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Ershov PV, Mezentsev YV, Kopylov AT, Yablokov EO, Svirid AV, Lushchyk AY, Kaluzhskiy LA, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Affinity Isolation and Mass Spectrometry Identification of Prostacyclin Synthase (PTGIS) Subinteractome. BIOLOGY 2019; 8:E49. [PMID: 31226805 PMCID: PMC6628129 DOI: 10.3390/biology8020049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/06/2019] [Accepted: 06/18/2019] [Indexed: 01/04/2023]
Abstract
Prostacyclin synthase (PTGIS; EC 5.3.99.4) catalyzes isomerization of prostaglandin H2 to prostacyclin, a potent vasodilator and inhibitor of platelet aggregation. At present, limited data exist on functional coupling and possible ways of regulating PTGIS due to insufficient information about protein-protein interactions in which this crucial enzyme is involved. The aim of this study is to isolate protein partners for PTGIS from rat tissue lysates. Using CNBr-activated Sepharose 4B with covalently immobilized PTGIS as an affinity sorbent, we confidently identified 58 unique proteins by mass spectrometry (LC-MS/MS). The participation of these proteins in lysate complex formation was characterized by SEC lysate profiling. Several potential members of the PTGIS subinteractome have been validated by surface plasmon resonance (SPR) analysis. SPR revealed that PTGIS interacted with full-length cytochrome P450 2J2 and glutathione S-transferase (GST). In addition, PTGIS was shown to bind synthetic peptides corresponding to sequences of for GSTA1, GSTM1, aldo-keto reductase (AKR1A1), glutaredoxin 3 (GLRX3) and histidine triad nucleotide binding protein 2 (HINT2). Prostacyclin synthase could potentially be involved in functional interactions with identified novel protein partners participating in iron and heme metabolism, oxidative stress, xenobiotic and drugs metabolism, glutathione and prostaglandin metabolism. The possible biological role of the recognized interaction is discussed in the context of PTGIS functioning.
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Affiliation(s)
- Pavel V Ershov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Yuri V Mezentsev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Arthur T Kopylov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Evgeniy O Yablokov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Andrey V Svirid
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Aliaksandr Ya Lushchyk
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Leonid A Kaluzhskiy
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Andrei A Gilep
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Sergey A Usanov
- Laboratory of Molecular Diagnostics and Biotechnology, Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 5, bld. 2 V.F. Kuprevich str., 220141 Minsk, Belarus.
| | - Alexey E Medvedev
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
| | - Alexis S Ivanov
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya str., 119121 Moscow, Russia.
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2
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhskiy LA, Florinskaya AV, Gnedenko OV, Zgoda VG, Vakhrushev IV, Raeva OS, Yarygin KN, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of Protein Partners for Proteins Encoded by Genes of Human Chromosome 18 in HepG2 Cell Lysate. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Pleshakova TO, Kaysheva AL, Shumov ID, Ziborov VS, Bayzyanova JM, Konev VA, Uchaikin VF, Archakov AI, Ivanov YD. Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips. MICROMACHINES 2019; 10:E129. [PMID: 30781415 PMCID: PMC6413090 DOI: 10.3390/mi10020129] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/24/2022]
Abstract
In the present study, we demonstrate atomic force microscopy (AFM)-based detection of hepatitis C virus (HCV) particles in serum samples using a chip with aptamer-functionalized surface (apta-based AFM chip). The target particles, containing core antigen of HCV (HCVcoreAg protein), were biospecifically captured onto the chip surface from 1 mL of test solution containing 10 µL of serum collected from a hepatitis C patient. The registration of aptamer/antigen complexes on the chip surface was performed by AFM. The aptamers used in the present study were initially developed for therapeutic purposes; herein, these aptamers have been successfully utilized as probe molecules for HCVcoreAg detection in the presence of a complex protein matrix (human serum). The results obtained herein can be used for the development of detection systems that employ affine enrichment for protein detection.
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Affiliation(s)
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia.
| | - Jana M Bayzyanova
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vladimir A Konev
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vasiliy F Uchaikin
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
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4
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Florinskaya A, Ershov P, Mezentsev Y, Kaluzhskiy L, Yablokov E, Medvedev A, Ivanov A. SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1616. [PMID: 29783662 PMCID: PMC5982148 DOI: 10.3390/s18051616] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/08/2023]
Abstract
We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.
