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An Exactly Solvable Stochastic Kinetic Theory of Single-Molecule Force Experiments.
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-08-12 , DOI: 10.1021/acs.jpcb.0c04386 Prasanta Kundu 1 , Soma Saha 2 , Gautam Gangopadhyay 1
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-08-12 , DOI: 10.1021/acs.jpcb.0c04386 Prasanta Kundu 1 , Soma Saha 2 , Gautam Gangopadhyay 1
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The unfolding of a protein in single-molecule pulling experiments subjected to a constant force (force-clamp) and constant velocity (force-ramp) is analyzed by introducing an exactly solvable two-state kinetic model framed based on the general stochastic approach of discrete state and continuous time formulation. The effect of perturbation is interpreted in the presence of dynamic disorder, resulting from intrinsic conformational fluctuations, by deriving an exact analytical expression for the unfolding time distribution, which in turn allowed us to calculate the expressions for the quantities of experimental interest explicitly. In particular, the novelty of our method lies in the fact that it reduced the need for a lengthy calculation, contrary to the previous dynamic disorder studies, and provides a fairly concise but sufficient mathematical analysis, which becomes much easier to implement quantitatively. We tested our results against the measured data from a number of force unfolding experiments on various proteins, ubiquitin, titin, and filamin, and the force unzipping of DNA and observed excellent agreement in each case. This asserts the reliability of the present technique, which suggests a plausible extension of the stochastic kinetic theory in single-molecule force experiments beyond its present-day widespread implications.
中文翻译：
单分子力实验的精确可解随机动力学理论。
通过引入基于离散离散的一般随机方法构建的可精确求解的二态动力学模型，分析了单分子拉伸实验中蛋白质在恒定力（力钳）和恒定速度（力斜坡）下的解折叠状态和连续时间公式。通过推导展开时间分布的精确解析表达式，可以解释由内在构象波动引起的动态紊乱引起的摄动效应，这反过来又使我们能够明确地计算出实验兴趣量的表达式。特别是，与以前的动态障碍研究相反，我们方法的新颖之处在于它减少了冗长计算的需要，并提供了一个相当简洁但足够的数学分析，这使得定量实施变得更加容易。我们针对来自各种蛋白质，泛素，肌动蛋白和丝蛋白的力解开实验的测量数据以及DNA的力解开，测试了我们的结果，并观察到了极好的一致性。这证明了本技术的可靠性，这暗示了随机动力学理论在单分子力实验中的合理扩展，超出了其当前广泛的含义。
更新日期：2020-09-10
中文翻译：
单分子力实验的精确可解随机动力学理论。
通过引入基于离散离散的一般随机方法构建的可精确求解的二态动力学模型，分析了单分子拉伸实验中蛋白质在恒定力（力钳）和恒定速度（力斜坡）下的解折叠状态和连续时间公式。通过推导展开时间分布的精确解析表达式，可以解释由内在构象波动引起的动态紊乱引起的摄动效应，这反过来又使我们能够明确地计算出实验兴趣量的表达式。特别是，与以前的动态障碍研究相反，我们方法的新颖之处在于它减少了冗长计算的需要，并提供了一个相当简洁但足够的数学分析，这使得定量实施变得更加容易。我们针对来自各种蛋白质，泛素，肌动蛋白和丝蛋白的力解开实验的测量数据以及DNA的力解开，测试了我们的结果，并观察到了极好的一致性。这证明了本技术的可靠性，这暗示了随机动力学理论在单分子力实验中的合理扩展，超出了其当前广泛的含义。
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