Reference : Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
Physical, chemical, mathematical & earth Sciences : Physics
Physics and Materials Science; Systems Biomedicine
http://hdl.handle.net/10993/35460
Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis–Menten
English
Wachtel, Artur mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
Rao, Riccardo mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
Esposito, Massimiliano mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Physics and Materials Science Research Unit >]
12-Apr-2018
New Journal of Physics
Institute of Physics
20
4
042002
Yes (verified by ORBilu)
International
1367-2630
Bristol
United Kingdom
[en] coarse graining ; biochemical reaction networks ; thermodynamics ; enzyme kinetics
[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.
Fonds National de la Recherche - FnR
Researchers
http://hdl.handle.net/10993/35460
10.1088/1367-2630/aab5c9
http://iopscience.iop.org/article/10.1088/1367-2630/aab5c9
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).
H2020 ; 681456 - NanoThermo - Energy Conversion and Information Processing at Small Scales
FnR ; FNR7865466 > Artur Wachtel > CNThermo > Thermodynamics of Chemical Networks > 01/07/2014 > 30/06/2018 > 2014; FNR9114110 > Riccardo Rao > ThermoAccu > Thermodynamic cost of Accuracy in Biological Processes > 01/11/2014 > 31/10/2018 > 2014

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