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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

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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.

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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Updated: Jul 18, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Approximating conformational Boltzmann distributions with AlphaFold2 predictions.

Benjamin P Brown^1,2,3, Richard A Stein^3,4, Jens Meiler^1,2,3,5

¹Department of Chemistry, Vanderbilt University, Nashville, TN, USA. Nashville, TN 37232, USA.

Biorxiv : the Preprint Server for Biology

|August 23, 2023

Summary

This summary is machine-generated.

AlphaFold2 contact distance distributions can approximate protein conformational Boltzmann distributions. This method predicts mutation effects and models thermodynamics in large biomolecular systems.

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Area of Science:

Structural biology
Computational biophysics
Protein dynamics

Background:

Protein dynamics are crucial for biological functions like signal transduction and enzyme catalysis.
Understanding protein conformational free energies is vital for disease treatment but limited by current methods.
Existing computational and experimental techniques are restricted to small biological systems.

Conclusions:

AlphaFold2 offers a promising method to model protein conformational thermodynamics beyond the limitations of current techniques.
This approach can aid in understanding protein dynamics and developing new therapeutic strategies.
The findings pave the way for applying AlphaFold2 to larger and more complex biomolecular systems.