1
|
Buneeva O, Kopylov A, Gnedenko O, Medvedeva M, Veselovsky A, Ivanov A, Zgoda V, Medvedev A. Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1? Int J Mol Sci 2023; 24:ijms24087634. [PMID: 37108803 PMCID: PMC10143413 DOI: 10.3390/ijms24087634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Affinity-based proteomic profiling is widely used for the identification of proteins involved in the formation of various interactomes. Since protein-protein interactions (PPIs) reflect the role of particular proteins in the cell, identification of interaction partners for a protein of interest can reveal its function. The latter is especially important for the characterization of multifunctional proteins, which can play different roles in the cell. Pyruvate kinase (PK), a classical glycolytic enzyme catalyzing the last step of glycolysis, exists in four isoforms: PKM1, PKM2, PKL, and PKR. The enzyme isoform expressed in actively dividing cells, PKM2, exhibits many moonlighting (noncanonical) functions. In contrast to PKM2, PKM1, predominantly expressed in adult differentiated tissues, lacks well-documented moonlighting functions. However, certain evidence exists that it can also perform some functions unrelated to glycolysis. In order to evaluate protein partners, bound to PKM1, in this study we have combined affinity-based separation of mouse brain proteins with mass spectrometry identification. The highly purified PKM1 and a 32-mer synthetic peptide (PK peptide), sharing high sequence homology with the interface contact region of all PK isoforms, were used as the affinity ligands. This proteomic profiling resulted in the identification of specific and common proteins bound to both affinity ligands. Quantitative affinity binding to the affinity ligands of selected identified proteins was validated using a surface plasmon resonance (SPR) biosensor. Bioinformatic analysis has shown that the identified proteins, bound to both full-length PKM1 and the PK peptide, form a protein network (interactome). Some of these interactions are relevant for the moonlighting functions of PKM1. The proteomic dataset is available via ProteomeXchange with the identifier PXD041321.
Collapse
Affiliation(s)
- Olga Buneeva
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Arthur Kopylov
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Oksana Gnedenko
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Marina Medvedeva
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russia
| | - Alexander Veselovsky
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Alexei Medvedev
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| |
Collapse
|
2
|
Murai Y, Hashimoto M. Heteroaromatic Diazirines Are Essential Building Blocks for Material and Medicinal Chemistry. Molecules 2023; 28:molecules28031408. [PMID: 36771073 PMCID: PMC9921084 DOI: 10.3390/molecules28031408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In materials (polymer) science and medicinal chemistry, heteroaromatic derivatives play the role of the central skeleton in development of novel devices and discovery of new drugs. On the other hand, (3-trifluoromethyl)phenyldiazirine (TPD) is a crucial chemical method for understanding biological processes such as ligand-receptor, nucleic acid-protein, lipid-protein, and protein-protein interactions. In particular, use of TPD has increased in recent materials science to create novel electric and polymer devices with comparative ease and reduced costs. Therefore, a combination of heteroaromatics and (3-trifluoromethyl)diazirine is a promising option for creating better materials and elucidating the unknown mechanisms of action of bioactive heteroaromatic compounds. In this review, a comprehensive synthesis of (3-trifluoromethyl)diazirine-substituted heteroaromatics is described.
Collapse
Affiliation(s)
- Yuta Murai
- Graduate School of Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
| |
Collapse
|
3
|
Lu KY, Mansfield CR, Fitzgerald MC, Derbyshire ER. Chemoproteomics for Plasmodium Parasite Drug Target Discovery. Chembiochem 2021; 22:2591-2599. [PMID: 33999499 PMCID: PMC8373781 DOI: 10.1002/cbic.202100155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/16/2021] [Indexed: 12/16/2022]
Abstract
Emerging Plasmodium parasite drug resistance is threatening progress towards malaria control and elimination. While recent efforts in cell-based, high-throughput drug screening have produced first-in-class drugs with promising activities against different Plasmodium life cycle stages, most of these antimalarial agents have elusive mechanisms of action. Though challenging to address, target identification can provide valuable information to facilitate lead optimization and preclinical drug prioritization. Recently, proteome-wide methods for direct assessment of drug-protein interactions have emerged as powerful tools in a number of systems, including Plasmodium. In this review, we will discuss current chemoproteomic strategies that have been adapted to antimalarial drug target discovery, including affinity- and activity-based protein profiling and the energetics-based techniques thermal proteome profiling and stability of proteins from rates of oxidation. The successful application of chemoproteomics to the Plasmodium blood stage highlights the potential of these methods to link inhibitors to their molecular targets in more elusive Plasmodium life stages and intracellular pathogens in the future.
