Recovering bond potentials and motor potentials, from what we can measure to what we like to know

本项目集中在两个密切相关的领域：1)从单分子实验数据中恢复蛋白质马达的运动电位；2)从原子力显微镜（AFM）拉伸实验中测量的断裂力中恢复键电位。在过去，单分子实验中测量到的马达位置的时间序列仅用于计算平均速度。这个项目旨在提取运动电位，充分利用运动位置的时间序列。一旦成功，通过检查运动电位的空间结构以及检查运动电位对各种环境参数（如对运动的负载力和化学浓度）的依赖性，将揭示有关运动机制的新信息。该项目还试图从AFM实验数据中提取键电位，利用在AFM实验中可以控制键上拉力的大小和时间模式的优势。恢复键电位将扩展AFM技术的能力，并提供一种探测亚纳米尺度构象变化的新方法。蛋白质马达在许多细胞功能中起着核心作用。了解蛋白质马达的工作原理是理解细胞内蛋白质运输和细胞运动的关键。蛋白质马达的电位分布描述了马达力的空间模式。例如，对于四冲程单缸摩托车，发动机仅在膨胀冲程期间提供正驱动力。虽然人们可以直接观察摩托车发动机的运行，但对于纳米级蛋白质马达来说，人们没有这样的奢侈。幸运的是，由于可以忽略的惯性，蛋白质马达的电位分布包含（隐藏）在马达的时间路径中。该项目旨在通过单分子实验中测量的时间路径来揭示运动电位。一旦成功，它将提供一种窥探纳米级蛋白质马达的新方法。该项目还试图通过间接和低分辨率AFM（原子力显微镜）实验数据的建模和推断，揭示分子键的潜在特征。这种间接探测分子键的新方法对于研究分子键非常重要，因为键断裂只涉及亚纳米尺度的构象变化。直接测量的分辨率不太可能远低于亚纳米尺度，从而直接解决键断裂问题。该项目还促进了代表性不足的群体参与科学，因为与首席研究员一起工作的两名研究生都来自代表性不足的群体。

This project is focused on two closely related areas: i) recovering motor potentials of protein motors from single molecule experimental data, and ii) recovering bond potentials from measured breaking forces in atomic force microscope (AFM) pulling experiments. In the past, the time series of motor positions measured in single molecule experiments were used only to calculate the average velocity. This project seeks to extract motor potentials, making full use of the time series of motor positions. Once successful, new information about motor mechanism will be revealed by examining the spatial structure of motor potential and by examining the dependence of motor potential on various environmental parameters, such as, the loading force on the motor and chemical concentrations. This project also seeks to extract bond potentials from AFM experimental data, utilizing the advantage that both the magnitude and the time pattern of pulling force on the bond can be controlled in AFM experiments. Recovering bond potentials will extend the capability of the AFM technologies and provide a novel way of probing sub-nanometer scale conformational changes.Protein motors play a central role in many cell functions. Understanding the operating principles of protein motors is crucial to comprehending intracellular protein transport and cell motility. The potential profile of a protein motor describes the spatial pattern of motor force. For example, for a four-stroke single cylinder motorcycle, the engine provides a positive driving force only during the expansion stroke. While one can observe directly the operation of a motorcycle engine, one does not have such a luxury for a nanometer scale protein motor. Fortunately, because of the negligible inertia, the potential profile of a protein motor is contained (hidden) in the time path of the motor. This project seeks to uncover motor potentials from measured time paths in single molecule experiments. Once successful, it will provide a new way of peeking into nanometer scale protein motors. This project also seeks to uncover potential profiles of molecular bonds, through modeling and inference, from indirect and low-resolution AFM (Atomic Force Microscopy) experimental data. This new way of indirectly probing is extremely important for studying molecular bonds since bond breaking involves only sub-nanometer scale conformational changes. The resolution of direct measurements is unlikely to go far below the sub-nanometer scale to resolve bond breaking directly. This project also promotes the participation of underrepresented groups in science as the two graduate students working with the principal investigator are both from underrepresented groups.