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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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Ivanov YD, Tatur VY, Pleshakova TO, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Repnikov VV, Stepanov IN, Ziborov VS. Effect of Spherical Elements of Biosensors and Bioreactors on the Physicochemical Properties of a Peroxidase Protein. Polymers (Basel) 2021; 13:1601. [PMID: 34063512 PMCID: PMC8155990 DOI: 10.3390/polym13101601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
External electromagnetic fields are known to be able to concentrate inside the construction elements of biosensors and bioreactors owing to reflection from their surface. This can lead to changes in the structure of biopolymers (such as proteins), incubated inside these elements, thus influencing their functional properties. Our present study concerned the revelation of the effect of spherical elements, commonly employed in biosensors and bioreactors, on the physicochemical properties of proteins with the example of the horseradish peroxidase (HRP) enzyme. In our experiments, a solution of HRP was incubated within a 30 cm-diameter titanium half-sphere, which was used as a model construction element. Atomic force microscopy (AFM) was employed for the single-molecule visualization of the HRP macromolecules, adsorbed from the test solution onto mica substrates in order to find out whether the incubation of the test HRP solution within the half-sphere influenced the HRP aggregation state. Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) was employed in order to reveal whether the incubation of HRP solution within the half-sphere led to any changes in its secondary structure. In parallel, spectrophotometry-based estimation of the HRP enzymatic activity was performed in order to find out if the HRP active site was affected by the electromagnetic field under the conditions of our experiments. We revealed an increased aggregation of HRP after the incubation of its solution within the half-sphere in comparison with the control sample incubated far outside the half-sphere. ATR-FTIR allowed us to reveal alterations in HRP's secondary structure. Such changes in the protein structure did not affect its active site, as was confirmed by spectrophotometry. The effect of spherical elements on a protein solution should be taken into account in the development of the optimized design of biosensors and bioreactors, intended for performing processes involving proteins in biomedicine and biotechnology, including highly sensitive biosensors intended for the diagnosis of socially significant diseases in humans (including oncology, cardiovascular diseases, etc.) at early stages.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | | | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
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Malsagova KA, Pleshakova TO, Popov VP, Kupriyanov IN, Galiullin RA, Kozlov AF, Shumov ID, Kaysheva AL, Tikhonenko FV, Archakov AI, Ivanov YD. Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides. MICROMACHINES 2021; 12:mi12020147. [PMID: 33546438 PMCID: PMC7913754 DOI: 10.3390/mi12020147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10−17 M) concentrations.
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Affiliation(s)
- Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
- Correspondence: ; Tel.: +7-499-246-3761
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Laboratory of Silicon Material Science, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Igor N. Kupriyanov
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences, Laboratory of Experimental Mineralogy and Crystallogenesis, 630090 Novosibirsk, Russia;
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Andrey F. Kozlov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Anna L. Kaysheva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Fedor V. Tikhonenko
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Laboratory of Silicon Material Science, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
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Ivanov Y, Pleshakova T, Malsagova K, Kurbatov L, Popov V, Glukhov A, Smirnov A, Enikeev D, Potoldykova N, Alekseev B, Dolotkazin D, Kaprin A, Ziborov V, Petrov O, Archakov A. Detection of Marker miRNAs, Associated with Prostate Cancer, in Plasma Using SOI-NW Biosensor in Direct and Inversion Modes. SENSORS (BASEL, SWITZERLAND) 2019; 19:E5248. [PMID: 31795306 PMCID: PMC6928824 DOI: 10.3390/s19235248] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been stored for either one or two years in a clean room. Potential to detect DNA oligonucleotides (oDNAs)-synthetic analogues of microRNAs (miRNAs) 198 and 429 that are associated with the development of prostate cancer (PCa)-in buffer solution was demonstrated using a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). To provide biospecific detection, nanowire surfaces were sensitized with oligonucleotide probes (oDNA probes) complimentary to the known sequences of miRNA 183 and 484. In this study it is demonstrated that freshly prepared SOI-NW biosensor chips with n-type conductance and immobilized oDNA probes exhibit responses to the addition of complimentary oDNAs in buffer, leading to decreases in chips' conductance at a concentration of 3.3 × 10-16 M. The influence of storage time on the characteristics of SOI-NW biosensor chips is also studied herein. It is shown that a two-year storage of the chips leads to significant changes in their characteristics, resulting in "inverse" sensitivity toward negatively charged oDNA probes (i.e., through an increase in chips' conductance). It is concluded that the surface layer makes the main contribution to conductance of the biosensor chip. Our results indicate that the detection of target nucleic acid molecules can be carried out with high sensitivity using sensor chips after long-term storage, but that changes in their surface properties, which lead to inversed detection signals, must be taken into account. Examples of the applications of such chips for the detection of cancer-associated microRNAs in plasma samples of patients with diagnosed prostate cancer are given. The results obtained herein are useful for the development of highly sensitive nanowire-based diagnostic systems for the revelation of (prostate) cancer-associated microRNAs in human plasma.
