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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...

Protein Folding

Protein Folding

Protein Folding

Protein Folding

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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.

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Related Experiment Video

Updated: May 22, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Folding helical proteins in explicit solvent using dihedral-biased tempering.

Cheng Zhang¹, Jianpeng Ma

¹Applied Physics Program and Department of Bioengineering, Rice University, Houston, TX 77005, USA.

Proceedings of the National Academy of Sciences of the United States of America

|May 11, 2012

Summary

Researchers successfully folded four helical proteins using a novel simulation method. This technique accurately predicts native protein structures and is applicable to other helical protein simulations.

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Last Updated: May 22, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

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Microfluidic Mixers for Studying Protein Folding

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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes

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Published on: January 16, 2016

Area of Science:

Biophysics
Computational Biology
Protein Folding

Background:

Protein folding is crucial for biological function.
Simulating protein folding remains a significant computational challenge.

Purpose of the Study:

To develop and validate a simulation protocol for folding helical proteins.
To assess the accuracy of the protocol in reproducing experimentally determined structures.

Main Methods:

Employed a single-trajectory-based tempering method with high-temperature dihedral bias.
Performed simulations in explicit solvent for several microseconds.
Analyzed folding trajectories using cluster analysis.

Main Results:

Successfully folded four helical proteins (α(3)D, α(3)W, Fap1-NR(α), S-836) and mutants.
Achieved low root-mean-square deviations (1.0–2.1 Å) from experimental structures.
Native conformations consistently occupied the most populated clusters in simulations.

Conclusions:

The developed simulation protocol is effective for folding helical proteins.
The method accurately predicts native protein conformations.
This protocol is scalable for large-scale simulations on accessible computing platforms.