F. Benedetti, C. Micheletti, G. Bussi, S. K. Sekatskii and G. Dietler
Non-kinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments
Biophys. J., 2011 101 p. 1504-1512

Abstract We introduce and discuss a novel approach, named back-calculation, for analyzing force spectroscopy experiments on multimodular proteins. The relationship between the histograms of the unfolding forces for different peaks, corresponding to a different number of not-yet-unfolded protein modules, is exploited in such a manner that the sole distribution of the forces for one unfolding peak can be used to predict the unfolding forces for other peaks. The scheme is based on a bootstrap prediction method and does not rely on any specific kinetic model for multimodular unfolding. It is tested and validated both in theoretical/computational contexts (based on stochastic simulations) and in atomic force microscope experiments on (GB1)_8 multimodular protein constructs. The prediction accuracy is so high that the predicted average unfolding forces corresponding to each peak for the GB1 construct are within only 5 pN of the averaged directly-measured values. Experimental data are also used to illustrate how the limitations of standard kinetic models can be aptly circumvented by the proposed approach.