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arXiv · 2501.01662

Acceleration of enzymatic reactions due to nearby inactive binding sites

Hila Katznelson·Saar Rahav
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Abstract

Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. We study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive site. Our approach is based on comparing the steady-state current in simple models to reference models without an inactive site. We identify two parameter regimes in which the reaction is accelerated. We then find the transition rates that maximize this acceleration, and use them to determine the underlying mechanisms in each region. In the first regime, the inactive site stores a molecule in order to release it following a reaction, when the neighboring catalytic site is empty. In the second regime, the inactive site releases a molecule when the catalytic site is full, in order to impede the molecules from leaving the active site before they react. For the storage mechanism, which is more likely to be biologically relevant, the acceleration can reach up to 15%, depending on parameters.

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Hila Katznelson, Saar Rahav. 2025-01-03. Acceleration of enzymatic reactions due to nearby inactive binding sites. https://doi.org/10.1103/physrevresearch.6.043330

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