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Affiliation(s)
| | - Pavel Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia.
| | - Yuri Mezentsev
- Institute of Biomedical Chemistry, 119121 Moscow, Russia.
| | | | | | | | - Alexis Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia.
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5
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Yantsevich AV, Dzichenka YV, Ivanchik AV, Shapiro MA, Trawkina M, Shkel TV, Gilep AA, Sergeev GV, Usanov SA. [Proteomic analysis of contaminants in recombinant membrane hemeproteins expressed in E. coli and isolated by metal affinity chromatography]. APPL BIOCHEM MICRO+ 2018; 53:173-87. [PMID: 29508978 DOI: 10.1134/s000368381702017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Contaminating proteins have been identified by “shotgun” proteomic analysis in 14 recombinant preparations of human membrane heme- and flavoproteins expressed in Escherichia coli and purified by immobilized metal ion affinity chromatography. Immobilized metal ion affinity chromatography of ten proteins was performed on Ni2+-NTA-sepharose 6B, and the remaining four proteins were purified by ligand affinity chromatography on 2',5'-ADP-sepharose 4B. Proteomic analysis allowed to detect 50 protein impurities from E. coli. The most common contaminant was Elongation factor Tu2. It is characterized by a large dipole moment and a cluster arrangement of acidic amino acid residues that mediate the specific interaction with the sorbent. Peptidyl prolyl-cis-trans isomerase SlyD, glutamine-fructose-6-phosphate aminotransferase, and catalase HPII that contained repeating HxH, QxQ, and RxR fragments capable of specific interaction with the sorbent were identified among the protein contaminants as well. GroL/GroS chaperonins were probably copurified due to the formation of complexes with the target proteins. The Ni2+ cations leakage from the sorbent during lead to formation of free carboxyl groups that is the reason of cation exchanger properties of the sorbent. This was the putative reason for the copurification of basic proteins, such as the ribosomal proteins of E. coli and the widely occurring uncharacterized protein YqjD. The results of the analysis revealed variation in the contaminant composition related to the type of protein expressed. This is probably related to the reaction of E. coli cell proteome to the expression of a foreign protein. We concluded that the nature of the protein contaminants in a preparation of a recombinant protein purified by immobilized metal ion affinity chromatography on a certain sorbent could be predicted if information on the host cell proteome were available.
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Mikurova AV, Novikova SE, Skvortsov VS, Alekseychuk NN, Rybina AV, Miroshnichenko YV. [The sequence coverage in different methods of mass spectrometry data analysis obtained on model proteins]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:397-404. [PMID: 29080871 DOI: 10.18097/pbmc20176305397] [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
The aim of this study was to evaluate sequence coverage of five model proteins (CYB5A, SMAD4, RAB27B, FECH, and CXXC1) by means of shotgun proteomic data analysis employing different methods of data treatment including database-dependent search engines (MASCOT and X!Tandem) and de novo sequencing software ((PEAKS, Novor, and PepNovo+). In order to achieve maximal results, multiprotease hydrolysis including enzymes trypsin, LYS-C, ASPN and GluC was performed in solution and using the FASP method. High resolution mass spectrometry was carried out with a Q EXACTIVE HF hybrid mass spectrometer in the positive ionization mode; parent ions with the highest intensity and a charge range from +2 to +6 were fragmented in the HCD mode. 27 experiments were carried out (hydrolysis with each of 5 enzymes in solution, 4 for the FASP protocol, three technical repeats). Using parameters limiting false identification of peptides, the search engines and de novo sequencing software gave similar results. The degree of sequence coverage was not at least 40%, and in the best cases it reached 80-90%. The use of de novo sequencing software resulted in identification of the Y12H amino acid substitution in one model protein (CYB5A).
