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Pleshakova TO, Ershova MO, Valueva AA, Ivanova IA, Ivanov YD, Archakov AI. AFM-fishing technology for protein detection in solutions. BIOMEDITSINSKAIA KHIMIIA 2024; 70:273-286. [PMID: 39324193 DOI: 10.18097/pbmc20247005273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
The review considers the possibility of using atomic force microscopy (AFM) as a basic method for protein detection in solutions with low protein concentrations. The demand for new bioanalytical approaches is determined by the problem of insufficient sensitivity of systems used in routine practice for protein detection. Special attention is paid to demonstration of the use in bioanalysis of a combination of AFM and fishing methods as an approach of concentrating biomolecules from a large volume of the analyzed solution on a small surface area.
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Affiliation(s)
| | - M O Ershova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Valueva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - I A Ivanova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Archakov AI, Aseev AL, Bykov VA, Grigoriev AI, Govorun VM, Ilgisonis EV, Ivanov YD, Ivanov VT, Kiseleva OI, Kopylov AT, Lisitsa AV, Mazurenko SN, Makarov AA, Naryzhny SN, Pleshakova TO, Ponomarenko EA, Poverennaya EV, Pyatnitskii MA, Sagdeev RZ, Skryabin KG, Zgoda VG. Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium. J Proteome Res 2019; 18:4206-4214. [PMID: 31599598 DOI: 10.1021/acs.jproteome.9b00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.
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Affiliation(s)
| | | | | | | | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine , Moscow 119435 , Russia
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| | - Vadim T Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow 117997 , Russia
| | | | | | | | - Sergey N Mazurenko
- Joint Institute for Nuclear Research , Dubna, Moscow region 141980 , Russia
| | | | | | | | | | | | | | - Renad Z Sagdeev
- International Tomography Center , Novosibirsk 630090 , Russia
| | - Konstantin G Skryabin
- The Federal Research Centre "Fundamentals of Biotechnology" , Moscow 119071 , Russia
| | - Victor G Zgoda
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
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Ivanov YD, Pleshakova TO, Malsagova KA, Kaysheva AL, Kopylov AT, Izotov AA, Tatur VY, Vesnin SG, Ivanova ND, Ziborov VS, Archakov AI. [AFM fishing of proteins under impulse electric field]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:439-46. [PMID: 27562998 DOI: 10.18097/pbmc20166204439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A combination of (atomic force microscopy)-based fishing (AFM-fishing) and mass spectrometry allows to capture protein molecules from solutions, concentrate and visualize them on an atomically flat surface of the AFM chip and identify by subsequent mass spectrometric analysis. In order to increase the AFM-fishing efficiency we have applied pulsed voltage with the rise time of the front of about 1 ns to the AFM chip. The AFM-chip was made using a conductive material, highly oriented pyrolytic graphite (HOPG). The increased efficiency of AFM-fishing has been demonstrated using detection of cytochrome b5 protein. Selection of the stimulating pulse with a rise time of 1 ns, corresponding to the GHz frequency range, by the effect of intrinsic emission from water observed in this frequency range during water injection into the cell.
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Affiliation(s)
- Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - A L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A T Kopylov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Izotov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V Yu Tatur
- Foundation of Perspective Technologies and Innovations, Moscow, Russia
| | | | - N D Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnjlogy (FSGEI of HPE), Moscow, Russia
| | - V S Ziborov
- Joint Institute for High Temperatures of RAS, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. [AFM-based technologies as the way towards the reverse Avogadro number]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:239-53. [PMID: 25978390 DOI: 10.18097/pbmc20156102239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Achievement of the concentration detection limit for proteins at the level of the reverse Avogadro number determines the modern development of proteomics. In this review, the possibility of approximating the reverse Avogadro number by using nanotechnological methods (AFM-based fishing with mechanical and electrical stimulation, nanowire detectors, and other methods) are discussed. The ability of AFM to detect, count, visualize and characterize physico-chemical properties of proteins at concentrations up to 10(-17)-10(-18) M is demonstrated. The combination of AFM-fishing with mass-spectrometry allows the identification of proteins not only in pure solutions, but also in multi-component biological fluids (serum). The possibilities to improve the biospecific fishing efficiency by use of SOMAmers in both AFM and nanowire systems are discussed. The paper also provides criteria for evaluation of the sensitivity of fishing-based detection systems. The fishing efficiency depending on the detection system parameters is estimated. The practical implementation of protein fishing depending on the ratio of the sample solution volume and the surface of the detection system is discussed. The advantages and disadvantages of today's promising nanotechnological protein detection methods implemented on the basis of these schemes.
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Affiliation(s)
| | - I D Shumov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Malsagova KA, Ivanov YD, Pleshakova TO, Kozlov AF, Krohin NV, Kaysheva AL, Shumov ID, Popov VP, Naumova OV, Fomin BI, Nasimov DA. [SOI-nanowire biosensor for the detection of D-NFAT 1 protein]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:462-7. [PMID: 26350736 DOI: 10.18097/pbmc20156104462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The nanowire (NW) detection is one of fast-acting and high-sensitive methods allowing to reveal potentially relevant protein molecules. A NW biosensor based on the silicon-on-insulator (SOI)-structures was used for biospecific label-free detection of NFAT 1 (D-NFAT 1) oncomarker in real time. For this purpose, SOI-nanowires (NWs) were modified with aptamers against NFAT 1 used as molecular probes. It was shown that using this biosensor it is possible to reach the sensitivity of ~10(-15) M. This sensitivity was comparable with that of the NW biosensor with immobilized antibodies used as macromolecular probes. The results demonstrate promising approaches used to form the sensor elements for high-sensitive disease diagnostics.
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Affiliation(s)
| | - Yu D Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A F Kozlov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - N V Krohin
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - I D Shumov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V P Popov
- Rzhanov Institute of Semiconductor Physics, Novosibirsk, Russia
| | - O V Naumova
- Rzhanov Institute of Semiconductor Physics, Novosibirsk, Russia
| | - B I Fomin
- Rzhanov Institute of Semiconductor Physics, Novosibirsk, Russia
| | - D A Nasimov
- Rzhanov Institute of Semiconductor Physics, Novosibirsk, Russia
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Pleshakova TO, Shumov ID, Ivanov YD, Malsagova KA, Kaysheva AL, Archakov AI. AFM-based technologies as the way towards the reverse Avogadro number. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815030063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ivanov YD, Pleshakova TO, Malsagova KA, Kaysheva AL, Kopylov AT, Izotov AA, Tatur VY, Vesnin SG, Ivanova ND, Ziborov VS, Archakov AI. AFM-based protein fishing in the pulsed electric field. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815020080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ivanov YD, Bukharina NS, Pleshakova TO, Frantsuzov PA, Andreeva EY, Kaysheva AL, Zgoda VG, Izotov AA, Pavlova TI, Ziborov VS, Radko SP, Moshkovskii SA, Archakov AI. Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers. Int J Nanomedicine 2014; 9:4659-70. [PMID: 25336946 PMCID: PMC4200055 DOI: 10.2147/ijn.s66946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.
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Affiliation(s)
- Yuri D Ivanov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Natalia S Bukharina
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana O Pleshakova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Pavel A Frantsuzov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Elena Yu Andreeva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Anna L Kaysheva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
- PostgenTech Ltd., Moscow, Russia
| | - Victor G Zgoda
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander A Izotov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana I Pavlova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Vadim S Ziborov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey P Radko
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergei A Moshkovskii
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander I Archakov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
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