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Gordeeva AI, Valueva AA, Rybakova EE, Ershova MO, Shumov ID, Kozlov AF, Ziborov VS, Kozlova AS, Zgoda VG, Ivanov YD, Ilgisonis EV, Kiseleva OI, Ponomarenko EA, Lisitsa AV, Archakov AI, Pleshakova TO. MS Identification of Blood Plasma Proteins Concentrated on a Photocrosslinker-Modified Surface. Int J Mol Sci 2023; 25:409. [PMID: 38203578 PMCID: PMC10778900 DOI: 10.3390/ijms25010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
This work demonstrates the use of a modified mica to concentrate proteins, which is required for proteomic profiling of blood plasma by mass spectrometry (MS). The surface of mica substrates, which are routinely used in atomic force microscopy (AFM), was modified with a photocrosslinker to allow "irreversible" binding of proteins via covalent bond formation. This modified substrate was called the AFM chip. This study aimed to determine the role of the surface and crosslinker in the efficient concentration of various types of proteins in plasma over a wide concentration range. The substrate surface was modified with a 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) photocrosslinker, activated by UV irradiation. AFM chips were incubated with plasma samples from a healthy volunteer at various dilution ratios (102X, 104X, and 106X). Control experiments were performed without UV irradiation to evaluate the contribution of physical protein adsorption to the concentration efficiency. AFM imaging confirmed the presence of protein layers on the chip surface after incubation with the samples. MS analysis of different samples indicated that the proteomic profile of the AFM-visualized layers contained common and unique proteins. In the working series of experiments, 228 proteins were identified on the chip surface for all samples, and 21 proteins were not identified in the control series. In the control series, a total of 220 proteins were identified on the chip surface, seven of which were not found in the working series. In plasma samples at various dilution ratios, a total of 146 proteins were identified without the concentration step, while 17 proteins were not detected in the series using AFM chips. The introduction of a concentration step using AFM chips allowed us to identify more proteins than in plasma samples without this step. We found that AFM chips with a modified surface facilitate the efficient concentration of proteins owing to the adsorption factor and the formation of covalent bonds between the proteins and the chip surface. The results of our study can be applied in the development of highly sensitive analytical systems for determining the complete composition of the plasma proteome.
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Affiliation(s)
| | | | | | | | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (A.I.G.); (A.A.V.); (E.E.R.); (M.O.E.); (A.F.K.); (V.S.Z.); (A.S.K.); (V.G.Z.); (Y.D.I.); (E.V.I.); (O.I.K.); (E.A.P.); (A.V.L.); (A.I.A.); (T.O.P.)
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Gordeeva AI, Valueva AA, Ershova MO, Rybakova EE, Shumov ID, Kozlov AF, Ziborov VS, Zavialova MG, Zgoda VG, Ivanov YD, Archakov AI, Pleshakova TO. Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy. Int J Mol Sci 2023; 24:ijms24108999. [PMID: 37240343 DOI: 10.3390/ijms24108999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mass spectrometry (MS) is one of the main techniques for protein identification. Herein, MS has been employed for the identification of bovine serum albumin (BSA), which was covalently immobilized on the surface of a mica chip intended for investigation by atomic force microscopy (AFM). For the immobilization, two different types of crosslinkers have been used: 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) and dithiobis(succinimidyl propionate) (DSP). According to the data obtained by using an AFM-based molecular detector, the SuccBB crosslinker was more efficient in BSA immobilization than the DSP. The type of crosslinker used for protein capturing has been found to affect the results of MS identification. The results obtained herein can be applied in the development of novel systems intended for the highly sensitive analysis of proteins with molecular detectors.
