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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...
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.
Conformations of Ethane and Propane02:18

Conformations of Ethane and Propane

In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, the...
IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration01:16

IR Spectroscopy: Hooke's Law Approximation of Molecular Vibration

A covalently bonded heteronuclear diatomic molecule can be modeled as two vibrating masses connected by a spring. The vibrational frequency of the bond can be expressed using an equation derived from Hooke's law, which describes how the force applied to stretch or compress a spring is proportional to the displacement of the spring. In this case, the atoms behave like masses, and the bond acts like a spring.
According to Hooke's law, the vibrational frequency is directly proportional to the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...

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Related Experiment Video

Updated: May 23, 2026

Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules

Published on: April 25, 2025

Conformational modes in biomolecules: dynamics and approximate invariance.

Alex Potapov1, Maria Stepanova

  • 1Centre for Mathematical Biology, University of Alberta, Edmonton, Alberta, Canada.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|April 3, 2012
PubMed
Summary

This study introduces a new theoretical framework to understand biomolecular dynamics and conformational changes. It analyzes stable properties of macromolecules like the human prion protein using advanced statistical mechanics.

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Area of Science:

  • Soft matter theory
  • Statistical mechanics
  • Biophysics

Background:

  • Understanding biomolecular folding and conformational dynamics remains a significant challenge in soft matter theory.
  • Existing methods may not fully capture the complex dynamics of macromolecules.

Purpose of the Study:

  • To introduce a novel theoretical framework for analyzing biomolecular dynamics.
  • To identify invariant properties and stable dynamical characteristics of biomolecules.
  • To provide a platform for modeling conformational changes and complementing simulations.

Main Methods:

  • Utilizing statistical mechanics, dimensionality reduction, perturbation theory, and matrix theory.
  • Representing biomolecular dynamics through time-dependent orthogonal conformational modes.
  • Analyzing mode dynamics and identifying persistent invariant properties.
  • Applying a multiscale approach using short molecular dynamics trajectory segments.

Main Results:

  • A theoretical framework for biomolecular dynamics is established.
  • Invariant properties of conformational modes are identified.
  • The dynamics of a human prion protein are analyzed as a case study.
  • Stable dynamical properties and coarse-grained structures are assessed.

Conclusions:

  • The developed theory offers a rigorous approach to understanding biomolecular dynamics.
  • It provides a foundation for modeling conformational changes in macromolecules.
  • The framework can complement existing molecular dynamics simulations.