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Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

ABSTRACT: The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

SUBMITTER: Holme P

PROVIDER: S-EPMC3089637 | biostudies-other | 2011

REPOSITORIES: biostudies-other

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Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

Holme Petter P Huss Mikael M Lee Sang Hoon SH

PloS one 20110506 5

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic ...[more]

PMID: 21573072

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Project description:MotivationThe growing complexity of reaction-based models necessitates early detection and resolution of model errors. Considerable work has been done on the detection of mass balance errors, especially atomic mass analysis (AMA) (which compares the counts of atoms in the reactants and products) and Linear Programming analysis (which detects stoichiometric inconsistencies). This article extends model error checking to include: (i) certain structural errors in reaction networks and (ii) error isolation. First, we consider the balance of chemical structures (moieties) between reactants and products. This balance is expected in many biochemical reactions, but the imbalance of chemical structures cannot be detected if the analysis is done in units of atomic masses. Second, we improve on error isolation for stoichiometric inconsistencies by identifying a small number of reactions and/or species that cause the error. Doing so simplifies error remediation.ResultsWe propose two algorithms that address isolating structural errors in reaction networks. Moiety analysis finds imbalances of moieties using the same algorithm as AMA, but moiety analysis works in units of moieties instead of atomic masses. We argue for the value of checking moiety balance, and discuss two approaches to decomposing chemical species into moieties. Graphical Analysis of Mass Equivalence Sets (GAMES) provides isolation for stoichiometric inconsistencies by constructing explanations that relate errors in the structure of the reaction network to elements of the reaction network. We study the effectiveness of moiety analysis and GAMES on curated models in the BioModels repository. We have created open source codes for moiety analysis and GAMES.Availability and implementationOur project is hosted at https://github.com/ModelEngineering/SBMLLint, which contains examples, documentation, source code files and build scripts used to create SBMLLint. Our source code is licensed under the MIT open source license.Supplementary informationSupplementary data are available at Bioinformatics online.

Project description:Understanding the mechanism of hydrazine oxidation reaction by OH radical along with the rate constants of all possible pathways leads to explain the fate of hydrazine in the atmosphere. In this article, the comprehensive mechanisms and kinetics of the hydrazine plus hydroxyl radical reaction have been investigated theoretically at different temperatures and pressures. To achieve the main goals, a series of high levels of quantum chemical calculations have been widely implemented in reliable channels of the H-abstraction, SN2, and addition/elimination reactions. The energy profile of all pathways accompanied by the molecular properties of the involved stationary points has been characterized at the MP2, M06-2X, and CCSD(T)/CBS levels. To estimate accurate barrier energies of the H-abstraction channels, large numbers of the CCSD (T) calculations in conjunction with various augmented basis sets have been implemented. The direct dynamic calculations have been carried out using the validated M06-2X/maug-cc-pVTZ level, and also by the CCSD(T) (energies) + MP2 (partition functions) level. The pressure-dependent rate constants of the barrierless pathways have been investigated by the strong collision approach. Therefore, the main behaviors of the N2H4 + OH reaction have been explored according to the influences of temperature and pressure on the computed rate coefficients within the well-behaved theoretical frameworks of the TST, VTST, and RRKM theories. It has been found that the H-abstraction mechanism (to form N2H3) is dominant relative to the SN2 reaction and OH-addition to the N center of N2H4 moiety (to form H2NOH + NH2). The computed high pressure limit rate constant of the main reaction pathway, k(298.15) = 7.31 × 10-11 cm3 molecule-1 s-1, has an excellent agreement with the experimental value (k (298.15) = (6.50 ± 1.3) × 10-11 cm3 molecule-1 s-1) recommended by Vaghjiani. Also, the atmospheric lifetime of hydrazine degradation by OH radicals has been demonstrated to be 32.80 to 1161.11 h at the altitudes of 0-50 km. Finally, the disagreement in the calculated rate constants between the previous theoretical study and experimental results has been rectified.

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Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

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Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

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