Collapse
Affiliation(s)
- Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Christopher R Mansfield
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R Derbyshire
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| |
Collapse
|
4
|
Poverennaya EV, Kiseleva OI, Ivanov AS, Ponomarenko EA. Methods of Computational Interactomics for Investigating Interactions of Human Proteoforms. BIOCHEMISTRY (MOSCOW) 2020; 85:68-79. [PMID: 32079518 DOI: 10.1134/s000629792001006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human genome contains ca. 20,000 protein-coding genes that could be translated into millions of unique protein species (proteoforms). Proteoforms coded by a single gene often have different functions, which implies different protein partners. By interacting with each other, proteoforms create a network reflecting the dynamics of cellular processes in an organism. Perturbations of protein-protein interactions change the network topology, which often triggers pathological processes. Studying proteoforms is a relatively new research area in proteomics, and this is why there are comparatively few experimental studies on the interaction of proteoforms. Bioinformatics tools can facilitate such studies by providing valuable complementary information to the experimental data and, in particular, expanding the possibilities of the studies of proteoform interactions.
Collapse
Affiliation(s)
| | - O I Kiseleva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | | |
Collapse
|
5
|
Wilkinson IVL, Perkins KJ, Dugdale H, Moir L, Vuorinen A, Chatzopoulou M, Squire SE, Monecke S, Lomow A, Geese M, Charles PD, Burch P, Tinsley JM, Wynne GM, Davies SG, Wilson FX, Rastinejad F, Mohammed S, Davies KE, Russell AJ. Chemical Proteomics and Phenotypic Profiling Identifies the Aryl Hydrocarbon Receptor as a Molecular Target of the Utrophin Modulator Ezutromid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel V. L. Wilkinson
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Kelly J. Perkins
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene Function South Parks Road Oxford OX1 3PT UK
| | - Hannah Dugdale
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene Function South Parks Road Oxford OX1 3PT UK
| | - Lee Moir
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene Function South Parks Road Oxford OX1 3PT UK
| | - Aini Vuorinen
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Maria Chatzopoulou
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Sarah E. Squire
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene Function South Parks Road Oxford OX1 3PT UK
| | - Sebastian Monecke
- Evotec International GmbHManfred Eigen Campus Essener Bogen 7 22419 Hamburg Germany
| | - Alexander Lomow
- Evotec International GmbHManfred Eigen Campus Essener Bogen 7 22419 Hamburg Germany
| | - Marcus Geese
- Evotec International GmbHManfred Eigen Campus Essener Bogen 7 22419 Hamburg Germany
| | - Philip D. Charles
- Department of BiochemistryUniversity of Oxford South Parks Rd Oxford OX1 3QU UK
- Target Discovery InstituteUniversity of OxfordOld Road Campus Roosevelt Drive Oxford OX3 7FZ UK
| | - Peter Burch
- Summit Therapeutics plc. 136a Eastern Avenue, Milton Park Abingdon Oxfordshire OX14 4SB UK
| | - Jonathan M. Tinsley
- Summit Therapeutics plc. 136a Eastern Avenue, Milton Park Abingdon Oxfordshire OX14 4SB UK
| | - Graham M. Wynne
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Stephen G. Davies
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
| | - Francis X. Wilson
- Summit Therapeutics plc. 136a Eastern Avenue, Milton Park Abingdon Oxfordshire OX14 4SB UK
| | - Fraydoon Rastinejad
- Target Discovery InstituteUniversity of OxfordOld Road Campus Roosevelt Drive Oxford OX3 7FZ UK
| | - Shabaz Mohammed
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Department of BiochemistryUniversity of Oxford South Parks Rd Oxford OX1 3QU UK
| | - Kay E. Davies
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene Function South Parks Road Oxford OX1 3PT UK
| | - Angela J. Russell
