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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.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

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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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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
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Thermodynamic potentials are state functions that are extremely useful in analyzing a thermodynamic system. They have dimensions of energy. The four important thermodynamic potentials are internal energy, enthalpy, Helmholtz free energy, and Gibbs free energy. These thermodynamic potentials can be expressed using two of the following variables: pressure, volume, temperature, and entropy. These two variables are expressed as the rate of change of the thermodynamic potential with respect to other...

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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
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Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.

Agustí Emperador1, Tim Meyer, Modesto Orozco

  • 1Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona, Spain.

Proteins
|October 10, 2009
PubMed
Summary

Discrete molecular dynamics (DMD) accurately simulates protein flexibility using physical potentials and secondary structure information. This method enhances protein dynamics studies, including conformational changes upon ligand binding.

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Area of Science:

  • Computational biology
  • Biophysics
  • Molecular dynamics

Background:

  • Atomistic molecular dynamics (MD) simulations are computationally expensive for studying protein flexibility.
  • Existing coarse-grained methods have limitations in accurately reproducing protein dynamics.

Purpose of the Study:

  • To evaluate the accuracy of all-atom discrete molecular dynamics (DMD) for protein flexibility studies.
  • To compare DMD performance against atomistic MD simulations and coarse-grained methods.

Main Methods:

  • Utilized all-atom discrete molecular dynamics (DMD) with a quasi-physical potential.
  • Incorporated secondary structure information to enhance the physical potential.
  • Validated the method against existing atomistic MD simulation data for a diverse protein set.

Main Results:

  • DMD accurately reproduces the dynamics of proteins in solution.
  • The method shows significant improvement over structure-based coarse-grained approaches.
  • DMD successfully captures protein conformational changes induced by ligand interactions.

Conclusions:

  • All-atom DMD offers a computationally efficient and accurate approach for studying protein flexibility and dynamics.
  • DMD enables exploration of non-equilibrium protein dynamics and ligand-induced conformational changes.
  • This method provides a valuable tool for understanding protein behavior in various biological contexts.