Quantum chemistry reveals thermodynamic principles of redox biochemistry

PLoS Comput Biol. 2018 Oct 24;14(10):e1006471. doi: 10.1371/journal.pcbi.1006471. eCollection 2018 Oct.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biochemical Phenomena*
  • Linear Models
  • Models, Chemical*
  • NAD / chemistry
  • NAD / metabolism
  • NADP / chemistry
  • NADP / metabolism
  • Oxidation-Reduction*
  • Thermodynamics*

Substances

  • NAD
  • NADP

Grants and funding

AAG and AJ and BSL acknowledge support from SEAS^NVIDIA, Massively Parallel Programming and Computing (332986). ABE and CC are funded by the Max Planck Society. AF was supported by an NSF Graduate Research Fellowship. EN is funded by the Swiss Initiative in Systems Biology (SystemsX.ch) TPdF fellowship (2014-230). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.