Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification

Bukharina, N. S.; Иванов, Ю Д; Pleshakova, Tatyana O.; Frantsuzov, P. A.; Андреева, Е Ю; Кайшева, Анна Леонидовна; Izotov, Alexander; Pavlova, Tatyana I; Ziborov, Vadim S.; Radko, Sergey P.; Archakov, Alexander I.

doi:10.18097/pbmc20156103363

Cited by 4 publications

(4 citation statements)

References 28 publications

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“…In order for AFM to detect specific targets, the AFM probe has to be functionalized with a molecule of high affinity [33,167]. The force applied to break the chemical bond between the probe and the target molecule is quantitatively determined from the force-distance curve [168][169][170]. Previous studies have demonstrated that a silicon nitride cantilever tip functionalized with DNA aptamers and cyclo-RGD peptides is able to detect their cognate α-thrombin, IgE molecules, and integrin α5β1 with high accuracy upto ~90 % [33,171].…”

Section: Molecular Recognition Imagingmentioning

confidence: 99%

Nano-scientific Application of Atomic Force Microscopy in Pathology: from Molecules to Tissues

Kiio

Park

2020

Int. J. Med. Sci.

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The advantages of atomic force microscopy (AFM) in biological research are its high imaging resolution, sensitivity, and ability to operate in physiological conditions. Over the past decades, rigorous studies have been performed to determine the potential applications of AFM techniques in disease diagnosis and prognosis. Many pathological conditions are accompanied by alterations in the morphology, adhesion properties, mechanical compliances, and molecular composition of cells and tissues. The accurate determination of such alterations can be utilized as a diagnostic and prognostic marker. Alteration in cell morphology represents changes in cell structure and membrane proteins induced by pathologic progression of diseases. Mechanical compliances are also modulated by the active rearrangements of cytoskeleton or extracellular matrix triggered by disease pathogenesis. In addition, adhesion is a critical step in the progression of many diseases including infectious and neurodegenerative diseases. Recent advances in AFM techniques have demonstrated their ability to obtain molecular composition as well as topographic information. The quantitative characterization of molecular alteration in biological specimens in terms of disease progression provides a new avenue to understand the underlying mechanisms of disease onset and progression. In this review, we have highlighted the application of diverse AFM techniques in pathological investigations.

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Section: Molecular Recognition Imagingmentioning

confidence: 99%

Nano-scientific Application of Atomic Force Microscopy in Pathology: from Molecules to Tissues

Kiio

Park

2020

Int. J. Med. Sci.

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“…53 At V = 1 mL, C v = 10 −13 M, S = 0.4 mm 2 , and h = 2 nm, the obtained concentration C vs was 1.25 × 10 −4 M, confirming the ability of this approach to overcome the sensitivity limitations of proteomic analytical methods. Furthermore, the proteins concentrated on the AFM chip surface can be identified using MS. 54,55 The ability to detect proteins present in biological fluid using a combination of AFM and MS methods has already been shown. 56 For example, using this technique, viral hepatitis C marker proteins are registered and identified in the blood serum of patients.…”

Section: Future Strategies To Resolve the Human Proteomementioning

confidence: 99%

“…At V = 1 mL, C v = 10 –13 M, S = 0.4 mm 2 , and h = 2 nm, the obtained concentration C vs was 1.25 × 10 –4 M, confirming the ability of this approach to overcome the sensitivity limitations of proteomic analytical methods. Furthermore, the proteins concentrated on the AFM chip surface can be identified using MS. , …”

Section: Introductionmentioning

confidence: 99%

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

Archakov

Aseev

Быков³

et al. 2019

J. Proteome Res.

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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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“…The identification of surfaceanchored proteins is a separate area of proteomic analysis that is of great significance for biotechnology and bioengineering with regards to the investigation of the functional properties of surface-localized biosystems. Developed surfaces, such as chromatographic columns [2] and microbeads [3], as well as planar surfaces [4,5], in particular atomically smooth ones [6,7], can be considered in this respect.…”

Section: Introductionmentioning

confidence: 99%

Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy

Gordeeva,

Valueva,

Ershova

et al. 2023

IJMS

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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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Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification

Cited by 4 publications

References 28 publications

Nano-scientific Application of Atomic Force Microscopy in Pathology: from Molecules to Tissues

Nano-scientific Application of Atomic Force Microscopy in Pathology: from Molecules to Tissues

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy

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