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Quantum chemistry reveals thermodynamic principles of redox biochemistry

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...

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Autores principales: Jinich, Adrian, Flamholz, Avi, Ren, Haniu, Kim, Sung-Jin, Sanchez-Lengeling, Benjamin, Cotton, Charles A. R., Noor, Elad, Aspuru-Guzik, Alán, Bar-Even, Arren
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218094/
https://www.ncbi.nlm.nih.gov/pubmed/30356318
http://dx.doi.org/10.1371/journal.pcbi.1006471
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author Jinich, Adrian
Flamholz, Avi
Ren, Haniu
Kim, Sung-Jin
Sanchez-Lengeling, Benjamin
Cotton, Charles A. R.
Noor, Elad
Aspuru-Guzik, Alán
Bar-Even, Arren
author_facet Jinich, Adrian
Flamholz, Avi
Ren, Haniu
Kim, Sung-Jin
Sanchez-Lengeling, Benjamin
Cotton, Charles A. R.
Noor, Elad
Aspuru-Guzik, Alán
Bar-Even, Arren
author_sort Jinich, Adrian
collection PubMed
description 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.
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spelling pubmed-62180942018-11-19 Quantum chemistry reveals thermodynamic principles of redox biochemistry Jinich, Adrian Flamholz, Avi Ren, Haniu Kim, Sung-Jin Sanchez-Lengeling, Benjamin Cotton, Charles A. R. Noor, Elad Aspuru-Guzik, Alán Bar-Even, Arren PLoS Comput Biol Research Article 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. Public Library of Science 2018-10-24 /pmc/articles/PMC6218094/ /pubmed/30356318 http://dx.doi.org/10.1371/journal.pcbi.1006471 Text en © 2018 Jinich et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Jinich, Adrian
Flamholz, Avi
Ren, Haniu
Kim, Sung-Jin
Sanchez-Lengeling, Benjamin
Cotton, Charles A. R.
Noor, Elad
Aspuru-Guzik, Alán
Bar-Even, Arren
Quantum chemistry reveals thermodynamic principles of redox biochemistry
title Quantum chemistry reveals thermodynamic principles of redox biochemistry
title_full Quantum chemistry reveals thermodynamic principles of redox biochemistry
title_fullStr Quantum chemistry reveals thermodynamic principles of redox biochemistry
title_full_unstemmed Quantum chemistry reveals thermodynamic principles of redox biochemistry
title_short Quantum chemistry reveals thermodynamic principles of redox biochemistry
title_sort quantum chemistry reveals thermodynamic principles of redox biochemistry
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218094/
https://www.ncbi.nlm.nih.gov/pubmed/30356318
http://dx.doi.org/10.1371/journal.pcbi.1006471
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