Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis-Menten
Thermodynamically consistent coarse graining of biocatalysts beyond Michaelis-Menten
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DOI：
10.1088/1367-2630/aab5c9
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发表时间：
2018-04-12
影响因子：
3.3
通讯作者：
Esposito, Massimiliano
中科院分区：
文献类型：
--
作者：
Wachtel, Artur;Rao, Riccardo;Esposito, Massimiliano
从生物催化剂的详细催化机理出发，我们提供了一个粗粒化的过程，通过构建，是化学上一致的。这个过程提供了化学计量，反应通量（速率定律），和反应力（吉布斯反应能）的粗粒度的水平。它可以治疗主动转运蛋白和分子机器，从而扩展了起源于酶动力学的思想的适用性。我们的结果为系统研究大规模生化反应网络的热力学奠定了基础。此外，我们确定的条件下，单向通量和力之间的关系，持有在粗粒度的水平，因为它持有在详细的水平。在这样做的时候，我们澄清了在文献中关于这样一个一般的通量-力关系的推测和广泛的主张。作为进一步的结果，我们表明，在一般的信念相反，热力学第二定律并不要求电流和生化反应网络的力量总是对齐。
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.