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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...

Third Law of Thermodynamics

Third Law of Thermodynamics

A pure, perfectly crystalline solid possessing no kinetic energy (that is, at a temperature of absolute zero, 0 K) may be described by a single microstate, as its purity, perfect crystallinity,and complete lack of motion means there is but one possible location for each identical atom or molecule comprising the crystal (W = 1). According to the Boltzmann equation, the entropy of this system is zero.

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

No description available

Second Law of Thermodynamics

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In the quest to identify a property that may reliably predict the spontaneity of a process, a promising candidate has been identified: entropy. Processes that involve an increase in entropy of the system (ΔS > 0) are very often spontaneous; however, examples to the contrary are plentiful. By expanding consideration of entropy changes to include the surroundings, a significant conclusion regarding the relation between this property and spontaneity may be reached. In thermodynamic models, the...

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Determining the Thermodynamic and Kinetic Association of a DNA Aptamer and Tetracycline Using Isothermal Titration Calorimetry

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Protein folding kinetics and thermodynamics from atomistic simulation.

Stefano Piana¹, Kresten Lindorff-Larsen, David E Shaw

¹DE Shaw Research, New York, NY 10036, USA. Stefano.Piana-Agostinetti@DEShawResearch.com

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

|July 24, 2012

Summary

Advanced simulations now accurately predict protein folding dynamics and thermodynamics. This study shows computational methods can quantitatively complement experimental data for protein folding research.

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Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

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Published on: April 28, 2011

Area of Science:

Biophysics
Computational Biology
Biochemistry

Background:

Protein folding is crucial for biological function.
Advances in computing enable simulations at biologically relevant timescales.
Atomic-level simulations can now access protein folding events.

Purpose of the Study:

To demonstrate the utility of molecular dynamics simulations for studying protein folding.
To quantitatively compare simulation data with experimental results.
To investigate the folding pathways and kinetics of villin headpiece variants.

Main Methods:

Utilized atomic-level simulations for spontaneous folding and unfolding.
Calculated thermodynamic and kinetic quantities (folding rates, free energies, Φ-values).
Performed quantitative comparisons between simulation outputs and experimental data.

Main Results:

Simulations provided direct access to key folding parameters.
Accurate prediction of folding rates, free energies, and Φ-values was achieved.
A norleucine double mutant of villin was found to fold five times faster than wild-type, with a distinct pathway.

Conclusions:

Computer simulations are a mature tool for quantitative protein folding studies.
Simulation results provide structural interpretation for experimental observations.
Computational methods offer a valuable complement to experimental techniques in protein dynamics research.