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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

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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.
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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...
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

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

Protein conformational transitions explored by mixed elastic network models.

Wenjun Zheng1, Bernard R Brooks, Gerhard Hummer

  • 1Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

Proteins
|June 29, 2007
PubMed
Summary

We developed a mixed elastic network model (MENM) to study protein conformational changes. This model efficiently reveals transition paths and molecular motions for large protein systems.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Proteins undergo large-scale conformational transitions essential for their function.
  • Studying these transitions computationally is challenging due to system size and complexity.

Purpose of the Study:

  • To develop a novel computational model for analyzing protein conformational transitions.
  • To efficiently characterize the dynamics and pathways of large-scale protein movements.

Main Methods:

  • Developed a mixed elastic network model (MENM) by combining elastic network potentials of initial and final states.
  • Utilized analytic methods to determine saddle points, transition paths, and potentials of mean force.
  • Applied the MENM to study conformational changes in motor proteins KIF1A kinesin and myosin II.

Main Results:

  • The MENM effectively interpolates between known protein structures, maintaining them as local minima.
  • Generated transition paths for KIF1A kinesin and myosin II, detailing their conformational motions.
  • Demonstrated the model's computational efficiency and applicability to large, complex protein systems.

Conclusions:

  • The mixed elastic network model (MENM) provides an efficient and generalizable framework for studying protein conformational changes.
  • MENM facilitates the detailed characterization of molecular motions during large-scale transitions.
  • This approach is valuable for understanding the function of motor proteins and other systems with collective structural dynamics.