Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.
Division of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, New York, New York, United States of America.
PLoS Comput Biol. 2018 Oct 24;14(10):e1006471. doi: 10.1371/journal.pcbi.1006471. eCollection 2018 Oct.
Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal design principles that shape cellular metabolism. However, only few redox potentials have been measured, and mostly with inconsistent experimental setups. Here, we develop a quantum chemistry approach to calculate redox potentials of biochemical reactions and demonstrate our method predicts experimentally measured potentials with unparalleled accuracy. We then calculate the potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental trends in redox biochemistry. We further address the question of why NAD/NADP are used as primary electron carriers, demonstrating how their physiological potential range fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry can revolutionize our understanding of biochemical phenomena by enabling fast and accurate calculation of thermodynamic values.
热力学决定了新陈代谢的结构和功能。氧化还原反应驱动着细胞的能量和物质流动。因此,准确地量化氧化还原反应的热力学应该能够揭示塑造细胞代谢的设计原则。然而,只有少数氧化还原电位被测量出来,而且大多数都是使用不一致的实验装置。在这里,我们开发了一种量子化学方法来计算生化反应的氧化还原电位,并证明我们的方法能够以前所未有的准确性预测实验测量的电位。然后,我们计算了所有可以从生物化学相关化合物中生成的氧化还原对的电位,并强调了氧化还原生物化学中的基本趋势。我们进一步探讨了为什么 NAD/NADP 被用作主要电子载体的问题,证明了它们的生理潜能范围如何适应中心代谢反应并最小化反应性羰基化合物的浓度。量子化学的使用可以通过快速准确地计算热力学值来彻底改变我们对生化现象的理解。