Glycolysis model shows that allostery maintains high ATP and limits accumulation of intermediates

Creators: Choe, Mangyu¹; Einav, Tal^{2, 3, 4}; Phillips, Rob²; Titov, Denis V.¹

1. University of California, Berkeley
2. California Institute of Technology
3. Fred Hutchinson Cancer Research Center
4. La Jolla Institute For Allergy & Immunology

Abstract

Glycolysis is a conserved metabolic pathway that produces ATP and biosynthetic precursors. It is not well understood how the control of mammalian glycolytic enzymes through allosteric feedback and mass action accomplishes various tasks of ATP homeostasis, such as controlling the rate of ATP production, maintaining high and stable ATP levels, ensuring that ATP hydrolysis generates a net excess of energy, and maintaining glycolytic intermediate concentrations within physiological levels. To investigate these questions, we developed a biophysical model of glycolysis based on enzyme rate equations derived from in vitro kinetic data. This is the first biophysical model of human glycolysis that successfully recapitulates the above tasks of ATP homeostasis and predicts absolute concentrations of glycolytic intermediates and isotope tracing kinetics that align with experimental measurements in human cells. We use the model to show that mass action alone is sufficient to control the ATP production rate and maintain the high energy of ATP hydrolysis. Meanwhile, allosteric regulation of hexokinase (HK) and phosphofructokinase (PFK) by ATP, ADP, inorganic phosphate, and glucose-6-phosphate is required to maintain high ATP levels and to prevent uncontrolled accumulation of phosphorylated intermediates of glycolysis. Allosteric feedback achieves the latter by maintaining HK and PFK enzyme activity at one-half of ATP demand and, thus, inhibiting the reaction of Harden and Young, which otherwise converts glucose to supraphysiological levels of phosphorylated glycolytic intermediates at the expense of ATP. Our methodology provides a roadmap for a quantitative understanding of how metabolic homeostasis emerges from the activities of individual enzymes.

Copyright and License (English)

Acknowledgement (English)

We thank the students and instructors of the 2017 Marine Biological Laboratory course on Physical Biology of the Cell for their comments on the early version of this project, participants of the 2019 Kavli Institute for Theoretical Physics workshop on Cellular Energetics for fruitful discussions, Bradley Webb for discussions about PFK regulation, James Mbata for contributions in identifying code errors, and members of the Titov and Phillips labs for many helpful suggestions. This research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California, Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award nos. DP2 GM132933 and R35 GM152114 to D.V.T., and R35 GM118043 to R.P. T.E. is supported by Damon Runyon Cancer Research Foundation Fellowship DRQ 01-20.

Data Availability

All data reported in this paper are provided as supporting material, Data S1 and S2.

Code Availability

All original code required to reproduce all the figures is publicly available at https://github.com/DenisTitovLab/CellMetabolism.jl

Supplemental Material

Supporting material:

Document S1. Figures S1–S11 and Tables S1–S14 : 1-s2.0-S0006349525002115-mmc1.pdf
Data S1. Enzymes, metabolites, and isotope tracing : 1-s2.0-S0006349525002115-mmc2.xlsx
Data S2. Kinetic rate data for glycolytic enzymes : 1-s2.0-S0006349525002115-mmc3.xlsx

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