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Affiliation(s)
- A V Mikurova
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - A V Rybina
- Institute of Biomedical Chemistry, Moscow, Russia
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7
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Pleshakova TO, Kaysheva AL, Bayzyanova JМ, Anashkina АS, Uchaikin VF, Ziborov VS, Konev VA, Archakov AI, Ivanov YD. The detection of hepatitis c virus core antigen using afm chips with immobolized aptamers. J Virol Methods 2017; 251:99-105. [PMID: 29042217 DOI: 10.1016/j.jviromet.2017.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/09/2017] [Accepted: 10/14/2017] [Indexed: 10/18/2022]
Abstract
In the present study, the possibility of hepatitis C virus core antigen (HCVcoreAg) detection in buffer solution, using atomic force microscope chip (AFM-chip) with immobilized aptamers, has been demonstrated. The target protein was detected in 1mL of solution at concentrations from 10-10М to 10-13М. The registration of aptamer/antigen complexes on the chip surface was carried out by atomic force microscopy (AFM). The further mass-spectrometric (MS) identification of AFM-registered objects on the chip surface allowed reliable identification of HCVcoreAg target protein in the complexes. Aptamers, which were designed for therapeutic purposes, have been shown to be effective in HCVcoreAg detection as probe molecules.
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Affiliation(s)
- T O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - A L Kaysheva
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia.
| | - J М Bayzyanova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - А S Anashkina
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V F Uchaikin
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V S Ziborov
- Joint Institute for High Temperatures RAS, Izhorskaya St. 13/19, Moscow, 125412, Russia
| | - V A Konev
- Pirogov Russian National Research Medical University (RNRMU), Ostrovitianov str. 1, Moscow, 117997, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - Y D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
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8
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Echterbille J, Gilles N, Araóz R, Mourier G, Amar M, Servent D, De Pauw E, Quinton L. Discovery and characterization of EII B, a new α-conotoxin from Conus ermineus venom by nAChRs affinity capture monitored by MALDI-TOF/TOF mass spectrometry. Toxicon 2017; 130:1-10. [PMID: 28238803 DOI: 10.1016/j.toxicon.2017.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 12/13/2022]
Abstract
Animal toxins are peptides that often bind with remarkable affinity and selectivity to membrane receptors such as nicotinic acetylcholine receptors (nAChRs). The latter are, for example, targeted by α-conotoxins, a family of peptide toxins produced by venomous cone snails. nAChRs are implicated in numerous physiological processes explaining why the design of new pharmacological tools and the discovery of potential innovative drugs targeting these receptor channels appear so important. This work describes a methodology developed to discover new ligands of nAChRs from complex mixtures of peptides. The methodology was set up by the incubation of Torpedo marmorata electrocyte membranes rich in nAChRs with BSA tryptic digests (>100 peptides) doped by small amounts of known nAChRs ligands (α-conotoxins). Peptides that bind to the receptors were purified and analyzed by MALDI-TOF/TOF mass spectrometry which revealed an enrichment of α-conotoxins in membrane-containing fractions. This result exhibits the binding of α-conotoxins to nAChRs. Negative controls were performed to demonstrate the specificity of the binding. The usefulness and the power of the methodology were also investigated for a discovery issue. The workflow was then applied to the screening of Conus ermineus crude venom, aiming at characterizing new nAChRs ligands from this venom, which has not been extensively investigated to date. The methodology validated our experiments by allowing us to bind two α-conotoxins (α-EI and α-EIIA) which have already been described as nAChRs ligands. Moreover, a new conotoxin, never described to date, was also captured, identified and sequenced from this venom. Classical pharmacology tests by radioligand binding using a synthetic homologue of the toxin confirm the activity of the new peptide, called α-EIIB. The Ki value of this peptide for Torpedo nicotinic receptors was measured at 2.2 ± 0.7 nM.
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Affiliation(s)
- Julien Echterbille
- Laboratory of Mass Spectrometry- MolSys, Department of Chemistry, University of Liege, Liege, Belgium
| | - Nicolas Gilles
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Romulo Araóz
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Gilles Mourier
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Muriel Amar
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Denis Servent
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), IBITECS, CEA, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry- MolSys, Department of Chemistry, University of Liege, Liege, Belgium
| | - Loic Quinton
- Laboratory of Mass Spectrometry- MolSys, Department of Chemistry, University of Liege, Liege, Belgium.
