Bayesian field theoretic reconstruction of bond potential and bond mobility in single molecule force spectroscopy

Abstract

Quantifying the forces between and within macromolecules is a necessary first step in understanding the mechanics of molecular structure, protein folding, and enzyme function and performance. In such macromolecular settings, dynamic single-molecule force spectroscopy (DFS) has been used to distort bonds. The resulting responses, in the form of rupture forces, work applied, and trajectories of displacements, have been used to reconstruct bond potentials. Such approaches often rely on simple parameterizations of one-dimensional bond potentials, assumptions on equilibrium starting states, and/or large amounts of trajectory data. Parametric approaches typically fail at inferring complex-shaped bond potentials with multiple minima, while piecewise estimation may not guarantee smooth results with the appropriate behavior at large distances. Existing techniques, particularly those based on work theorems, also do not address spatial variations in the diffusivity that may arise from spatially inhomogeneous coupling to other degrees of freedom in the macromolecule, thereby presenting an incomplete picture of the overall bond dynamics. To solve these challenges, we have developed a comprehensive empirical Bayesian approach that incorporates data and regularization terms directly into a path integral. All experiemental and statistical parameters in our method are estimated empirically directly from the data. Upon testing our method on simulated data, our regularized approach requires fewer data and allows simultaneous inference of both complex bond potentials and diffusivity profiles.