Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis

Area of Science:

• Computational Biophysics
• Single-Molecule Biophysics
• Chemical Physics

Background:

• Transition paths in molecular systems are crucial for understanding dynamics between stable states.
• Direct experimental observation of transition paths is challenging due to their transient nature and low population.
• Single-molecule techniques like Förster resonance energy transfer (FRET) offer insights into transition path durations.

Purpose of the Study:

• To evaluate the accuracy of single-molecule FRET methodology for determining transition path information.
• To assess the impact of model assumptions on transition path time estimations.
• To identify strategies for improving the accuracy of transition path time and shape analysis.

Main Methods:

• Molecular simulations were employed to generate distance trajectories.
• Photon trajectories were simulated from distance trajectories to mimic single-molecule FRET experiments.
• Maximum likelihood analysis was used to estimate transition path times from simulated photon trajectories.

Main Results:

• Maximum likelihood analysis provided transition path times within a factor of 2-4 of simulation estimates using a good folding coordinate.
• A systematic underestimation of transition path times was observed, partly due to early large changes in end-end distance.
• Assuming a step-function shape for the transition path led to underestimation, even with an optimal reaction coordinate.

Conclusions:

• Flexible transition path models significantly improve the accuracy of extracted transition path times.
• The study highlights limitations of current FRET analysis methods and suggests avenues for refinement.
• Improved methods are needed for accurate estimation of transition path time and shape in molecular systems.