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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

Calculating Standard Free Energy Changes

Calculating Standard Free Energy Changes

The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...

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...

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...

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Related Experiment Video

Updated: May 25, 2026

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

Published on: April 28, 2011

Predicting folding free energy changes upon single point mutations.

Zhe Zhang¹, Lin Wang, Yang Gao

¹Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA.

Bioinformatics (Oxford, England)

|January 13, 2012

Summary

This summary is machine-generated.

Predicting protein folding free energy changes from mutations is crucial for understanding disease and designing experiments. Our scaled molecular mechanics Generalized Born (sMMGB) method accurately predicts these changes using protein 3D structures.

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Area of Science:

Computational Biology
Biophysics
Protein Engineering

Background:

Protein folding free energy is vital for protein stability and function.
Missense mutations altering protein stability are often linked to diseases.
Predicting free energy changes upon mutation aids in understanding disease mechanisms and guiding experimental design.

Purpose of the Study:

To develop and validate a computational method for predicting the change in protein folding free energy upon single point mutations.
To assess the accuracy of the proposed method against experimental data.

Main Methods:

Utilized a scaled version of the molecular mechanics Generalized Born (sMMGB) method.
Incorporated a specific model for the unfolded protein state.
Built in silico mutations and compared predictions with a large dataset of 1109 experimentally determined mutations.

Main Results:

Achieved a root mean square deviation of 1.78 kcal/mol.
Demonstrated a strong linear correlation between predicted and experimental data (slope = 1.04).
Benchmarked sMMGB against other leading prediction methods.

Conclusions:

The sMMGB approach provides accurate predictions of folding free energy changes upon single point mutations.
This method can be a valuable tool for researchers studying protein stability, disease mutations, and protein design.