Related Experiment Video
Updated: May 14, 2026
10:09
Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
Published on: April 28, 2011
Quantifying protein folding transition States with φ(t)
1Departments of Chemistry, University of Illinois at Urbana-Champaign, IL 61801 USA.
Journal of Biological Physics
|January 25, 2013
Summary
This study details the entropic reaction coordinate Φ(T), a tool for analyzing protein folding. While useful for understanding mutations and transition states, its interpretation requires care, especially near cold denaturation points.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Protein folding free energy surfaces are complex.
- Reduced-dimensionality representations are crucial for analysis.
- The entropic reaction coordinate Φ(T) offers a novel approach.
Purpose of the Study:
- To discuss the entropic reaction coordinate Φ(T) in detail.
- To evaluate the advantages and limitations of Φ(T) for protein folding studies.
- To explore the application of Φ(T) in quantifying mutation conservation and transition state location.
Main Methods:
- Analysis of experimental temperature-tuning data.
- Numerical simulations to illustrate Φ(T) utility and constraints.
- Comparison of Φ(T) derived from experiment, computation, and theory.
Main Results:
- Φ(T) can be determined through multiple approaches (experiment, computation, theory).
- Φ(T) effectively quantifies mutation conservation and folding transition state location.
- Φ(T) can investigate localized perturbations on the protein free energy surface.
Conclusions:
- Φ(T) is a valuable, experimentally accessible reaction coordinate for protein folding.
- Limitations include its relative nature and interpretation challenges near cold denaturation.
- Careful consideration of heat capacity is needed when interpreting Φ(T) data.
Related Concept Videos
01:22Protein Folding
Overview
01:22Protein Folding
Overview
01:25Protein 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 Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
03:00Molecular 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...
The...
01:19Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
02:39Phase Transitions: Melting and Freezing
Heating a crystalline solid increases the average energy of its atoms, molecules, or ions, and the solid gets hotter. At some point, the added energy becomes large enough to partially overcome the forces holding the molecules or ions of the solid in their fixed positions, and the solid begins the process of transitioning to the liquid state or melting. At this point, the temperature of the solid stops rising, despite the continual input of heat, and it remains constant until all of the solid is...