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory Mansfield Road Oxford OX1 3TA UK
- Department of PharmacologyUniversity of Oxford Mansfield Road Oxford OX1 3PQ UK
| |
Collapse
|
6
|
Wilkinson IVL, Perkins KJ, Dugdale H, Moir L, Vuorinen A, Chatzopoulou M, Squire SE, Monecke S, Lomow A, Geese M, Charles PD, Burch P, Tinsley JM, Wynne GM, Davies SG, Wilson FX, Rastinejad F, Mohammed S, Davies KE, Russell AJ. Chemical Proteomics and Phenotypic Profiling Identifies the Aryl Hydrocarbon Receptor as a Molecular Target of the Utrophin Modulator Ezutromid. Angew Chem Int Ed Engl 2020; 59:2420-2428. [PMID: 31755636 PMCID: PMC7003794 DOI: 10.1002/anie.201912392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/13/2019] [Indexed: 12/20/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disease arising from mutations in the dystrophin gene. Upregulation of utrophin to compensate for the missing dystrophin offers a potential therapy independent of patient genotype. The first-in-class utrophin modulator ezutromid/SMT C1100 was developed from a phenotypic screen through to a Phase 2 clinical trial. Promising efficacy and evidence of target engagement was observed in DMD patients after 24 weeks of treatment, however trial endpoints were not met after 48 weeks. The objective of this study was to understand the mechanism of action of ezutromid which could explain the lack of sustained efficacy and help development of new generations of utrophin modulators. Using chemical proteomics and phenotypic profiling we show that the aryl hydrocarbon receptor (AhR) is a target of ezutromid. Several lines of evidence demonstrate that ezutromid binds AhR with an apparent KD of 50 nm and behaves as an AhR antagonist. Furthermore, other reported AhR antagonists also upregulate utrophin, showing that this pathway, which is currently being explored in other clinical applications including oncology and rheumatoid arthritis, could also be exploited in future DMD therapies.
Collapse
Affiliation(s)
- Isabel V. L. Wilkinson
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Kelly J. Perkins
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene FunctionSouth Parks RoadOxfordOX1 3PTUK
| | - Hannah Dugdale
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene FunctionSouth Parks RoadOxfordOX1 3PTUK
| | - Lee Moir
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene FunctionSouth Parks RoadOxfordOX1 3PTUK
| | - Aini Vuorinen
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Maria Chatzopoulou
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Sarah E. Squire
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene FunctionSouth Parks RoadOxfordOX1 3PTUK
| | - Sebastian Monecke
- Evotec International GmbHManfred Eigen CampusEssener Bogen 722419HamburgGermany
| | - Alexander Lomow
- Evotec International GmbHManfred Eigen CampusEssener Bogen 722419HamburgGermany
| | - Marcus Geese
- Evotec International GmbHManfred Eigen CampusEssener Bogen 722419HamburgGermany
| | - Philip D. Charles
- Department of BiochemistryUniversity of OxfordSouth Parks RdOxfordOX1 3QUUK
- Target Discovery InstituteUniversity of OxfordOld Road CampusRoosevelt DriveOxfordOX3 7FZUK
| | - Peter Burch
- Summit Therapeutics plc.136a Eastern Avenue, Milton ParkAbingdonOxfordshireOX14 4SBUK
| | - Jonathan M. Tinsley
- Summit Therapeutics plc.136a Eastern Avenue, Milton ParkAbingdonOxfordshireOX14 4SBUK
| | - Graham M. Wynne
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Stephen G. Davies
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Francis X. Wilson
- Summit Therapeutics plc.136a Eastern Avenue, Milton ParkAbingdonOxfordshireOX14 4SBUK
| | - Fraydoon Rastinejad
- Target Discovery InstituteUniversity of OxfordOld Road CampusRoosevelt DriveOxfordOX3 7FZUK
| | - Shabaz Mohammed
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Department of BiochemistryUniversity of OxfordSouth Parks RdOxfordOX1 3QUUK
| | - Kay E. Davies
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordSir Henry Wellcome Building of Gene FunctionSouth Parks RoadOxfordOX1 3PTUK