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Affiliation(s)
- Yuri Ivanov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia; (Y.I.); (T.P.); (L.K.); (A.A.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia; (V.Z.)
| | - Tatyana Pleshakova
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia; (Y.I.); (T.P.); (L.K.); (A.A.)
| | - Kristina Malsagova
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia; (Y.I.); (T.P.); (L.K.); (A.A.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia; (Y.I.); (T.P.); (L.K.); (A.A.)
| | - Vladimir Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia;
| | - Alexander Glukhov
- Joint-Stock Company “Novosibirsk Plant of Semiconductor Devices & DC”, Novosibirsk 630082, Russia;
| | - Alexander Smirnov
- Russian Union of Industrialists and Entrepreneurs, Moscow 109240, Russia;
| | - Dmitry Enikeev
- Institute for Urology and Reproductive Health, Sechenov University, Moscow 119992, Russia; (D.E.); (N.P.)
| | - Natalia Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, Moscow 119992, Russia; (D.E.); (N.P.)
| | - Boris Alekseev
- Federal State Budgetary Institution National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Moscow 125284, Russia; (B.A.); (D.D.); (A.K.)
| | - Daniyar Dolotkazin
- Federal State Budgetary Institution National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Moscow 125284, Russia; (B.A.); (D.D.); (A.K.)
| | - Andrey Kaprin
- Federal State Budgetary Institution National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Moscow 125284, Russia; (B.A.); (D.D.); (A.K.)
| | - Vadim Ziborov
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia; (V.Z.)
| | - Oleg Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia; (V.Z.)
| | - Alexander Archakov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia; (Y.I.); (T.P.); (L.K.); (A.A.)
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Taniguchi M, Ohshiro T. Nanopore Device for Single-Molecule Sensing Method and Its Application. Bioanalysis 2019. [DOI: 10.1007/978-981-13-6229-3_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Pleshakova TO, Bukharina NS, Archakov AI, Ivanov YD. Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization. Int J Mol Sci 2018; 19:E1142. [PMID: 29642632 PMCID: PMC5979402 DOI: 10.3390/ijms19041142] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.
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Affiliation(s)
| | - Natalia S Bukharina
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
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Bukharina NS, Ivanov YD, Pleshakova TO, Frantsuzov PA, Andreeva EY, Kaysheva AL, Izotov AA, Pavlova TI, Ziborov VS, Radko SP, Archakov AI. [Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016. [PMID: 26215414 DOI: 10.18097/pbmc20156103363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A method of atomic force microscopy-based fishing (AFM fishing) has been developed for protein detection in the analyte solution using a chip with an immobilized aptamer. This method is based on the biospecific fishing of a target protein from a bulk solution onto the small AFM chip area with the immobilized aptamer to this protein used as the molecular probe. Such aptamer-based approach allows to increase an AFM image contrast compared to the antibody-based approach. Mass spectrometry analysis used after the biospecific fishing to identify the target protein on the AFM chip has proved complex formation. Use of the AFM chip with the immobilized aptamer avoids interference of the antibody and target protein peaks in a mass spectrum.
