A quantitative analysis of single protein-ligand complex separation with the atomic force microscope

Force measurements on and within single macromolecular complexes utilizing techniques such as atomic force microscopy, optical trapping, flexible glass fibers, and magnetic beads provide a rich source of quantitative data on biomolecular processes. Stochastic thermal fluctuations, an undesirable source of noise in macroscopic biochemical experiments, are an essential element of these sensitive and novel experiments. With the proper analysis, a great deal of information can be gleaned from measurements of these fluctuations. A quantitative framework for analyzing such measurements, based on Kramers' theory of molecular dissociation, is developed. The analysis reveals the kinetic origin and stochastic nature of the measurements. This framework is presented in the context of protein-ligand separation with the atomic force microscope.