University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 8, 2000, Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška Cesta 160, 2000, Maribor, Slovenia.
University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Energy Technology, Hočevarjev Trg 1, 8270, Krško, Slovenia.
Comput Biol Chem. 2021 Apr;91:107449. doi: 10.1016/j.compbiolchem.2021.107449. Epub 2021 Feb 5.
We investigate the relations between the enzyme kinetic flexibility, the rate of entropy production, and the Shannon information entropy in a steady-state enzyme reaction. All these quantities are maximized with respect to enzyme rate constants. We show that the steady-state, which is characterized by the most flexible enzymatic transitions between the enzyme conformational states, coincides with the global maxima of the Shannon information entropy and the rate of entropy production. This steady-state of an enzyme is referred to as globally optimal. This theoretical approach is then used for the analysis of the kinetic and the thermodynamic performance of the enzyme triose-phosphate isomerase. The analysis reveals that there exist well-defined maxima of the kinetic flexibility, the rate of entropy production, and the Shannon information entropy with respect to any arbitrarily chosen rate constant of the enzyme and that these maxima, calculated from the measured kinetic rate constants for the triose-phosphate isomerase are lower, however of the same order of magnitude, as the maxima of the globally optimal state of the enzyme. This suggests that the triose-phosphate isomerase could be a well, but not fully evolved enzyme, as it was previously claimed. Herein presented theoretical investigations also provide clear evidence that the flexibility of enzymatic transitions between the enzyme conformational states is a requirement for the maximal Shannon information entropy and the maximal rate of entropy production.
我们研究了在稳态酶反应中酶动力学灵活性、熵产生率和香农信息熵之间的关系。所有这些量都针对酶速率常数进行了最大化。我们表明，以酶构象状态之间最灵活的酶转变为特征的稳态与香农信息熵和熵产生率的全局最大值重合。这种酶的稳态被称为全局最优。然后，我们使用这种理论方法来分析磷酸丙糖异构酶的动力学和热力学性能。分析表明，对于酶的任何任意选择的速率常数，存在明确的动力学灵活性、熵产生率和香农信息熵的最大值，并且这些最大值是从磷酸丙糖异构酶的测量动力学速率常数计算得出的，然而，与酶的全局最优状态的最大值具有相同的数量级，这表明磷酸丙糖异构酶可能是一种良好的、但不是完全进化的酶，正如之前所声称的那样。本文提出的理论研究还提供了明确的证据，证明酶构象状态之间的酶转变的灵活性是最大香农信息熵和最大熵产生率的要求。
