Thermodynamics of hydrolysis of sugar phosphates.

Tewari, Yadu D.; Steckler, D K.; Goldberg, Robert N.; Gitomer, William L.

doi:10.1016/s0021-9258(18)68977-x

Cited by 25 publications

(30 citation statements)

References 19 publications

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“…The impact of pH on the quality of the 31 P spectrum was quite dramatic and is likely attributed to changes in both the stability and ionization state of the phosphate group. This is consistent with previous reports that the stability of ATP is increased at either acidic or basic pH values. , Accordingly, a pH of 4 was determined to be optimal for collecting a 31 P spectrum of metabolomics samples. Importantly, a low pH is also compatible with the sample conditions we previously reported for detecting nitrogen-containing metabolites.…”

Section: Resultssupporting

confidence: 91%

“…Phosphorylated metabolites are prone to hydrolysis, which leads to the accumulation of inorganic phosphate and its related substrate. , The rate and extent of chemical hydrolysis is influenced by pH, temperature, and the presence of counterions . Phosphorylated metabolites are also prone to enzymatic hydrolysis .…”

Section: Resultsmentioning

confidence: 99%

“…13 C-carbon and 15 N-nitrogen labeled nutrients are convenient sources of isotope tracers and are commonly added as supplements to a variety of biological systems ranging from cell cultures to animal models. Unlike 13 C and 15 N, 31 Pphosphorus is a naturally abundant and NMR active isotope that does not require an external supplemental source. To date, 31 P NMR has seen limited usage in metabolomics because of a lack of reference spectra, difficulties in sample preparation, and an absence of two-dimensional (2D) NMR experiments, but 31 P NMR has the potential of expanding the coverage of the metabolome by detecting phosphorus-containing metabolites.…”

mentioning

confidence: 99%

“…Unlike 13 C and 15 N, 31 Pphosphorus is a naturally abundant and NMR active isotope that does not require an external supplemental source. To date, 31 P NMR has seen limited usage in metabolomics because of a lack of reference spectra, difficulties in sample preparation, and an absence of two-dimensional (2D) NMR experiments, but 31 P NMR has the potential of expanding the coverage of the metabolome by detecting phosphorus-containing metabolites. Phosphorylated metabolites regulate key cellular processes, serve as a surrogate for intracellular pH conditions, and provide a measure of a cell's metabolic energy and redox state, among other processes.…”

mentioning

confidence: 99%

“…Phosphorylated metabolites regulate key cellular processes, serve as a surrogate for intracellular pH conditions, and provide a measure of a cell's metabolic energy and redox state, among other processes. Thus, incorporating 31 P NMR into a metabolomics investigation will enable the detection of these key cellular processes. To facilitate the application of 31 P NMR in metabolomics, we present a unified protocol that allows for the simultaneous and efficient detection of 1 H-, 13 C-, 15 N-, and 31 P-labeled metabolites.…”

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confidence: 99%

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Phosphorus NMR and Its Application to Metabolomics

et al. 2020

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Stable isotopes are routinely employed by NMR metabolomics to highlight specific metabolic processes and to monitor pathway flux. 13C-carbon and 15N-nitrogen labeled nutrients are convenient sources of isotope tracers and are commonly added as supplements to a variety of biological systems ranging from cell cultures to animal models. Unlike 13C and 15N, 31P-phosphorus is a naturally abundant and NMR active isotope that does not require an external supplemental source. To date, 31P NMR has seen limited usage in metabolomics because of a lack of reference spectra, difficulties in sample preparation, and an absence of two-dimensional (2D) NMR experiments, but 31P NMR has the potential of expanding the coverage of the metabolome by detecting phosphorus-containing metabolites. Phosphorylated metabolites regulate key cellular processes, serve as a surrogate for intracellular pH conditions, and provide a measure of a cell’s metabolic energy and redox state, among other processes. Thus, incorporating 31P NMR into a metabolomics investigation will enable the detection of these key cellular processes. To facilitate the application of 31P NMR in metabolomics, we present a unified protocol that allows for the simultaneous and efficient detection of 1H-, 13C-, 15N-, and 31P-labeled metabolites. The protocol includes the application of a 2D 1H–31P HSQC-TOCSY experiment to detect 31P-labeled metabolites from heterogeneous biological mixtures, methods for sample preparation to detect 1H-, 13C-, 15N-, and 31P-labeled metabolites from a single NMR sample, and a data set of one-dimensional (1D) 31P NMR and 2D 1H–31P HSQC-TOCSY spectra of 38 common phosphorus-containing metabolites to assist in metabolite assignments.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Phosphorus NMR and Its Application to Metabolomics

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Catalytic Conversion of Sugars to Fuels

Tompsett

Huber

2011

Thermochemical Processing of Biomass

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Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

Vojinović

Stockar

2009

Biotech & Bioengineering

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Thermodynamic feasibility analysis (TFA) has been used as a tool capable of providing additional constraints to the mass balance-based methods of analysis of metabolic networks (e.g., flux balance analysis). Several publications have recently appeared in which TFA of different metabolic pathways from relatively simple to the genome-scale networks was described as a means of detecting the possible metabolic control steps. However, in order to perform TFA, many simplifying assumptions were necessary. On the other hand, it has been shown by applying TFA to the well-known pathway of glycolysis that erroneous simplifying assumptions may seriously bias the results of the analysis. A quantitative analysis of the influence of non-ideality of the biochemical system, pH, temperature, and complexation of the metabolites with Mg(2+) ions as well as a number of other factors on the TFA is reported. It is shown that the feasibility of glycolysis is very seriously limited by the reaction of oxidative phosphorylation of glyceraldehyde phosphate, and that the intracellular concentration of the main product of this reaction, biphosphoglycerate, must be anywhere from 10 to 100 times lower than published values. In addition, the driving force for this reaction, and consequently the feasibility of the entire pathway depend strongly on the intracellular pH and ionic strength and to a lesser extent on pMg and temperature. The analysis may also be influenced by uncertainties of the dissociation and magnesium complexation constants of glyceraldehyde phosphate. The analysis demonstrates the crucial importance of taking such factors into account when performing TFA. It also suggests an urgent need for experimental determinations of such factors as a prerequisite for sensible thermodynamic analysis of metabolism on a genome-wide scale.

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Thermodynamics of hydrolysis of sugar phosphates.

Cited by 25 publications

References 19 publications

Phosphorus NMR and Its Application to Metabolomics

Phosphorus NMR and Its Application to Metabolomics

Catalytic Conversion of Sugars to Fuels

Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

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