Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

Non-Markov bond model for dynamic force spectroscopy

Single-molecule force spectroscopy data are conventionally analyzed using a schematic model, wherein a molecular bond is represented as a virtual particle diffusing in a one-dimensional free-energy landscape. However, this simple and efficient approach is unable to account for the "anomalous" bond-breaking kinetics increasingly observed in force spectroscopy experiments and simulations, e.g., in the form of non-exponential distributions of bond lifetimes under constant load. Here, we show that such characteristic traits arise naturally in a rigorous extension of the one-dimensional theory that accounts for the transient dynamics of a generic set of coupled degrees of freedom. These "hidden modes" affect the reaction dynamics in various ways, depending on their relaxation spectrum and the loading protocol, giving rise, in particular, to apparent static and dynamic disorder. In two complementary asymptotic limits, we are able to find exact analytical expressions for pertinent experimental observables, such as the mean rupture force and the rupture-force distribution. Intriguingly, our asymptotic results become unconditionally exact at high loading rates, thus providing us with a microscopically consistent theory of rapid force spectroscopy that avoids the usual Markov assumption.

Stretching of single poly-ubiquitin molecules revisited: dynamic disorder in the non-exponential unfolding kinetics

A theoretical framework based on a generalized Langevin equation (GLE) with fractional Gaussian noise (fGn) and a power-law memory kernel is presented to describe the non-exponential kinetics of the unfolding of a single poly-ubiquitin molecule under a constant force [T.-L. Kuo, S. Garcia-Manyes, J. Li, I. Barel, H. Lu, B. J. Berne, M. Urbakh, J. Klafter, and J. M. Fernández, Proc. Natl. Acad. Sci. U.S.A. 107, 11336 (2010)]. Such a GLE-fGn strategy is made on the basis that the pulling coordinate variable x undergoes subdiffusion, usually resulting from conformational fluctuations, over a one-dimensional force-modified free-energy surface U(x, F). By using the Kramers' rate theory, we have obtained analytical formulae for the time-dependent rate coefficient k(t, F), the survival probability S(t, F) as well as the waiting time distribution function f(t, F) as functions of time t and force F. We find that our results can fit the experimental data of f(t, F) perfectly in the whole time range with a power-law exponent γ = 1/2, the characteristic of typical anomalous subdiffusion. In addition, the fitting of the survival probabilities for different forces facilitates us to reach rather reasonable estimations for intrinsic properties of the system, such as the free-energy barrier and the distance between the native conformation and the transition state conformation along the reaction coordinate, which are in good agreements with molecular dynamics simulations in the literatures. Although static disorder has been implicated in the original work of Kuo et al., our work suggests a sound and plausible alternative interpretation for the non-exponential kinetics in the stretching of poly-ubiquitin molecules, associated with dynamic disorder.