Mathematical Modelling of the Influence of Different Concentrations of Oxaloacetate to Glycerol-3-Phosphate Dehydrogenase Structure

Nataliya A. Kolotyeva; Frida N. Gilmiyarova; Oksana A. Gusyakova; Marina V. Komarova; Nikita V. Remizov; Elena A. Ryskina

doi:10.18287/JBPE22.08.010302

Authors

Nataliya A. Kolotyeva Samara State Medical University, Russia http://orcid.org/0000-0002-7853-6222 (unauthenticated)
Frida N. Gilmiyarova Samara State Medical University, Russia http://orcid.org/0000-0001-5992-3609 (unauthenticated)
Oksana A. Gusyakova Samara State Medical University, Russia
Marina V. Komarova Samara National Research University, Russia http://orcid.org/0000-0001-6545-0035 (unauthenticated)
Nikita V. Remizov Samara National Research University, Russia
Elena A. Ryskina Higher School of Economics, Moscow, Russia http://orcid.org/0000-0002-8752-3837 (unauthenticated)

DOI:

https://doi.org/10.18287/JBPE22.08.010302

Keywords:

glycerol-3-phosphate dehydrogenase, oxaloacetate, differential scanning fluorimetry, conformation structure, mathematical modelling

Abstract

The study was devoted to the influence of different concentrations of oxaloacetate on the conformational structure of glycerol-3-phosphate dehydrogenase in a temperature gradient, using differential scanning fluorimetry on a Prometheus NT.48 device (NanoTemper Technologies, Germany). We studied the fluorescence ratio (350/330 nm) of glycerol-3-phosphate dehydrogenase in the presence of oxaloacetate at concentrations of 0.5–16 µM in a temperature gradient of 20–95 °C. We built linear regression models for the physiological temperature range and nonlinear models (polynomial of the third degree) for the temperature range corresponding to protein melting. Temperature was the independent variable; fluorescence ratio was the variable. The effect of different oxaloacetate concentrations on glycerol-3-phosphate dehydrogenase thermostability was evaluated by comparing the parameters of obtained regression models. At the physiological temperature range of 20–40 °C, the fluorescence ratios and their growth rates at oxaloacetate concentrations of 0.5-8 µM (p < 0.001) were found to be lower than those of controls. Higher average fluorescence ratios and growth rates were detected at oxaloacetate concentrations of 16 µM (p < 0.001). When heating over 45 °C, no differences were found in the average denaturation temperature of glycerol-3-phosphate dehydrogenase between the oxaloacetate concentrations studied. The experiment demonstrates the change in the total amplitude of the fluorescence signal in the process of heating the enzyme. The effect of biologically active compounds on fluorescence ratio differs in the area of low concentrations (0.5 and 1 µM) and high concentrations (16 µM). Oxaloacetate at a final concentration of 0.5–1 µM contributes to the thermodynamic stability of glycerol-3-phosphate dehydrogenase, while the concentration of 16 µM causes a decrease in its thermostability.

Author Biographies

Nataliya A. Kolotyeva, Samara State Medical University, Russia

Department of Fundamental and Clinical Biochemistry with Laboratory Diagnostics, Associate Professor, Doctor of Medical Sciences
Frida N. Gilmiyarova, Samara State Medical University, Russia

Department of Fundamental and Clinical Biochemistry with Laboratory Diagnostics, Professor, Doctor of Medical Sciences
Oksana A. Gusyakova, Samara State Medical University, Russia

Department of Fundamental and Clinical Biochemistry with Laboratory Diagnostics, Head of the department, Doctor of Medical Sciences
Marina V. Komarova, Samara National Research University, Russia

Department of Laser and Biotechnology Systems, Associate Professor, Candidate of Biological Sciences
Elena A. Ryskina, Higher School of Economics, Moscow, Russia

Department of Biology and Biotechnology, Professor, Doctor of Biological Sciences

References

E. L. Van Nostrand, S. C. Huelga, and G. W. Yeo, “Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions,” Advances in Experimental Medicine and Biology 907, 1–28 (2016).

E. A. Ryskina, N. A. Kolotyeva, F. N. Gilmiyarova, and N. N. Chernov, “Intermolecular interaction of proteins and small molecules (review),” European Journal of Natural History 3, 8–13 (2016).

K. Rooijers, C. M. Markodimitraki, F. J. Rang, S. S. de Vries, A. Chialastri, K. L. de Luca, D. Mooijman, S. S. Dey, and J. Kind, “Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells,” Nature Biotechnology 37(7), 766–772 (2019).

Q. Xu, R. L. Dunbrack Jr., “ProtCID: a data resource for structural information on protein interactions,” Nature Communications 11(1), 711 (2020).

