The use of artificial solid-state pores for measurement of catalytic activity of individual molecules of horseradish peroxidase
https://doi.org/10.18384/2949-5067-2025-1-40-51
Abstract
Aim. Determination of the catalytic activity of a single molecule of horseradish peroxidase (HRP) in the oxidation reaction of the substrate 2,2ʹ-azino-bis-[3-ethylbenzthiazoline-6- sulfonate] (ABTS) with hydrogen peroxide.
Methodology. To determine (monitor) the catalytic activity of HRP, pore technology has been used; it has allowed us to analyze the activity of a single HRP molecule without introducing additional components into the system to enhance the signal. For this purpose, a solid-state pore of about 5 nm in size, formed by electron-beam drilling in a silicon nitride plate of ~40 nm thickness, has been used. A HRP molecule has been embedded in this pore, after which the catalytic activity of the molecule embedded in the pore in the presence of ABTS and H2O2 has been analyzed by measuring the ion current through the pore with the HRP molecule embedded in it.
Results. A pore detector has been proposed to study the catalytic activity of HRP in the reaction of ABTS oxidation. It has been found that this detector made it possible to monitor the activity of this enzyme by registering of ion current through the pore.
Research implications. It has been shown that the manufactured pore can be used to monitor HRP activity. The results obtained are important for the development of work in the field of enzyme research at the level of single molecules.
About the Authors
Yu. D. IvanovRussian Federation
Yuri D. Ivanov – Dr. Sci. (Biology), Prof., Laboratory Head, Laboratory of Nanobiotechnology; Leading Researcher, Laboratory No. 6.2. – Shock wave impacts
Moscow
A. N. Ableev
Russian Federation
Alexander N. Ableev – Leading Engineer, Laboratory of Nanobiotechnology
Moscow
V. V. Shumyantseva
Russian Federation
Victoria V. Shumyantseva – Dr. Sci. (Biology), Prof., Laboratory Head, Laboratory of Bioelectrochemistry
Moscow
I. D. Shumov
Russian Federation
Ivan D. Shumov – Cand. Sci. (Biology), Researcher, Laboratory of Nanobiotechnology
Moscow
V. S. Ziborov
Russian Federation
Vadim S. Ziborov – Cand. Sci. (Phys.-Math.), Senior Researcher, Laboratory No. 6.2. – shock wave impacts; Leading Specialist, Laboratory of Nanobiotechnology
Moscow
E. D. Nevedrova
Russian Federation
Ekaterina D. Nevedrova – Research Assistant, Laboratory of Nanobiotechnology
Moscow
A. V. Vinogradova
Russian Federation
Angelina V. Vinogradova – Research Assistant, Laboratory of Nanobiotechnology
Moscow
I. A. Ivanova
Russian Federation
Irina A. Ivanova – Research Assistant, Laboratory for Research of Single Biomacromolecules
Moscow
N. V. Vaulin
Russian Federation
Nikita V. Vaulin – Laboratory Assistant, Laboratory for Renewable Energy Sources
Saint-Petersburg
D. V. Lebedev
Russian Federation
Denis V. Lebedev – Cand. Sci. (Phys.-Math.), Senior Researcher, Laboratory for Renewable Energy Sources
Saint-Petersburg
A. S. Bukatin
Russian Federation
Anton S. Bukatin – Cand. Sci. (Phys.-Math.), Assoc. Prof., Senior Researcher, Laboratory for Renewable Energy Sources
Saint-Petersburg
I. S. Mukhin
Russian Federation
Ivan S. Mukhin – Dr. Sci. (Phys.-Math.), Prof., Laboratory Head, Laboratory for Renewable Energy Sources
Saint-Petersburg
I. N. Saraeva
Russian Federation
Irina N. Saraeva – Cand. Sci. (Phys.-Math.), Researcher, Laboratory for Laser Nanophysics and Biomedicine, Department of Quantum Radiophysics named after N. G. Basov
Moscow
P. Y. Apel
Russian Federation
Pavel Yu. Apel – Dr. Sci. (Chemistry), Head of the Center for Applied Physics, Flerov Laboratory of Nuclear Reactions
Dubna, Moscow Region
E. S. Yushkov
Russian Federation
Evgeniy S. Yushkov – Cand. Sci. (Engineering), Assoc. Prof., Department No. 71 “Economics and Management in Industry”
Moscow
A. I. Archakov
Russian Federation
Alexander I. Archakov – Dr. Sci. (Biology), Prof., Scientific Leader
Moscow
References
1. Ivanov, Y. D., Bukharina, N. S., Pleshakova, T. O., Frantsuzov, P. A., Krokhin, N. V., Ziborov, V. S. & Archakov, A. I. (2011). Atomic force microscopy visualization and measurement of the activity and physicochemical properties of single monomeric and oligomeric enzymes. In: Biophysics, 56 (5), 939–944 (in Russ.).