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9
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Ershov P, Yablokov E, Mezentsev Y, Kalushskiy L, Florinskaya A, Veselovsky A, Gnedenko O, Gilep A, Usanov S, Medvedev A, Ivanov A. The effect of isatin on protein-protein interactions between cytochrome b5 and cytochromes P450. ACTA ACUST UNITED AC 2017; 63:170-175. [DOI: 10.18097/pbmc20176302170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cytochromes P450 (CYP) are involved in numerous biochemical processes including metabolism of xenobiotics, biosynthesis of cholesterol, steroid hormones etc. Since some CYP catalyze indol oxidation to isatin, we have hypothesized that isatin can regulate protein-protein interactions (PPI) between components of the CYP system thus representing a (negative?) feedback mechanism. The aim of this study was to investigate a possible effect of isatin on interaction of human CYP with cytochrome b5 (CYB5A). Using the optical biosensor test system employing surface plasmon resonance (SPR) we have investigated interaction of immobilized CYB5A with various CYP in the absence and in the presence of isatin. The SPR-based experiments have shown that a high concentration of isatin (270 mM) increases Kd values for complexes CYB5A/CYP3А5 and CYB5A/CYP3A4 (twofold and threefold, respectively), but has no influence on complex formation between CYB5A and other CYP (including indol-metabolizing CYP2C19 and CYP2E1). Isatin injection to the optical biosensor chip with the preformed molecular complex CYB5A/CYP3A4 caused a 30%-increase in its dissociation rate. Molecular docking manipulations have shown that isatin can influence interaction of CYP3А5 or CYP3A4 with CYB5A acting at the contact region of CYB5A/CYP.
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Affiliation(s)
- P.V. Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | | | | | | | - A.A. Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - S.A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - A.S. Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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10
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Michalek P, Dostalova S, Buchtelova H, Cernei N, Krejcova L, Hynek D, Milosavljevic V, Jimenez AMJ, Kopel P, Heger Z, Adam V. A two-step protocol for isolation of influenza A (H7N7) virions and their RNA for PCR diagnostics based on modified paramagnetic particles. Electrophoresis 2016; 37:2025-35. [PMID: 27130152 DOI: 10.1002/elps.201600044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 01/18/2023]
Abstract
Annual epidemics of influenza cause death of hundreds of thousands people and they also have a significant economic impact. Hence, a need for fast and cheap influenza diagnostic method is arising. The conventional methods for an isolation of the viruses are time-consuming and require expensive instrumentation as well as trained personnel. In this study, we modified the surface of nanomaghemite (γ-Fe2 O3 ) paramagnetic core with tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane and the resulting particles were utilized for the isolation of H7N7 influenza virions. Consequently, we designed γ-Fe2 O3 paramagnetic core modified with calcium tripolyphosphate which was employed for the isolation of viral nucleic acid after virion's lysis. Both of these procedures can be performed rapidly in less than 10 min and, in combination with the RT-PCR, the whole influenza detection can be shortened to few hours. Moreover, the whole protocol could be easily automated and/or miniaturized, and thus can serve as a basis for use in a lab-on-a-chip device. We assume that magnetic isolation is an exceptional procedure which can significantly accelerate the diagnostic possibilities of a broad spectrum of diseases.
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Affiliation(s)
- Petr Michalek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Simona Dostalova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Hana Buchtelova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
| | - Natalia Cernei
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ludmila Krejcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - David Hynek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vedran Milosavljevic
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ana Maria Jimenez Jimenez
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Pavel Kopel
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic.,Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
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11
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Ivanov AS, Ershov PV, Molnar AA, Mezentsev YV, Kaluzhskiy LA, Yablokov EO, Florinskaya AV, Gnedenko OV, Medvedev AE, Kozin SA, Mitkevich VA, Makarov AA, Gilep AA, Luschik AY, Gaidukevich IV, Usanov SA. Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Ivanov AS, Medvedev AE. [Optical surface plasmon resonance biosensors in molecular fishing]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:231-8. [PMID: 25978389 DOI: 10.18097/pbmc20156102231] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An optical biosensor employing surface plasmon resonance is a highly efficient instrument applicable for direct real time registration of molecular interactions without additional use of any labels or coupled processes. As an independent approach it is especially effective in analysis of various ligand receptor interactions. SPR-biosensors are used for validation of studies on intermolecular interactions in complex biological systems (affinity profiling of various groups of proteins, etc.). Recently, potential application of the SPR-biosensor for molecular fishing (direct affinity binding of target molecules from complex biological mixtures on the optical biosensor surface followed by their elution for identification by LC-MS/MS) has been demonstrated. Using SPR-biosensors in such studies it is possible to solve the following tasks: (a) SPR-based selection of immobilization conditions required for the most effective affinity separation of a particular biological sample; (b) SPR-based molecular fishing for subsequent protein identification by mass spectrometry; (c) SPR-based validation of the interaction of identified proteins with immobilized ligand. This review considers practical application of the SPR technology in the context of recent studies performed in the Institute of Biomedical Chemistry on molecular fishing of real biological objects.
