Biological molecular motors carry out mechanical functions by coupling conformational changes to substeps in chemical fuel consumption. Gyrase is an essential motor that harnesses the free energy of ATP hydrolysis to introduce negative supercoils into DNA. Here we propose a comprehensive biophysical approach for studying gyrase dynamics and mechanochemical coupling. Our goal is to define a set of functionally relevant structural intermediates of the gyrase nucleoprotein complex, and characterize the mechanics and chemistry of transitions between these intermediates. In recent work, we have measured structural dynamics using a single molecule assay in which gyrase drives the processive, stepwise rotation of a submicron fluorescent sphere attached to the side of a stretched DNA molecule. Analysis of rotational pauses and simultaneous measurements of DNA contraction revealed multiple ATP-modulated structural transitions. We showed that a critical DNA wrapping step is coordinated with the ATPase cycle and proceeds via an unanticipated structural intermediate that dominates the kinetics of supercoiling. We proposed a mechanochemical model that quantitatively explained our findings, featuring a conformational landscape of loosely coupled transitions funneling the motor toward productive energy transduction. Our model provides a new framework that guides the investigations in this proposal. In the proposed work, we will exploit new instrumentation and methods that we have recently developed. We can now measure twist and torque in individual stretched DNA molecules with spatiotemporal resolutions that far exceed any previously reported methods, using gold nanospheres as low-drag rotational probes. This technology provides access to millisecond-resolution dynamics of DNA gyrase. We further propose to complement our DNA-centric measurements of nucleoprotein dynamics (relying on observations of changes in twist and extension) with simultaneous measurements of protein domain movements using single molecule fluorescence. Finally, we will use complementary structural approaches to characterize the architectures of substates identified in our single molecule studies. The methods established in this proposal are expected to be an important contribution in themselves, and should be directly applicable to observing the structural dynamics of diverse nucleoprotein complexes ranging from nucleosomes to preinitation complexes.

Public Health Relevance

This project addresses the detailed mechanism of a molecular machine that is essential for bacterial life and a validated target for antibiotic drugs. The work will provide insights into steps in the gyrase mechanism that may be inhibited by small molecules, and the single-molecule methods we propose are directly applicable to characterizing the mode of action of compounds that inhibit the enzyme. The methods we are developing may be used to dissect the structural dynamics of a wide range of DNA-associated macromolecular machines, and this work investigates fundamental mechanisms for coupling conformational changes to energy consumption, a function that is central to many biological processes.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function C Study Section (MSFC)
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Preusch, Peter
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Stanford University
Biomedical Engineering
Schools of Medicine
United States
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Ivanov, Ivan E; Lebel, Paul; Oberstrass, Florian C et al. (2018) Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT. Biophys J 114:278-282
Basu, Aakash; Hobson, Matthew; Lebel, Paul et al. (2018) Dynamic coupling between conformations and nucleotide states in DNA gyrase. Nat Chem Biol 14:565-574
Basu, Aakash; Parente, Angelica C; Bryant, Zev (2016) Structural Dynamics and Mechanochemical Coupling in DNA Gyrase. J Mol Biol 428:1833-45
Lebel, Paul; Basu, Aakash; Oberstrass, Florian C et al. (2014) Gold rotor bead tracking for high-speed measurements of DNA twist, torque and extension. Nat Methods 11:456-62