TY - JOUR
T1 - Extending Bell's model
T2 - How force transducer stiffness alters measured unbinding forces and kinetics of molecular complexes
AU - Walton, Emily B.
AU - Lee, Sunyoung
AU - Van Vliet, Krystyn J.
N1 - Funding Information:
The authors thank the National Defense Science and Engineering Graduate Fellowship program (to E.B.W.), as well as the National Science Foundation Nanoscale Exploratory Research program and National Science Foundation CAREER Award, and the Arnold and Mabel Beckman Foundation Young Investigator Program (to K.J.V.V.). Computational support for this project was provided by the National Science Foundation though grant No. IMR-0414849.
PY - 2008/4
Y1 - 2008/4
N2 - 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 F R 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.
AB - 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 F R 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.
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U2 - 10.1529/biophysj.107.114454
DO - 10.1529/biophysj.107.114454
M3 - Article
C2 - 18178658
AN - SCOPUS:41649121704
SN - 0006-3495
VL - 94
SP - 2621
EP - 2630
JO - Biophysical journal
JF - Biophysical journal
IS - 7
ER -