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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 A Izotov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - T I Pavlova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V S Ziborov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Ivanov YD, Kaysheva AL, Frantsuzov PA, Pleshakova TO, Krohin NV, Izotov AA, Shumov ID, Uchaikin VF, Konev VA, Ziborov VS, Archakov AI. Detection of hepatitis C virus core protein in serum by atomic force microscopy combined with mass spectrometry. Int J Nanomedicine 2015; 10:1597-608. [PMID: 25759582 PMCID: PMC4346358 DOI: 10.2147/ijn.s71776] [Citation(s) in RCA: 8] [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: 11/23/2022] Open
Abstract
A method for detection and identification of core antigen of hepatitis C virus (HCVcoreAg)-containing particles in the serum was proposed, with due account taken of the interactions of proteotypic peptides with Na(+), K(+), and Cl(-) ions. The method is based on a combination of reversible biospecific atomic force microscopy (AFM)-fishing and mass spectrometry (MS). AFM-fishing enables concentration, detection, and counting of protein complexes captured on the AFM chip surface, with their subsequent MS identification. Biospecific AFM-fishing of HCVcoreAg-containing particles from serum samples was carried out using AFM chips with immobilized antibodies against HCVcoreAg (HCVcoreAgim). Formation of complexes between anti-HCVcoreAgim and HCVcoreAg-containing particles on the AFM chip surface during the fishing process was demonstrated. These complexes were registered and counted by AFM. Further MS analysis allowed reliable identification of HCVcoreAg within the complexes formed on the AFM chip surface. It was shown that MS data processing, with account taken of the interactions between HCVcoreAg peptides and Na(+), K(+) cations, and Cl(-) anions, allows an increase in the number of peptides identified.
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Affiliation(s)
| | - Anna L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
- PostgenTech Ltd, Moscow, Russia
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Senapati S, Manna S, Lindsay S, Zhang P. Application of catalyst-free click reactions in attaching affinity molecules to tips of atomic force microscopy for detection of protein biomarkers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14622-30. [PMID: 24180289 PMCID: PMC3886287 DOI: 10.1021/la4039667] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Atomic force microscopy (AFM) has been extensively used in studies of biological interactions. Particularly, AFM based force spectroscopy and recognition imaging can sense biomolecules on a single molecule level, having great potential to become a tool for molecular diagnostics in clinics. These techniques, however, require affinity molecules to be attached to AFM tips in order to specifically detect their targets. The attachment chemistry currently used on silicon tips involves multiple steps of reactions and moisture sensitive chemicals, such as (3-aminopropyl)triethoxysilane (APTES) and N-hydroxysuccinimide (NHS) ester, making the process difficult to operate in aqueous solutions. In the present study, we have developed a user-friendly protocol to functionalize the AFM tips with affinity molecules. A key feature of it is that all reactions are carried out in aqueous solutions. In summary, we first synthesized a molecular anchor composed of cyclooctyne and silatrane for introduction of a chemically reactive function to AFM tips and a bifunctional polyethylene glycol linker that harnesses two orthogonal click reactions, copper free alkyne-azide cycloaddition and thiol-vinylsulfone Michael addition, for attaching affinity molecules to AFM tips. The attachment chemistry was then validated by attaching antithrombin DNA aptamers and cyclo-RGD peptides to silicon nitride (SiN) tips, respectively, and measuring forces of unbinding these affinity molecules from their protein cognates human α-thrombin and human α5β1-integrin immobilized on mica surfaces. In turn, we used the same attachment chemistry to functionalize silicon tips with the same affinity molecules for AFM based recognition imaging, showing that the disease-relevant biomarkers such as α-thrombin and α5β1-integrin can be detected with high sensitivity and specificity by the single molecule technique. These studies demonstrate the feasibility of our attachment chemistry for the use in functionalization of AFM tips with affinity molecules.
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Affiliation(s)
- Subhadip Senapati
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Saikat Manna
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Stuart Lindsay
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Peiming Zhang
- Center for Single Molecule Biophysics of the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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Ivanov YD, Danichev VV, Pleshakova TO, Shumov ID, Ziborov VS, Krokhin NV, Zagumenniy MN, Ustinov VS, Smirnov LP, Shironin AV, Archakov AI. Irreversible chemical AFM-based fishing for detection of low-copied proteins. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2013. [DOI: 10.1134/s1990750813010071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Maojo V, Fritts M, de la Iglesia D, Cachau RE, Garcia-Remesal M, Mitchell JA, Kulikowski C. Nanoinformatics: a new area of research in nanomedicine. Int J Nanomedicine 2012; 7:3867-90. [PMID: 22866003 PMCID: PMC3410693 DOI: 10.2147/ijn.s24582] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and -omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings.
