Laboratory of Biophotonics and Quantum Biology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, USA.
Laboratory of Chemical Physics, National Institute for Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
J Chem Phys. 2021 Mar 21;154(11):115101. doi: 10.1063/5.0040949.
In a two-state molecular system, transition paths comprise the portions of trajectories during which the system transits from one stable state to the other. Because of their low population, it is essentially impossible to obtain information on transition paths from experiments on a large sample of molecules. However, single-molecule experiments such as laser optical tweezers or Förster resonance energy transfer (FRET) spectroscopy have allowed transition-path durations to be estimated. Here, we use molecular simulations to test the methodology for obtaining information on transition paths in single-molecule FRET by generating photon trajectories from the distance trajectories obtained in the simulation. Encouragingly, we find that this maximum likelihood analysis yields transition-path times within a factor of 2-4 of the values estimated using a good coordinate for folding, but tends to systematically underestimate them. The underestimation can be attributed partly to the fact that the large changes in the end-end distance occur mostly early in a folding trajectory. However, even if the transfer efficiency is a good reaction coordinate for folding, the assumption that the transition-path shape is a step function still leads to an underestimation of the transition-path time as defined here. We find that allowing more flexibility in the form of the transition path model allows more accurate transition-path times to be extracted and points the way toward further improvements in methods for estimating transition-path time and transition-path shape.
在二态分子体系中，跃迁路径包含体系从一个稳定状态过渡到另一个稳定状态的轨迹部分。由于其低人口密度，从大量分子的实验中获得跃迁路径的信息基本上是不可能的。然而，激光光学镊子或Förster 共振能量转移（FRET）光谱等单分子实验已经允许估计跃迁路径持续时间。在这里，我们使用分子模拟来测试通过从模拟中获得的距离轨迹生成光子轨迹来获取单分子 FRET 中跃迁路径信息的方法。令人鼓舞的是，我们发现这种最大似然分析得出的跃迁路径时间与使用良好的折叠坐标估计的值相差 2-4 倍，但往往会系统地低估它们。这种低估部分归因于这样一个事实，即末端距离的大变化主要发生在折叠轨迹的早期。然而，即使转移效率是折叠的良好反应坐标，假设跃迁路径形状是阶跃函数仍然会导致如这里定义的跃迁路径时间的低估。我们发现，允许跃迁路径模型的形式更加灵活，可以提取更准确的跃迁路径时间，并为估计跃迁路径时间和跃迁路径形状的方法的进一步改进指明了方向。
