Enzymes are central to both metabolism and information processing in cells. In both cases, an enzyme’s ability to accelerate a reaction without being consumed in the reaction is crucial. Nevertheless, enzymes are transiently sequestered when they bind to their substrates; this sequestration limits activity and potentially compromises information processing and signal transduction. In this article, we analyse the mechanism of enzyme–substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, while maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies of the enzyme–substrate and enzyme–product reaction intermediates minimize the fraction of enzymes sequestered in complexes, while sustaining a certain minimal flux? Under reasonable biophysical assumptions, we find that the optimal design will saturate the bound on the minimal flux and reflects a basic trade-off in catalytic operation. If both binding free energies are too high, there is low sequestration, but the effective progress of the reaction is hampered. If both binding free energies are too low, there is high sequestration, and the reaction flux may also be suppressed in extreme cases. The optimal binding free energies are therefore neither too high nor too low, but in fact moderate. Moreover, the optimal difference in substrate and product binding free energies, which contributes to the thermodynamic driving force of the reaction, is in general strongly constrained by the intrinsic free-energy difference between products and reactants. Both the strategies of using a negative binding free-energy difference to drive the catalyst-bound reaction forward and of using a positive binding free-energy difference to enhance detachment of the product are limited in their efficacy.

酶是细胞代谢和信息处理的核心。在这两种情况下，酶加速反应而不在反应中被消耗的能力是至关重要的。然而，酶在与其底物结合时会被暂时隔离。这种隔离限制了活动，并可能危及信息处理和信号转导。在本文中，我们从通过螯合使酶的负荷最小化的角度分析酶-底物催化的机理，同时至少保持最小的反应通量。我们特别要问：酶-底物和酶-产物反应中间体的哪些结合自由能使复合物中螯合的酶比例最小化，同时保持一定的最小通量？在合理的生物物理假设下，我们发现优化设计将使最小通量的界限饱和，并反映催化操作的基本权衡。如果两个结合自由能都太高，则螯合量低，但会阻碍反应的有效进行。如果两个结合自由能都太低，则螯合度高，在极端情况下也可能抑制反应通量。因此，最佳结合自由能既不太高也不太低，实际上适中。此外，有助于反应热力学驱动力的底物和产物结合自由能的最佳差异通常受到产物和反应物之间固有自由能差异的强烈限制。