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Affiliation(s)
- Victor Maojo
- Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Spain.
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Maojo V, García-Remesal M, de la Iglesia D, Crespo J, Pérez-Rey D, Chiesa S, Fritts M, Kulikowski CA. Nanoinformatics: Developing Advanced Informatics Applications for Nanomedicine. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-94-007-1248-5_26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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13
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Kaĭsheva AL, Ivanov ID, Zgoda VG, Frantsuzov PA, Pleshakova TO, Krokhin NV, Ziborov VS, Archakov AI. [Visualization and identification of hepatitis C viral particles by atomic force microscopy combined with MS/MS analysis]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2011; 56:26-39. [PMID: 21328909 DOI: 10.18097/pbmc20105601026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Possibility of detection and identification of hepatitis C viral particles with mass spectrometry (MS) in combination with atomic force microscopy (AFM) had been investigated. AFM/MS approach is based on two technologies: (1) AFM-biospecific fishing that allows to detect, concentrate from solution and to count protein complexes on a surface of AFM-nanochip; (2) mass spectrometric identification of these complexes. AFM-biospecific fishing of HCVcoreAg from solution was carried onto surface of AFM-nanochips with immobilized anti-HCVcoreAg. It was shown that HCVcoreAg/anti-HCVcore(im) complexes were formed onto AFM-nanochips in quantity sufficient for mass spectrometric identification. Thus, AFM/MS approach allows to identify fragments of hepatitis C virus fished onto a surface of AFM-nanochip from serum.
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14
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Rodriguez H, Rivers R, Kinsinger C, Mesri M, Hiltke T, Rahbar A, Boja E. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective. Proteomics Clin Appl 2010; 4:904-14. [PMID: 21137031 DOI: 10.1002/prca.201000057] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 01/10/2023]
Abstract
Proteomics holds great promise in personalized medicine for cancer in the post-genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high-quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution-MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next-generation high-throughput protein biomarker measurements for diagnostics and therapeutics.
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Affiliation(s)
- Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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15
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Archakov AI, Ivanov YD. Application of AFM and optical biosensor for investigation of complexes formed in P450-containing monooxygenase systems. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:102-10. [PMID: 20832504 DOI: 10.1016/j.bbapap.2010.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/20/2010] [Accepted: 08/29/2010] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) allows to visualize and count the individual protein molecules and their complexes within multiprotein systems. On the other hand, optical biosensor (OB) provides information on complex formation kinetics as well as complex lifetime (τ(LT)) and affinity. Comparison of complex lifetime τ(LT) with the time required for enzyme's catalytic cycle (τ(cat)) enables to characterize productive complexes and distinguish them from non-productive ones. Both these approaches were applied for the analysis of the three cytochrome P450-containing monooxygenase systems: cytochrome P450 101, cytochrome P450 11A1 and cytochrome P450 2B4. By using AFM, the formation of binary and ternary protein complexes was registered in all the three systems. OB analysis enabled to kinetically characterize these binary and ternary complexes. It was shown that the binary complexes putidaredoxin reductase (PdR)/putidaredoxin (Pd) and Pd/cytochrome P450 101 (P450 101) formed within the P450 101 system and, also, the binary complexes adrenodoxin reductase (AdR)/adrenodoxin (Ad) and Ad/cytochrome P450 11A1 (P450 11A1) formed within the P450 11A1 system are non-productive (deadlock). At the same time, the ternary PdR/Pd/P450 101 and AdR/Ad/P450 11A1 complexes proved to be productive. The binary cytochrome P450 reductase (Fp)/cytochrome P450 2B4 (2B4) complexes and the ternary Fp/2B4/cytochrome b5 (b5) complexes formed within P450 2B4 system were productive.
