Fold catastrophes and the dependence of free-energy barriers to conformational transitions on applied force
| Autor: | Daniel J. Lacks, Michael-Paul Robinson, Joshua J. Willis |
|---|---|
| Rok vydání: | 2010 |
| Předmět: |
Conformational change
Protein Folding Chemistry Fold (geology) Molecular Dynamics Simulation Mechanical force Molecular physics Surfaces Coatings and Films Biomechanical Phenomena Protein Structure Tertiary Maxima and minima Molecular dynamics Crystallography Materials Chemistry Molecule Thermodynamics Physical and Theoretical Chemistry Umbrella sampling Scaling Mechanical Phenomena |
| Zdroj: | The journal of physical chemistry. B. 114(33) |
| ISSN: | 1520-5207 |
| Popis: | Applied mechanical force (f) can activate conformational change in molecules by reducing the height of a free-energy barrier (DeltaG(b)). In this paper, molecular dynamics simulations are carried out with umbrella sampling and self-consistent histogram methods to determine free-energy profiles for a coarse-grained model of a protein under an applied force. Applied force is shown to cause fold catastrophes, where free-energy minima are destabilized until they disappear. It is well-known that a fold catastrophe at force f = B implies the scaling DeltaG(b) approximately |B - f|(3/2) in the limit of DeltaG(b) --0, but it is not clear whether this scaling is accurate for physically relevant barrier heights. The simulation results show that the fold catastrophe scaling is in fact accurate in the physically relevant regime and that the two-parameter function DeltaG(b) = A(B - f)(3/2) is superior to the two-parameter linear function for parametrizing changes in free-energy barriers with applied force. |
| Databáze: | OpenAIRE |
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