Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds

Abstract

Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via ''slip bonds,'' so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo ''facilitated dissociation,'' in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a ''catch bond,'' for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip-and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.

Force-dependent interactions between talin and full-length vinculin

“…In contrast to an isolated VBS helix, which exists in a force-free environment, the mechanically exposed VBS in talin are under forces of several pN 12,13,16 , which may alter the conformation of the VBS helix significantly impacting on the binding affinity 29 and kinetics 30 . Hence, further studies on the force-dependent conformations of VBSs under a few pN forces and the resulting effects on the vinculin-talin VBS interaction may provide insight into this important linkage.…”

Calculating the force-dependent unbinding rate of biological macromolecular bonds from force-ramp optical trapping assays

“…Of the 50 simulations, we found that only 24 of the 𝑓 = 0.3 pN/s, 33 of the 𝑓 = 10 pN/s, and 5 of the 𝑓 = 30 pN/s simulated data sets were well-fit by equation (18b) (Table 4). * 𝑘 off,c-s (𝐹 = 0) = 𝑘 0,c + 𝑘 0,s = 1.05 per equation (17) for the parameters used in the simulation As we observed for the simulated data without accounting for the effect of experimental noise (Table 3), the cumulative distribution function-like analysis technique was able to resolve the catch-bond fitting parameters reasonably well (despite a 17%, P value = 0.02 two-tailed ttest, error in resolving the force sensitivity of the catch bond) with low s.e.m. of the fits in low loading rate simulations, and the slip-bond fitting parameters (despite a low number of well-fit data sets) in the high loading rate simulation (Table 4).…”

“…We also discuss the implications of our results on using optical tweezers to collect force-dependent dissociation data.force 16 . Catch bonds have a lifetime that increases with applied force 10,17 . Ideal bonds have a 42 lifetime that is independent of applied force 10 .…”

“…force 16 . Catch bonds have a lifetime that increases with applied force 10,17 . Ideal bonds have a 42 lifetime that is independent of applied force 10 .…”

Calculating the force-dependent unbinding rate of biological macromolecular bonds from the force-ramp optical trapping assays

“…Slip bonds have a lifetime that decreases with the increasing applied force 16 . Catch bonds have a lifetime that increases with applied force 10,17 . Ideal bonds have a lifetime that is independent of applied force 10 .…”