Y. Mugabo, S. Zhao, A. Seifried, S. Gezzar, A. Al-Mass, D. Zhang, J. Lamontagne, C. Attane, P. Poursharifi, J. Iglesias, E. Joly, M.-L. Peyot, A. Gohla, S. R. Murthy Madiraju, and M. Prentki, “Identification of a mammalian glycerol-3-phosphate phosphatase: role in metabolism and signaling in pancreatic beta-cells and hepatocytes,” Proceedings of the National Academy of Sciences 113(4), 430–439 (2016).

E. Possik, S. R. Murthy Madiraju, and M. Prentki, “Glycerol-3-phosphate phosphatase/PGP: Role in intermediary metabolism and target for cardiometabolic diseases,” Biochimie 143, 18–28 (2017).

P. K. Langston, A. Nambu, J. Jung, M. Shibata, H. I. Aksoylar, J. Lei, P. Xu, M. T. Doan, H. Jiang, M. R. MacArthur, X. Gao, Y. Kong, E. T. Chouchani, J. W. Locasale, N. W. Snyder, and T. Horng, “Glycerol phosphate shuttle enzyme GPD2 regulates macrophage inflammatory responses,” Nature Immunology 20(9), 1186–1195 (2019).

J. Lu, Z. Xu, H. Duan, H. Ji, Z. Zhen, B. Li, H. Wang, H. Tang, J. Zhou, T. Guo, B. Wu, D. Wang, Y. Liu, Y. Niu, and R. Zhang, “Tumor-associated macrophage interleukin-β promotes glycerol-3-phosphate dehydrogenase activation, glycolysis and tumorigenesis in glioma cells,” Cancer Science 111(6), 1979–1990 (2020).

C. Zhou, J. Yu, M. Wang, J. Yang, H. Xiong, H. Huang, D. Wu, S. Hu, Y. Wang, X.-Z. Chen, and J. Tang, “Identification of glycerol-3-phosphate dehydrogenase 1 as a tumour suppressor in human breast cancer,” Oncotarget 8(60), 101309–101324 (2017).

P. Rusu, C. Shao, A. Neuerburg, A. A. Acikgöz, Y. Wu, P. Zou, P. Phapale, T. S. Shankar, K. Döring, S. Dettling, H. Körkel-Qu, G. Bekki, B. Costa, T. Guo, O. Friesen, M. Schlotter, M. Heikenwalder, D. F. Tschaharganeh, B. Bukau, G. Kramer, P. Angel, C. Herold-Mende, B. Radlwimmer, and H.-K. Liu, “GPD1 Specifically Marks Dormant Glioma Stem Cells with a Distinct Metabolic Profile,” Cell Stem Cell 25(2), 241–257 (2019).

F. Lorenzetti, A. M. Capiglioni, R. A. Marinelli, M. C. Carrillo, and M. de Luján Alvarez, “Hepatic glycerol metabolism is early reprogrammed in rat liver cancer development,” Biochimie 170, 88–93 (2020).

D. L. Nelson, M. M. Cox, and A. L. Lehninger, Lehninger principles of biochemistry, W. H. Freeman, New York, 2013.

F. Campos, T. Sobrino, P. Ramos-Cabrer, and J. Castillo, “Oxaloacetate: A novel neuroprotective for acute ischemic stroke,” The International Journal of Biochemistry & Cell Biology 44(2), 262–265 (2012).

R. H. Swerdlow, R. Bothwell, L. Hutfles, J. M. Burns, and G. A. Reed, “Tolerability and pharmacokinetics of oxaloacetate 100 mg capsules in Alzheimer’s subjects,” BBA Clinical 5, 120–123 (2016).

H. M. Wilkins, S. Koppel, S. M. Carl, S. Ramanujan, I. Weidling, M. L. Michaelis, E. K. Michaelis, and R. H. Swerdlow, “Oxaloacetate enhances neuronal cell bioenergetic fluxes and infrastructure,” Journal of Neurochemistry 137(1), 76–87 (2016).

G. R. Grimsley, S. R. Trevino, R. L. Thurlkill, and J. M. Scholtz, “Determining the conformational stability of a protein from urea and thermal unfolding curves,” Current Protocols in Protein Science 71(1), 28.4.1–28.4.14 (2013).

C. G. Alexander, R. Wanner, C. M. Johnson, D. Breitsprecherc, G. Winterb, S. Duhrc, P. Baaskec, and N. Fergusona, “Novel microscale approaches for easy, rapid determination of protein stability in academic and commercial settings,” Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 1844(12), 2241–2250 (2014).