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Force-induced remodelling of proteins and their complexes.

Chen Y, Radford SE, Brockwell DJ - Curr. Opin. Struct. Biol. (2015)

Bottom Line: The effects of force on the biophysical properties of biological systems can be large and varied.As these effects are only apparent in the presence of force, studies on the same proteins using traditional ensemble biophysical methods can yield apparently conflicting results.Where appropriate, therefore, force measurements should be integrated with other experimental approaches to understand the physiological context of the system under study.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

No MeSH data available.


Related in: MedlinePlus

Models used to interpret DFS data. The assumed energy landscape and the resultant theoretical force versus loading rate relationship (insets) are shown above each model where F(v) is the most probable rupture force at a loading rate v, kB is Boltzmann’s constant, T is temperature, xβ indicates the location of the energy barrier, and koff is the off rate constant at zero force. In Dudko-Hummer-Szabo model (centre), ks is the harmonic force constant scaled by kBT and S(t) is the rupture probability as a function of the time t. In Friddle-De Yoreo model (right), feq indicates the force at which the dissociation and association are in equilibrium, and koff(feq) is the off rate constant at feq.
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Figure 2: Models used to interpret DFS data. The assumed energy landscape and the resultant theoretical force versus loading rate relationship (insets) are shown above each model where F(v) is the most probable rupture force at a loading rate v, kB is Boltzmann’s constant, T is temperature, xβ indicates the location of the energy barrier, and koff is the off rate constant at zero force. In Dudko-Hummer-Szabo model (centre), ks is the harmonic force constant scaled by kBT and S(t) is the rupture probability as a function of the time t. In Friddle-De Yoreo model (right), feq indicates the force at which the dissociation and association are in equilibrium, and koff(feq) is the off rate constant at feq.

Mentions: For most interactions, force acts to decrease the stability of the folded or bound state of a protein or complex relative to the unfolded or dissociated state. The effect of force can be thought of as a mechanical lever that tilts the underlying energy landscape with a magnitude that increases with distance from the native (or bound) state. Thus, in addition to stabilising the unfolded state, force also reduces the free energy barrier to unfolding (or unbinding). As these experiments are usually carried out far-from-equilibrium at a variety of extension rates, it is necessary to calculate the parameters that describe the unperturbed energy landscape (koff and xβ, see Figure 2) so that the results from different experiments can be compared. In order to reveal kinetic parameters for the reactions of interest a dynamic force spectrum is measured by performing single molecule force spectroscopy at different loading rates [3]. A plot of most likely rupture force versus force loading rate can be fitted to different analytical models. In the Bell–Evans model (Figure 2 left), it is assumed that the energy barrier is so deep that its position does not change, but the height of the escape barrier is lowered by the applied force. The most probable rupture force is then proportional to the natural logarithm of the loading rate [17,18]. A modification of the Bell–Evans model by applying Kramer’s diffusion theory was later proposed (Figure 2 middle) to avoid this assumption [19,20]. Both models above ignore the possibility of reversible bond formation during the force spectroscopy, and have been challenged by the Friddle-De Yoreo model (Figure 2 right) [21]. In this recently developed model, it is assumed that at relatively low loading rates, there is another shallow barrier for rebinding; while at higher loading rates, this secondary barrier increases so that the probability of rebinding is reduced.


Force-induced remodelling of proteins and their complexes.

Chen Y, Radford SE, Brockwell DJ - Curr. Opin. Struct. Biol. (2015)

Models used to interpret DFS data. The assumed energy landscape and the resultant theoretical force versus loading rate relationship (insets) are shown above each model where F(v) is the most probable rupture force at a loading rate v, kB is Boltzmann’s constant, T is temperature, xβ indicates the location of the energy barrier, and koff is the off rate constant at zero force. In Dudko-Hummer-Szabo model (centre), ks is the harmonic force constant scaled by kBT and S(t) is the rupture probability as a function of the time t. In Friddle-De Yoreo model (right), feq indicates the force at which the dissociation and association are in equilibrium, and koff(feq) is the off rate constant at feq.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499843&req=5

Figure 2: Models used to interpret DFS data. The assumed energy landscape and the resultant theoretical force versus loading rate relationship (insets) are shown above each model where F(v) is the most probable rupture force at a loading rate v, kB is Boltzmann’s constant, T is temperature, xβ indicates the location of the energy barrier, and koff is the off rate constant at zero force. In Dudko-Hummer-Szabo model (centre), ks is the harmonic force constant scaled by kBT and S(t) is the rupture probability as a function of the time t. In Friddle-De Yoreo model (right), feq indicates the force at which the dissociation and association are in equilibrium, and koff(feq) is the off rate constant at feq.
Mentions: For most interactions, force acts to decrease the stability of the folded or bound state of a protein or complex relative to the unfolded or dissociated state. The effect of force can be thought of as a mechanical lever that tilts the underlying energy landscape with a magnitude that increases with distance from the native (or bound) state. Thus, in addition to stabilising the unfolded state, force also reduces the free energy barrier to unfolding (or unbinding). As these experiments are usually carried out far-from-equilibrium at a variety of extension rates, it is necessary to calculate the parameters that describe the unperturbed energy landscape (koff and xβ, see Figure 2) so that the results from different experiments can be compared. In order to reveal kinetic parameters for the reactions of interest a dynamic force spectrum is measured by performing single molecule force spectroscopy at different loading rates [3]. A plot of most likely rupture force versus force loading rate can be fitted to different analytical models. In the Bell–Evans model (Figure 2 left), it is assumed that the energy barrier is so deep that its position does not change, but the height of the escape barrier is lowered by the applied force. The most probable rupture force is then proportional to the natural logarithm of the loading rate [17,18]. A modification of the Bell–Evans model by applying Kramer’s diffusion theory was later proposed (Figure 2 middle) to avoid this assumption [19,20]. Both models above ignore the possibility of reversible bond formation during the force spectroscopy, and have been challenged by the Friddle-De Yoreo model (Figure 2 right) [21]. In this recently developed model, it is assumed that at relatively low loading rates, there is another shallow barrier for rebinding; while at higher loading rates, this secondary barrier increases so that the probability of rebinding is reduced.

Bottom Line: The effects of force on the biophysical properties of biological systems can be large and varied.As these effects are only apparent in the presence of force, studies on the same proteins using traditional ensemble biophysical methods can yield apparently conflicting results.Where appropriate, therefore, force measurements should be integrated with other experimental approaches to understand the physiological context of the system under study.

View Article: PubMed Central - PubMed

Affiliation: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

No MeSH data available.


Related in: MedlinePlus