration time step.
  • Applied the method to simulate the calcium-induced conformational change of the Calmodulin calcium binding domain.

Main Results:

  • The approximate MD method successfully captured intermediate conformations during the open-to-closed transition of Calmodulin.
  • Simulated structures showed a low root-mean-square deviation (rmsd) of 1.56 Å compared to experimental apo-calmodulin structures.
  • Identified helix rearrangements within Ca2+ binding pockets during the transition.

Conclusions:

  • The proposed approximate MD method is effective for studying large-scale protein conformational changes.
  • This approach enhances the applicability of MD simulations for complex biological systems.
  • Provides insights into the dynamic mechanisms of calcium binding proteins like Calmodulin.