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

Single-molecule force spectroscopy (SMFS) in optical tweezers is hard to interpret with standard steered molecular dynamics (SMD) because of a severe timescale mismatch: SMD trajectories span nanoseconds to microseconds while experiments unfold over milliseconds to seconds, forcing SMD to pull six to nine orders of magnitude faster than experiment. This systematically distorts rupture forces, molecular pathways, and kinetic intermediates.

The authors 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. To handle the resulting computational bottleneck, they develop a Predict-Correct Trajectory Propagation (PCTP) scheme that decouples fast molecular relaxation from 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. It further resolves how applied force reshapes the molecular escape pathway: cholesterol dissociates via a high-angle route at low force and a direct, small-angle route at high force. The authors describe this as 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 thereby offers a general route to simulating force-probe-coupled biomolecular mechanics at experimentally relevant timescales.