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Affiliation(s)
| | | | - Maria O Ershova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Yuri D Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
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Ivanov YD, Shumov ID, Tatur VY, Valueva AA, Kozlov AF, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. AFM Investigation of the Influence of Steam Flow through a Conical Coil Heat Exchanger on Enzyme Properties. MICROMACHINES 2022; 13:2041. [PMID: 36557340 PMCID: PMC9784692 DOI: 10.3390/mi13122041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
The present study is aimed at the revelation of subtle effects of steam flow through a conical coil heat exchanger on an enzyme, incubated near the heat exchanger, at the nanoscale. For this purpose, atomic force microscopy (AFM) has been employed. In our experiments, horseradish peroxidase (HRP) was used as a model enzyme. HRP is extensively employed as a model in food science in order to determine the influence of electromagnetic fields on enzymes. Adsorption properties of HRP on mica have been studied by AFM at the level of individual enzyme macromolecules, while the enzymatic activity of HRP has been studied by spectrophotometry. The solution of HRP was incubated either near the top or at the side of the conically wound aluminium pipe, through which steam flow passed. Our AFM data indicated an increase in the enzyme aggregation on mica after its incubation at either of the two points near the heat exchanger. At the same time, in the spectrophotometry experiments, a slight change in the shape of the curves, reflecting the HRP-catalyzed kinetics of ABTS oxidation by hydrogen peroxide, has also been observed after the incubation of the enzyme solution near the heat exchanger. These effects on the enzyme adsorption and kinetics can be explained by alterations in the enzyme hydration caused by the influence of the electromagnetic field, induced triboelectrically by the flow of steam through the heat exchanger. Our findings should thus be considered in the development of equipment involving conical heat exchangers, intended for either research or industrial use (including miniaturized bioreactors and biosensors). The increased aggregation of the HRP enzyme, observed after its incubation near the heat exchanger, should also be taken into account in analysis of possible adverse effects from steam-heated industrial equipment on the human body.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow 109472, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow 119991, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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Lim K, Nishide G, Yoshida T, Watanabe‐Nakayama T, Kobayashi A, Hazawa M, Hanayama R, Ando T, Wong RW. Millisecond dynamic of SARS-CoV-2 spike and its interaction with ACE2 receptor and small extracellular vesicles. J Extracell Vesicles 2021; 10:e12170. [PMID: 34874124 PMCID: PMC8650025 DOI: 10.1002/jev2.12170] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 spike protein (S) binds to human angiotensin-converting enzyme 2 (hACE2), allowing virus to dock on cell membrane follow by viral entry. Here, we use high-speed atomic force microscopy (HS-AFM) for real-time visualization of S, and its interaction with hACE2 and small extracellular vesicles (sEVs). Results show conformational heterogeneity of S, flexibility of S stalk and receptor-binding domain (RBD), and pH/temperature-induced conformational change of S. S in an S-ACE2 complex appears as an all-RBD up conformation. The complex acquires a distinct topology upon acidification. S and S2 subunit demonstrate different membrane docking mechanisms on sEVs. S-hACE2 interaction facilitates S to dock on sEVs, implying the feasibility of ACE2-expressing sEVs for viral neutralization. In contrary, S2 subunit docks on lipid layer and enters sEV using its fusion peptide, mimicking the viral entry scenario. Altogether, our study provides a platform that is suitable for real-time visualization of various entry inhibitors, neutralizing antibodies, and sEV-based decoy in blocking viral entry. Teaser: Comprehensive observation of SARS-CoV-2 spike and its interaction with receptor ACE2 and sEV-based decoy in real time using HS-AFM.
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Affiliation(s)
- Keesiang Lim
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Goro Nishide
- Division of Nano Life Science in the Graduate School of Frontier Science InitiativeWISE Program for Nano‐Precision MedicineScience and TechnologyKanazawa UniversityKanazawaIshikawaJapan
| | - Takeshi Yoshida
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | | | - Akiko Kobayashi
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Masaharu Hazawa
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
| | - Rikinari Hanayama
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Department of ImmunologyKanazawa University Graduate School of Medical SciencesKanazawaIshikawaJapan
| | - Toshio Ando
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
| | - Richard W. Wong
- WPI‐Nano Life Science InstituteKanazawa UniversityKanazawaIshikawaJapan
- Cell‐Bionomics Research UnitInstitute for Frontier Science Initiative (INFINITI)Kanazawa UniversityKanazawaIshikawaJapan
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