Simulating Bead-Tethered Biomolecules: Force-Probe Coupled Steered Molecular Dynamics (fp-SMD) in Optical Tweezers Force Spectroscopy

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 alternating a bead-propagation step, with the molecular center of mass (COM) held fixed, and a molecular step in which metadynamics and transition-state theory identify the kinetically resolved intermediate reached at each macroscopic time step. On the cholesterol--{beta}-cyclodextrin ({beta}-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: we find that 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 in a small host-guest system, a mechanism believed to underlie catch-slip bond behavior.