A solution to the subdiffusion-efficiency paradox: Inactive states enhance reaction efficiency at subdiffusion conditions in living cells

¹ Department of Physics, Technical University of Munich - James-Franck Straße, D-85747 Garching, Germany, EU
² MEMPHYS - Center for Biomembrane Physics, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark - Campusvej 55, DK-5230 Odense M, Denmark, EU
³ Institute for Physics and Astronomy, University of Potsdam - D-14476 Potsdam-Golm, Germany, EU
⁴ Department of Physics, Tampere University of Technology - FI-33101 Tampere, Finland, EU

^a rmetzler@uni-potsdam.de

Received: 19 October 2011
Accepted: 12 December 2011

Abstract

Macromolecular crowding in living biological cells effects subdiffusion of larger biomolecules such as proteins and enzymes. Mimicking this subdiffusion in terms of random walks on a critical percolation cluster, we here present a case study of EcoRV restriction enzymes involved in vital cellular defence. We show that due to its so far elusive propensity to an inactive state the enzyme avoids non-specific binding and remains well-distributed in the bulk cytoplasm of the cell. Despite the reduced volume exploration capability of subdiffusion processes, this mechanism guarantees a high efficiency of the enzyme. By variation of the non-specific binding constant and the bond occupation probability on the percolation network, we demonstrate that reduced non-specific binding are beneficial for efficient subdiffusive enzyme activity even in relatively small bacteria cells. Our results corroborate a more local picture of cellular regulation.