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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...

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.

Intrinsically Disordered Proteins

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

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A Structure-free Method for Quantifying Conformational Flexibility in proteins.

Virginia M Burger¹, Daniel J Arenas², Collin M Stultz^1,3

¹Research Laboratory for Electronics, Massachusetts Institute of Technology, 77 Massachusetts Ave. Cambridge MA 02139, USA.

Scientific Reports

|July 1, 2016

Summary

This summary is machine-generated.

This study introduces a new method using small-angle X-ray scattering (SAXS) to measure protein flexibility without needing complex structural models. This approach quantifies protein disorder and ligand binding effects, aiding in protein classification.

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Published on: July 16, 2017

Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Protein flexibility is crucial for function.
Understanding protein dynamics requires quantifying flexibility.
Existing methods may require complex structural ensembles.

Purpose of the Study:

To develop a novel, structure-free method for quantifying protein flexibility in solution.
To assess the impact of ligand binding on protein flexibility.
To establish a basis for a protein structure classification system.

Main Methods:

Utilized small-angle X-ray scattering (SAXS) data.
Developed a method to calculate effective entropy from SAXS data.
Quantified the diversity of radii of gyration without generating structural ensembles.

Main Results:

The novel approach successfully quantifies protein disorder.
Demonstrated the ability to measure the effects of ligand binding on protein flexibility.
Validated the method across over 200 experimental datasets.

Conclusions:

The structure-free SAXS method provides a robust way to quantify protein flexibility.
This quantitative description aids in understanding protein dynamics and function.
The approach supports the development of a rigorous protein structure taxonomy.