BIOPHYSICAL THEORY AND MODELING |
Extending Bell's model: how force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes
Emily B. Walton 1, Sunyoung Lee 1 and Krystyn J. Van Vliet 1*
1 Massachusetts Institute of Technology
* To whom correspondence should be addressed. E-mail: krystyn{at}mit.edu.
Submitted on June 9, 2007
Revised on July 26, 2007
Accepted on 4 December 2007
 |
Abstract |
|---|
Forced unbinding of complementary macromolecules such as ligand-receptor complexes can reveal energetic and kinetic details governing physiological processes ranging from cellular adhesion to drug metabolism. Although molecular-level experiments have enabled sampling of individual ligand-receptor complex dissociation events, disparities in measured unbinding force FR among these methods lead to marked variation in inferred binding energetics and kinetics at equilibrium. These discrepancies are documented for even the ubiquitous ligand-receptor pair, biotin-streptavidin. We investigated these disparities and examined atomic-level unbinding trajectories via steered molecular dynamics simulations as well as via molecular force spectroscopy experiments on biotin-streptavidin. In addition to the well-known loading rate dependence of FR predicted by Bell's model, we find that experimentally accessible parameters such as the effective stiffness of the force transducer k can significantly perturb the energy landscape and the apparent unbinding force of the complex for sufficiently stiff force transducers. Additionally, at least 20% variation in unbinding force can be attributed to minute differences in initial atomic positions among energetically and structurally comparable complexes. For force transducers typical of molecular force spectroscopy experiments and atomistic simulations, this energy barrier perturbation results in extrapolated energetic and kinetic parameters of the complex that depend strongly on k. We present a model that explicitly includes the effect of k on apparent unbinding force of the ligand-receptor complex, and demonstrate that this correction enables prediction of unbinding distances and dissociation rates that are decoupled from the stiffness of actual or simulated molecular linkers.
Key Words:
biotin, energy landscape, force spectroscopy, ligand-receptor, steered molecular dynamics, streptavidin
