Localization of the E. coli Dps protein molecules in a silicon wires matrix according to scanning electron microscopy and X-ray photoelectron spectroscopy

Keywords: Nanostructures, Biomolecules, Hybrid materials, Developed surface, Recombinant ferritin-like protein Dps, Silicon wires, Scanning Electron Microscopy, X-ray Photoelectron Spectroscopy

Abstract

     The work is related to the study of the morphological features of silicon wires arrays combined with a nanomaterial of natural origin, a bacterial ferritin-like protein Dps, and their relationship with the composition of the surface and interior.
     A silicon wires array was formed by metal-assisted wet chemical etching. To obtain recombinant protein, Escherichia coli BL21*(DE3) cells were used as producers, and purification was carried out by the chromatography method. The combination of silicon wires with protein molecules was carried out by layering under laboratory conditions, followed by drying. The resulting hybrid material was studied by scanning electron microscopy and X-ray photoelectron spectroscopy.
    The initial silicon wires array had sharp boundaries on the surface. The diameter of the silicon wires was about 100 nm, while the distances between the wires can vary widely, reaching several hundred nanometres or be less than 100 nanometres, depending on the formation conditions, in the absence of noticeable transition layers. The pores formed in this way are available for filling with protein during deposition.
     The effectiveness of using the scanning electron microscopy method to study the morphology of the hybrid material “silicon wires – bacterial protein Dps” as well as X-ray photoelectron spectroscopy method together with ion etching for the investigation of the composition and physico-chemical of the hybrid material was demonstrated. Complementary results have shown that the molecular culture, which is a solution of oligomers of the recombinant Dps protein of E.coli bacterial cells, can penetrate deep into the pores of the silicon wires array with an extremely developed surface. The possibility of the control of the filling of silicon wires arrays by varying the pore morphology and other modes of formation of structures
and their surface has been demonstrated.
      The obtained data can be used to study the possibilities of the functionalization of the developed surface of silicon wires by their driven coating with controlled delivery of biohybrid material.

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Author Biographies

Elena V. Parinova, Voronezh State University, 1 Universitetskaya pl., Voronezh, 394018, Russian Federation

Cand. Sci. (Phys.-Math.),
Assistant Professor, General Physics Department,
Voronezh State University (Voronezh, Russian
Federation).

Sergey S. Antipov, Voronezh State University, 1 Universitetskaya pl., Voronezh, 394018, Russian Federation; Institute of Cell Biophysics of the Russian Academy of Sciences, 3 Institutskaya st., Pushchino, 142290, Russian Federation

Dr. Sci. (Biology), Associate
Professor, Biophysics and Biotechnology Department,
Voronezh State University (Voronezh, Russian
Federation).

Vladimir Sivakov, Leibniz Institute of Photonic Technology, Department Functional Interfaces, 9 Albert Einstein st., Jena, 07745, Germany

PhD, Deputy Head, Leibniz
Institute of Photonic Technology (Jena, Germany).

Evgeny A. Belikov, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Engineer of Joint Laboratory
“Atomic and Electronic Structure of Functional
Materials”, Voronezh State University (Voronezh,
Russian Federation).

Olga A. Chuvenkova, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Cand. Sci. (Phys.-Math.),
Senior researcher of the Joint Laboratory “Atomic and
Electronic Structure of Functional Materials”,
Voronezh State University (Voronezh, Russian
Federation).

Iuliia S. Kakuliia, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Leading Engineer, General
Physics Department, Voronezh State University
(Voronezh, Russian Federation).

Sergey Yu. Trebunskikh, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Cand. Sci. (Phys.-Math.),
Researcher of the Joint Laboratory “Atomic and
Electronic Structure of Functional Materials”,
Voronezh State University (Voronezh, Russian
Federation).

Matvey S. Skorobogatov, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

bachelor student,
Biophysics and Biotechnology Department, Voronezh
State University (Voronezh, Russian Federation).

Ratibor G. Chumakov, National Research Center “Kurchatov Institute”, 1 Akademika Kurchatova pl., Moscow, 123182, Russian Federation

Cand. Sci. (Phys.–Math.),
Senior Researcher of the National Research Center
“Kurchatov Institute” (Moscow, Russian Federation).

Alexei M. Lebedev, National Research Center “Kurchatov Institute”, 1 Akademika Kurchatova pl., Moscow, 123182, Russian Federation

Cand. Sci. (Phys.–Math.), Senior
Researcher of the National Research Center “Kurchatov
Institute” (Moscow, Russian Federation).

Valerii G. Artyukhov, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Dr. Sci. (Biology), Professor,
Head of the Biophysics and Biotechnology Department,
Voronezh State University (Voronezh, Russian
Federation).

Sergey Yu. Turishchev, Voronezh State University, 1 Universitetskaya pl., Voronezh 394018, Russian Federation

Dr. Sci. (Phys.-Math.),
Associate Professor, Head of the General Physics
Department, Voronezh State University (Voronezh,
Russian Federation).

