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Title: Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system

Abstract

Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re-analyzing published data of different amino acids (AAs) in potato and in green alga. Our re-analysis shows that biosynthesis pathways could be the reason for an apparently close-to-equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose-cultured green algae than in the autotrophic ones. Application of the |Δα| matrix can help usmore » to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.« less

Authors:
ORCiD logo [1];  [1];  [1];  [1]
  1. Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Geology and Geophysics
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE
OSTI Identifier:
1543484
Resource Type:
Accepted Manuscript
Journal Name:
Rapid Communications in Mass Spectrometry
Additional Journal Information:
Journal Volume: 32; Journal Issue: 4; Journal ID: ISSN 0951-4198
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Chemistry; Spectroscopy

Citation Formats

He, Yuyang, Cao, Xiaobin, Wang, Jianwei, and Bao, Huiming. Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system. United States: N. p., 2018. Web. https://doi.org/10.1002/rcm.8040.
He, Yuyang, Cao, Xiaobin, Wang, Jianwei, & Bao, Huiming. Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system. United States. https://doi.org/10.1002/rcm.8040
He, Yuyang, Cao, Xiaobin, Wang, Jianwei, and Bao, Huiming. Tue . "Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system". United States. https://doi.org/10.1002/rcm.8040. https://www.osti.gov/servlets/purl/1543484.
@article{osti_1543484,
title = {Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system},
author = {He, Yuyang and Cao, Xiaobin and Wang, Jianwei and Bao, Huiming},
abstractNote = {Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re-analyzing published data of different amino acids (AAs) in potato and in green alga. Our re-analysis shows that biosynthesis pathways could be the reason for an apparently close-to-equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose-cultured green algae than in the autotrophic ones. Application of the |Δα| matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.},
doi = {10.1002/rcm.8040},
journal = {Rapid Communications in Mass Spectrometry},
number = 4,
volume = 32,
place = {United States},
year = {2018},
month = {1}
}

Journal Article:
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Cited by: 1 work
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Figures / Tables:

Fig. 1 Fig. 1: |Δα| matrix heat maps for carbon isotope composition of AAs in potato leaves (left) and tubers (right). Each cell corresponds to the apparent α difference (Δα) for correspondingly paired AAs. Its value is represented in a color scale, with black for close to apparent equilibrium and white formore » the largest deviation. Red squares mark paired AAs of the same synthetic family, ala, alanine; val, valine; asp, aspartic acid; lys, lysine; glu, glutamic acid; pro, proline; phe, phenylalanine; tyr, tyrosine; ser, serine.« less

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    Figures / Tables found in this record:

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.