Group seminar, 20.01.15

Orville Damaschke


Thermodynamically Consistent Coarse Graining of Biocatalysts beyond Michaelis--Menten

Virtually all processes in living cells involve catalytic molecules to enhance chemical reactions: various enzymes process metabolites and signalling molecules, catalytically active membrane proteins serve as transporters or receptors for chemical signals. While the thermodynamics of elementary mass--action reactions is quite well understood, there is some confusion in the literature about the proper thermodynamic treatment of enzymatic reactions.

In this talk we start from the detailed catalytic mechanism of a single biocatalyst and we provide a coarse-graining procedure which, by construction, is thermodynamically consistent even out of equilibrium:

This procedure provides stoichiometries, reaction fluxes (kinetic 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.

As a consequence, 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 elementary 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.

Our results lay the foundations for systematic studies of the energetics and information processing in large-scale biochemical reaction networks.

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