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Affiliation(s)
- A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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16
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Fuchs S, Winter G, Coester C. Ultrasonic resonator technology as a new quality control method evaluating gelatin nanoparticles. J Microencapsul 2010; 27:242-52. [PMID: 20406094 DOI: 10.3109/02652040903079534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Nanomedicine is a quickly evolving field where more and more possible applications become evident and start entering clinical trials or even the market. However, the analytic methods are not always able to keep pace with the new formulations' demands. One example of a promising medical implementation is oligodeoxynucleotide (ODN) delivery by gelatin nanoparticles (GNPs). Currently, quality control is dependent on either some time consuming or destructive spectrometric, chromatographic or electrophoretic methods. A possible enlargement of the portfolio by Ultrasonic Resonator Technology (URT) is investigated here by subjecting plain GNPs in various sizes and concentrations as well as ODN-loaded GNPs to URT analysis. If calibrated by photon correlation spectroscopy (PCS) and other spectroscopy methods for each single nanoparticle system parameter, URT is an efficient and non-destructive technique and serves as a broad characterization method. URT is emphasized to play a possible future part in the size, concentration and ODN loading monitoring, e.g. of gelatin nanoparticles in the course of formulation development.
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Affiliation(s)
- Sebastian Fuchs
- Department of Pharmacy, Pharmaceutical Technology and Biopharmacy, Ludwig Maximilians University, Munich, Germany
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17
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Koopmans RJ, Aggeli A. Nanobiotechnology—quo vadis? Curr Opin Microbiol 2010; 13:327-34. [DOI: 10.1016/j.mib.2010.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 01/18/2010] [Indexed: 01/12/2023]
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18
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Archakov AI. Nanobiotechnologies in medicine: Nanodiagnostics and nanodrugs. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2010. [DOI: 10.1134/s1990750810010026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Kaysheva AL, Ivanov YD, Zgoda VG, Frantsuzov PA, Pleshakova TO, Krokhin NV, Ziborov VS, Archakov AI. Visualization and identification of hepatitis C viral particles by atomic force microscopy combined with MS/MS analysis. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2010. [DOI: 10.1134/s1990750810010038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Brault ND, Gao C, Xue H, Piliarik M, Homola J, Jiang S, Yu Q. Ultra-low fouling and functionalizable zwitterionic coatings grafted onto SiO2 via a biomimetic adhesive group for sensing and detection in complex media. Biosens Bioelectron 2010; 25:2276-82. [PMID: 20359880 DOI: 10.1016/j.bios.2010.03.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/03/2010] [Accepted: 03/04/2010] [Indexed: 10/19/2022]
Abstract
Non-specific protein binding from human plasma and serum has severely hindered the full capabilities of biosensors concerned with cancer biomarker detection. Currently, there is a strong desire for developing new materials which allow for the convenient attachment of an ultra-low fouling and functionalizable surface coating which can be used for highly sensitive and label-free detection of target analytes directly from complex media. In this work, a short 20 min in situ "graft to" protocol using Tris pH 8.5 buffer was developed for zwitterionic carboxybetaine methacrylate (CBMA) polymer conjugates containing the adhesive biomimetic moiety, 3,4-dihydroxy-L-phenylalanine (DOPA), on SiO(2) substrates. Using a surface plasmon resonance (SPR) biosensor, different buffers, pH values, salt concentrations, and temperatures were investigated for determining the "graft to" conditions that yield dense polymer films which both minimize non-specific protein adsorption and maximize antibody immobilization. The optimized surface coatings were shown to be highly protein resistant to 100% human blood plasma and serum. Subsequent antibody functionalized surfaces without any blocking agents enabled the specific detection of the cancer biomarker ALCAM directly from undiluted human serum down to 64 ng/mL. The successful use of this zwitterionic surface coating for detection from complex media on SiO(2) surfaces indicates its potential for broad impacts in the development of implantable medical devices, in vivo diagnostics, and nano-scale biosensors.