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Affiliation(s)
- A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia; Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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Feng S, Zhou L, Huang C, Xie K, Nice EC. Interactomics: toward protein function and regulation. Expert Rev Proteomics 2015; 12:37-60. [DOI: 10.1586/14789450.2015.1000870] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Ivanov AS, Medvedev A, Ershov P, Molnar A, Mezentsev Y, Yablokov E, Kaluzhsky L, Gnedenko O, Buneeva O, Haidukevich I, Sergeev G, Lushchyk A, Yantsevich A, Medvedeva M, Kozin S, Popov I, Novikova S, Zgoda V, Gilep A, Usanov S, Lisitsa A, Archakov A. Protein interactomics based on direct molecular fishing on paramagnetic particles: practical realization and further SPR validation. Proteomics 2014; 14:2261-74. [PMID: 25044858 DOI: 10.1002/pmic.201400117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/27/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
There is increasing evidence that proteins function in the cell as integrated stable or temporally formed protein complexes, interactomes. Previously, using model systems we demonstrated applicability of direct molecular fishing on paramagnetic particles for protein interactomics (Ershov et al. Proteomics, 2012, 12, 3295). In the present study, we have used a combination of affinity-based molecular fishing and subsequent MS for investigation of human liver proteins involved in interactions with immobilized microsomal cytochrome b5 (CYB5A), and also transthyretin and BSA as alternative affinity ligands (baits). The LC-MS/MS identification of prey proteins fished on these baits revealed three sets of proteins: 98, 120, and 220, respectively. Comparison analysis of these sets revealed only three proteins common for all the baits. In the case of paired analysis, the number of common proteins varied from 2 to 9. The binding capacity of some identified proteins has been validated by a SPR-based biosensor. All the investigated proteins effectively interacted with the immobilized CYB5A (Kd values ranged from 0.07 to 1.1 μM). Results of this study suggest that direct molecular fishing is applicable for analysis of protein-protein interactions (PPI) under normal and pathological conditions, in which altered PPIs are especially important.
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Affiliation(s)
- Alexis S Ivanov
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
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15
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Hust M, Frenzel A, Schirrmann T, Dübel S. Selection of recombinant antibodies from antibody gene libraries. Methods Mol Biol 2014; 1101:305-20. [PMID: 24233787 DOI: 10.1007/978-1-62703-721-1_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Antibodies are indispensable detection reagents for research and diagnostics and represent the biggest class of biological therapeutics on the market. In vitro antibody selection systems offer many advantages over animal-based technologies because the whole selection process is independent of the in vivo immune response. In the last two decades antibody phage display has evolved to the most robust and widely used method and has already yielded thousands of antibodies. The selection of binders by phage display is also referred to as "panning" and based on the specific molecular interaction of antibody phage with an immobilized antigen thus allowing the enrichment and isolation of antigen-specific monoclonal binders from very large antibody gene libraries. Here, we give detailed protocols for the selection of recombinant antibody fragments from antibody gene libraries in microtiter plates.
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Affiliation(s)
- Michael Hust
- Abteilung Biotechnologie, Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Braunschweig, Germany
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16
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de Moraes MC, Vanzolini KL, Cardoso CL, Cass QB. New trends in LC protein ligand screening. J Pharm Biomed Anal 2014; 87:155-66. [DOI: 10.1016/j.jpba.2013.07.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
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