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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.
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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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules
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Published on: April 25, 2025

Protein conformational flexibility analysis with noisy data.

Anshul Nigham1, David Hsu

  • 1Computer Science Programme, Singapore-MIT Alliance, Singapore.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|July 26, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient algorithm to analyze noisy protein structural data, reliably detecting key conformational changes. The method uses statistical flexibility tests to identify significant movements crucial for biological functions.

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein conformational changes are vital for biological functions like ligand-protein and protein-protein interactions.
  • Analyzing these changes is challenging due to noise in structural data.
  • Reliable and efficient algorithms are needed to identify significant protein movements.

Purpose of the Study:

  • To develop an efficient algorithm for analyzing protein conformational changes from noisy structural data.
  • To reliably detect salient conformational alterations in proteins.
  • To provide a tool for understanding protein dynamics.

Main Methods:

  • Applied a statistical flexibility test to contiguous protein fragments.
  • Combined flexibility test results to compute a consensus flexibility measure for each residue.
  • Validated the algorithm using data from the Protein Data Bank and Macromolecular Movements Database.

Main Results:

  • The algorithm reliably detects different types of salient conformational changes.
  • Successfully identified well-known movements like hinge, shear, and the flap motion of HIV-1 protease.
  • Demonstrated efficiency and reliability in analyzing noisy protein structural data.

Conclusions:

  • The developed algorithm offers an efficient and reliable method for analyzing protein conformational changes.
  • It accurately identifies significant protein dynamics even with noisy structural data.
  • The software is publicly available for broader research use.