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Protein Folding

Protein Folding

Protein Folding

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...

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

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 Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein Organization

Protein Organization

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Updated: Mar 12, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Quantifying side-chain conformational variations in protein structure.

Zhichao Miao^1,2,3, Yang Cao⁴

¹Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France.

Scientific Reports

|November 16, 2016

Summary

This summary is machine-generated.

Protein side-chain flexibility, influenced by solvent exposure and hydrophilicity, varies significantly. This variability means predicting protein side-chain conformation is complex, requiring new assessment methods.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Protein side-chain conformation is crucial for biological function.
Accurate side-chain prediction is vital for protein design and structure optimization.
Existing prediction methods often overlook side-chain polymorphism.

Purpose of the Study:

To quantitatively study side-chain conformational variations in proteins.
To investigate the relationship between side-chain variability and residue features.
To re-evaluate current approaches for assessing side-chain prediction programs.

Main Methods:

Statistical analysis of large-scale protein data sets from the Protein Data Bank (PDB).
Quantification of different types of side-chain variabilities.
Correlation analysis between conformational flexibility and residue properties (solvent exposure, degree of freedom, hydrophilicity).

Main Results:

Side-chain conformational flexibility is significantly correlated with solvent exposure, degree of freedom, and hydrophilicity.
Identified and quantified various types of side-chain variabilities within protein structures.
Demonstrated that side-chain conformation is not a single fixed state.

Conclusions:

Protein side-chain prediction is inherently a multi-state problem, not a single-answer prediction.
The findings necessitate a reconsideration of how side-chain prediction programs are assessed.
Understanding side-chain polymorphism is key to advancing protein structure prediction and design.