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Affiliation(s)
- Norman D Brault
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-1750, USA
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21
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Selective chemical modification of silicon nitride/silicon oxide nanostructures to develop label-free biosensors. Biosens Bioelectron 2010; 25:1460-6. [DOI: 10.1016/j.bios.2009.10.048] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 10/28/2009] [Accepted: 10/29/2009] [Indexed: 11/22/2022]
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22
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Archakov A, Ivanov Y, Lisitsa A, Zgoda V. Biospecific irreversible fishing coupled with atomic force microscopy for detection of extremely low-abundant proteins. Proteomics 2009; 9:1326-43. [PMID: 19253286 DOI: 10.1002/pmic.200800598] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the absence of an analog of PCR for proteins, the concentration detection limit (DL) becomes a real challenge. The problem may be solved by means of a combination of biospecific irreversible fishing with atomic force microscopy (AFM). AFM offers the ability to register individual molecules and their complexes, while biospecific fishing takes advantage of an affine interaction between analyte molecules spread over a large volume of biomaterial and ligand molecules immobilized on the chip surface. Fishing may be conducted in Kd-dependent reversible mode and in Kd-independent irreversible mode. In this study, the DLs of two previously applied proteomic approaches were determined and compared to the DL of a newly developed analytical method. The first approach, based on MS analysis of biomaterial after 2-DE or LC separation of proteins, attained a DL at the level of 10(-8)-10(-10) M. The second approach, based on the optical biosensor analysis of molecular interactions in the format of proteomic microarrays, had a DL of 10(-9)-10(-10) M. Our proposed method which combines biospecific fishing with AFM allowed us to attain DL values of 10(-11) M under reversible binding conditions and 10(-16) M under irreversible binding conditions.
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Ponomarenko EA, Lisitsa AV, Petrak J, Moshkovskii SA, Archakov AI. Identification of differentially expressed proteins using automated meta-analysis of proteomic articles. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2009. [DOI: 10.1134/s1990750809010028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Meuwis MA, Fillet M, Chapelle JP, Malaise M, Louis E, Merville MP. New biomarkers of Crohn's disease: serum biomarkers and development of diagnostic tools. Expert Rev Mol Diagn 2008; 8:327-37. [PMID: 18598111 DOI: 10.1586/14737159.8.3.327] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crohn's disease (CD) is a complex and heterogeneous inflammatory disorder that is part of inflammatory bowel diseases. Its diagnosis is performed on clinical presentation and results of radiography, endoscopy and histological findings. New noninvasive diagnostic biomarkers are needed to allow rapid and accurate CD discrimination. Blood-derived biomarkers correlating with disease activity, supported by genetic evidences and valid for all CD patients subtypes are still missing. Hence, no biomarkers and no related diagnostic tests are recommended or used alone for CD diagnosis in clinical practice. This review describes diagnosis tests based on the detection/quantification of specific acute-phase reactant proteins, enzymes and derived antibody response developed by inflammatory bowel disease patients for pathogens or symbiotic flora determinant, as well as autoantibodies. Their power as diagnostic tools is discussed, as well as new high-throughput techniques, such as microarrays and proteomics, for the discovery of new CD clinical biomarkers and for the development of specific CD diagnostic tests. Some rapidly evolving nanotechnologies, mathematical analysis and bioinformatics methods are also mentioned to highlight their importance for further accurate CD diagnosis.
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Affiliation(s)
- Marie-Alice Meuwis
- Proteomic Platform, GIGA, GIGA-Research, University of Liège, 4000 Liège, Belgium.
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Robinson JM, Ackerman WE, Kniss DA, Takizawa T, Vandré DD. Proteomics of the human placenta: promises and realities. Placenta 2008; 29:135-43. [PMID: 18222537 DOI: 10.1016/j.placenta.2007.12.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/06/2007] [Accepted: 12/11/2007] [Indexed: 02/08/2023]
Abstract
Proteomics is an area of study that sets as its ultimate goal the global analysis of all of the proteins expressed in a biological system of interest. However, technical limitations currently hamper proteome-wide analyses of complex systems. In a more practical sense, a desired outcome of proteomics research is the translation of large protein data sets into formats that provide meaningful information regarding clinical conditions (e.g., biomarkers to serve as diagnostic and/or prognostic indicators of disease). Herein, we discuss placental proteomics by describing existing studies, pointing out their strengths and weaknesses. In so doing, we strive to inform investigators interested in this area of research about the current gap between hyperbolic promises and realities. Additionally, we discuss the utility of proteomics in discovery-based research, particularly as regards the capacity to unearth novel insights into placental biology. Importantly, when considering under studied systems such as the human placenta and diseases associated with abnormalities in placental function, proteomics can serve as a robust 'shortcut' to obtaining information unlikely to be garnered using traditional approaches.
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Affiliation(s)
- J M Robinson
- Department of Physiology and Cell Biology, Ohio State University, Columbus, OH 43210, USA.
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