References

Osminkina L. A., Gongalsky M. B., Motuzuk A. V., Timoshenko V. Y., Kudryavtsev A. A. Silicon nanocrystals as photo- and sono-sensitizers for biomedical applications. Applied Physics B. 2011;105: 665–668. https://doi.org/10.1007/s00340-011-4562‑8

Harrison P. M., Arosio P. The ferritins, molecular properties, iron storage and cellular regulation. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1996;1275(3): 161−203. https://doi.org/10.1016/0005-2728(96)00022-9

Sivakov V. A., Brönstrup G., Pecz B., Berger A., Radnoczi G. Z., Krause M., Christiansen S. H. Realization of vertical and zigzag single crystalline silicon nanowire architectures. The Journal of Physical Chemistry C. 2010;114: 3798–3803. https://doi.org/10.1021/jp909946x

Lo Faro M. J., Leonardi A. Al., D’Andrea C., … Irrera A. Low cost synthesis of silicon nanowires for photonic applications. Journal of Materials Science: Materials in Electronics. 2020;31: 34–40. https://doi.org/10.1007/s10854-019-00672-y

Ming T., Turishchev S., Schleusener A., … Sivakov V. Silicon suboxides as driving force for efficient light-nhanced hydrogen generation on silicon nanowires. Small. 2021;17(8): 2007650. https://doi.org/10.1002/smll.202007650

Parinova E. V., Antipov S. S., Sivakov V., … Turishchev S. Yu. Dps protein localization studies in nanostructured silicon matrix by scanning electron microscopy. Condensed Matter and Interphases. 2021;23(4): 644–648. https://doi.org/10.17308/kcmf.2021.23/3741

Parinova E. V., Antipov S. S., Belikov E. A., Chuvenkova O.A., Kakuliia I.S., Koyuda D.A., Trebunskikh S.Yu., Skorobogatov M.S., Chumakov R.G., Lebedev A.M., Sinelnikov A.A., Artiuhov V.G., Ovchinnikov O.V., Smirnov M.S., Turishchev S.Iu. TEM and XPS studies of bio-nanohybrid material based on bacterial ferritin-like protein Dps. Condensed Matter and Interphases. 2022;24(2): 265–272. https://doi.org/10.17308/kcmf.2022.24/9267

Parinova E. V., Antipov S. S., Belikov E. A., Kakuliia I. S., Trebunskikh S. Y., Turishchev S. Y., Sivakov V. Localization of DPS protein in porous silicon nanowires matrix. Results in Physics. 2022;35: 105348. https://doi.org/10.1016/j.rinp.2022.105348

Antipov S., Turishchev S., Purtov Yu., … Ozoline O. The oligomeric form of the Escherichia coli Dps 3 protein depends on the availability of iron ions. Molecules. 2017;22(11): 1904. https://doi.org/10.3390/molecules22111904

Zhang Y., Fu J., Chee S. Y., Ang E. X., Orner B. P. Rational disruption of the oligomerization of the miniferritin E. coli DPS through protein–protein interface mutation. Protein Science. 2011;20(11): 1907–1917. https://doi.org/10.1002/pro.731

Turishchev S. Yu., Antipov S. S., Novolokina N. V., … Domashevskaya E. P. A soft X-ray synchrotron study of the charge state of iron ions in the ferrihydrite core of the ferritin Dps protein in Escherichia coli. Biophysics. 2016;61(5): 705–710. https://doi.org/10.1134/s0006350916050286

Lebedev A. M., Menshikov K. A., Nazin V. G., Stankevich V. G., Tsetlin M. B., Chumakov R. G.. NanoPES photoelectron beamline of the Kurchatov Synchrotron Radiation Source. Journal of Surface Investigation: X-ray, Synchrotron and Neutron Techniques. 2021;15(5): 1039–1044. https://doi.org/10.1134/s1027451021050335

John F. Moulder handbook of X-ray photoelectron spectroscopy. Published by Perkin-Elmer Corporation Physical Electronics Division 6509 Flying Cloud Drive Eden Prairie, Minnesota 55344 United States of America; 1992.

Handbook of the elements and native oxide. XPS International, Inc.; 1999.

srdata.nist.gov/xps

Turishchev S. Yu., Chuvenkova O. A., Parinova E. V., … Sivakov V. XPS investigations of MOCVD tin oxide thin layers on Si nanowires array. Results in Physics. 2018;11: 507-509. https://doi.org/10.1016/j.rinp.2018.09.046

Hüfner S. Very high resolution photoelectron spectroscopy. In: Lecture Notes in Physics. Berlin Heidelberg: Springer; 2007. https://doi.org/10.1007/3-540-68133-7

Published
2023-05-11
How to Cite
Parinova, E. V., Antipov, S. S., Sivakov, V., Belikov, E. A., Chuvenkova, O. A., Kakuliia, I. S., Trebunskikh, S. Y., Skorobogatov, M. S., Chumakov, R. G., Lebedev, A. M., Artyukhov, V. G., & Turishchev, S. Y. (2023). Localization of the E. coli Dps protein molecules in a silicon wires matrix according to scanning electron microscopy and X-ray photoelectron spectroscopy. Condensed Matter and Interphases, 25(2), 207-214. https://doi.org/10.17308/kcmf.2023.25/11102
Section
Original articles

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