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

University Of California-Santa Cruz, Santa Cruz CA

Investigators

Abstract

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.