2. Ivanov, Y. D., Bukharina, N. S., Frantsuzov, P. A., Pleshakova, T. O., Munro, A. V., Hui Bon Hoa, G. & Archakov, A. I. (2010). ASN-nanotechnology for visualization, counting, determination of elasticity and activity of single proteins of cytochrome P 450-containing monooxygenase systems. In: Nanotechnology and Health Protection, 2 (1), 30–35 (in Russ.).
3. Radmacher, M., Fritz, M., Hansma, H. G. & Hansma, P. K. (1994). Direct Observation of enzyme activity with the atomic force microscope. In: Science, 265 (5178), 1577–1579. DOI: 10.1126/science.8079171.
4. Sheng, Y., Zhang, S., Liu, L. & Wu, H.-C. (2020). Measuring enzymatic activities with nanopores. In: ChemBioChem, 21 (15), 2089–2097. DOI: 10.1002/cbic.202000079.
5. Chen, H., Lin, Y., Long, Y.-T., Minteer, S. D. & Ying, Y.-L. (2022). Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level. In: Faraday Discussions, 233, 295–302. DOI: 10.1039/d1fd00042j.
6. Willems, K., van Meervelt, V., Wloka, C. & Maglia, G. (2017). Single-molecule nanopore enzymology. In: Philosophical transactions of the Royal Society B, Biological sciences, 372 (1726), 20160230. DOI: 10.1098/rstb.2016.0230.
7. Wloka, C., van Meervelt, V., Gelder, D. V., Danda, N., Jager, N., Williams, C. P. & Maglia, G. (2017). Label-free and real-time detection of protein ubiquitination with a biological nanopore. In: ACS Nano, 11 (5), 4387–4394. DOI: 10.1021/acsnano.6b07760.
8. Pham, B., Eron, S. J., Hill, M. E., Xin, Li, Fahie, M. A., Hardy, J. A. & Chen, Min (2019). A nanopore approach for analysis of caspase-7 activity in cell lysates. In: Biophysical Journal, 117 (5), 844–855. DOI: 10.1016/j.bpj.2019.07.045.
9. Fahie, M. A., Pham, B., Li, F. & Chen, M. (2021). A selective activity-based approach for analysis of enzymes with an OmpG nanopore. In: Methods in Molecular Biology, 2186, 115–133. DOI: 10.1007/978-1-0716-0806-7_9.
10. Rogozhin, V. V., Kutuzova, G. D. & Ugarova, N. N. (2000). Inhibition of horseradish peroxidase by W-ethylamide of o-sulfobenzoylacetic acid. In: Russian Journal of Bioorganic Chemistry, 26 (2), 156–160 (in Russ.).
11. Davies, P. F., Rennke, H. G. & Cotran R. S. (1981). Influence of molecular charge upon the endocytosis and intracellular fate of peroxidase activity in cultured arterial endothelium. In: Journal of Cell Science, 49 (1), 69–86. DOI: 10.1242/jcs.49.1.69.
12. Sander, S. A., Bray, R. C. & Smith, A. T. (1994). pH-dependent properties of a mutant horseradish peroxidase isoenzyme C in which Arg38 has been replaced with lysine. In: European Journal of Biochemistry, 224 (3), 1029–1037. DOI: 10.1111/j.1432-1033.1994.01029.x.