A DNA origami rotary ratchet motor

Journal article

Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, the bottom-up design of enzymes presents a daunting task that is far more challenging than making passive molecules with specific binding affinities or building nano-scale mechanically active devices. We present a thermodynamically consistent model for the operation of such a fueled enzyme, which uses the energy from a favorable reaction to undergo non-equilibrium conformational changes that in turn catalyze a chemical reaction on an attached substrate molecule. We show that enzymatic function can emerge through a bifurcation upon appropriate implementation of momentum conservation on the effective reaction coordinates of the low-dimensional description of the enzyme, and thanks to a generically present dissipative coupling. Our results can complement the recently developed strategies for de novo enzyme design based on machine learning approaches

Authors: Pumm, A-K; Engelen, W; Kopperger, E; Isensee, J; Vogt, M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Nature
• Volume: 607
• Issue: 7919
• Pages: 492-498
• Publication date: 2022-07-20
• DOI: 10.1038/s41586-022-04910-y
• EISSN: 1476-4687
• ISSN: 0028-0836
• Language: English
• Keywords: Thermodynamics; Thermal; Classical mechanics; Molecular machine; Materials science; Microscale chemistry; Molecular motor; Work (physics); Ratchet; DNA origami; Nanotechnology; Brownian motion; Physics; Thermal fluctuations; Mechanics