Abstract
Abstract
Interpreting single-molecule force spectroscopy (SMFS) data from optical tweezers with steered molecular dynamics (SMD) is hindered by a severe timescale mismatch: SMD trajectories span nanoseconds to microseconds, while SMFS experiments unfold over milliseconds to seconds, forcing SMD to pull six to nine orders of magnitude faster than experiment and systematically distorting rupture forces, molecular pathways, and kinetic intermediates. We introduce force-probe coupled steered molecular dynamics (fp-SMD), which explicitly propagates the force probe (the optically trapped bead) alongside the biomolecule within a single classical Hamiltonian description of the coupled molecule– linker–bead system. A Predict–Correct Trajectory Propagation (PCTP) scheme resolves the resulting computational bottleneck by decoupling the fast molecular relaxation from the slow, macroscopic bead motion, using metadynamics and transition-state theory to identify the kinetically resolved molecular intermediate reached at each macroscopic time step. On the cholesterol–β-cyclodextrin (β-CD) host–guest complex, fp-SMD reproduces the experimental rupture-force histogram directly at matched conditions, without extrapolation from standard SMD. fp-SMD further resolves how applied force reshapes the molecular escape pathway itself — cholesterol dissociates via a high-angle route at low force and a direct, small-angle route at high force — providing, to our knowledge, the first direct structural evidence for force-induced pathway switching within small host-guest systems believed to underlie catch-slip bond behavior. fp-SMD/PCTP thus offers a general route to simulating force-probe-coupled biomolecular mechanics at experimentally relevant timescales.
Significance Statement
Single-molecule experiments using optical tweezers reveal how mechanical forces unfold proteins, rupture bonds, and drive cell adhesion. Simulations that could explain these experiments at atomic resolution have been hindered by a basic mismatch: they must pull the molecule millions of times faster than a real experiment to be computationally tractable, distorting the forces and pathways they aim to explain. This work introduces a simulation method that explicitly includes the physical probe used in the experiment, not just the molecule, letting simulations match experimental timescales without sacrificing atomic detail. Applied to a cholesterol–cyclodextrin complex relevant to atherosclerosis and drug delivery, the method shows how force redirects a molecule’s escape pathway — a mechanism believed to underlie many force-sensitive switches.