[en] Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and reaction forces (Gibbs energies of reaction) for the coarse-grained level. It can treat active transporters and molecular machines, and thus extends the applicability of ideas that originated in enzyme kinetics. Our results lay the foundations for systematic studies of the thermodynamics of large-scale biochemical reaction networks. Moreover, we identify the conditions under which a relation between one-way fluxes and forces holds at the coarse-grained level as it holds at the detailed level. In doing so, we clarify the speculations and broad claims made in the literature about such a general flux–force relation. As a further consequence we show that, in contrast to common belief, the second law of thermodynamics does not require the currents and the forces of biochemical reaction networks to be always aligned.
Wachtel, Artur ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
Rao, Riccardo ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
Esposito, Massimiliano ; University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit
External co-authors :
no
Language :
English
Title :
Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten
H2020 - 681456 - NanoThermo - Energy Conversion and Information Processing at Small Scales
FnR Project :
FNR7865466 - Thermodynamics Of Chemical Networks, 2014 (01/07/2014-30/06/2018) - Artur Wachtel
Funders :
FNR - Fonds National de la Recherche [LU] CE - Commission Européenne [BE]
Commentary :
This work is financially supported by the National Research Fund of Luxembourg in the frame of AFR PhD
Grants No. 7865466 and No. 9114110. Furthermore, this research is funded by the European Research Council
project NanoThermo (ERC-2015-CoG Agreement No. 681456).