| | - Angela J. Russell
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
- Department of PharmacologyUniversity of OxfordMansfield RoadOxfordOX1 3PQUK
| |
Collapse
|
7
|
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]
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
Collapse
Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
| |
Collapse
|
10
|
Florinskaya AV, Ershov PV, Mezentsev YV, Kaluzhskiy LA, Yablokov EO, Buneeva OA, Zgoda VG, Medvedev AE, Ivanov AS. [The analysis of participation of individual proteins in the protein interactome formation]. BIOMEDITSINSKAIA KHIMIIA 2018; 64:169-174. [PMID: 29723146 DOI: 10.18097/pbmc20186402169] [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: 06/08/2023]
Abstract
It becomes increasingly clear that most proteins of living systems exist as components of various protein complexes rather than individual molecules. The use of various proteomic techniques significantly extended our knowledge not only about functioning of individual complexes but also formed a basis for systemic analysis of protein-protein interactions. In this study gel-filtration chromatography accompanied by mass-spectrometry was used for the interactome analysis of human liver proteins. In six fractions (with average molecular masses of 45 kDa, 60 kDa, 85 kDa, 150 kDa, 250 kDa, and 440 kDa) 797 proteins were identified. In dependence of their distribution profiles in the fractions, these proteins could be subdivided into four groups: (1) single monomeric proteins that are not involved in formation of stable protein complexes; (2) proteins existing as homodimers or heterodimers with comparable partners; (3) proteins that are partially exist as monomers and partially as components of protein complexes; (4) proteins that do not exist in the monomolecular state, but also exist within protein complexes containing three or more subunits. Application of this approach to known isatin-binding proteins resulted in identification of proteins involved in formation of the homo- and heterodimers and mixed protein complexes.
Collapse
Affiliation(s)
| | - P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
11
|
Zhang T, de Vries MP, Permentier HP, Bischoff R. Specific Affinity Enrichment of Electrochemically Cleaved Peptides Based on Cu(II)-Mediated Spirolactone Tagging. Anal Chem 2017; 89:7123-7129. [PMID: 28593756 PMCID: PMC5510089 DOI: 10.1021/acs.analchem.7b01039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/08/2017] [Indexed: 12/15/2022]
Abstract
Specific digestion of proteins is an essential step for mass spectrometry-based proteomics, and the chemical labeling of the resulting peptides is often used for peptide enrichment or the introduction of desirable tags. Electrochemical oxidation yielding specific cleavage C-terminal to tyrosine (Tyr) and tryptophan (Trp) residues provides a potential alternative to enzymatic digestion and a possibility for further chemical labeling by introducing reactive spirolactone moieties. However, spirolactone-containing peptides suffer from low stability due to hydrolysis and intramolecular side reactions. We found that Cu(II) ions stabilize the spirolactone and prevent intramolecular side reactions during chemical labeling, allowing efficient chemical tagging with a reduced excess of labeling reagent without intramolecular side reactions. On the basis of this reaction, we developed an analytical procedure combining electrochemical digestion, Cu(II)-mediated spirolactone biotinylation, and enrichment by avidin affinity chromatography with mass spectrometry. The method was optimized with the tripeptide LWL and subsequently applied to chicken egg white lysozyme, in which one biotinylated electrochemistry (EC)-cleaved peptide was identified after affinity enrichment. This proof-of-principle shows that specific enrichment of electrochemically cleaved spirolactone-containing peptides can be used for protein identification and notably that inclusion of Cu(II) ions is essential for stabilizing spirolactones for subsequent biotinylation.
Collapse
Affiliation(s)
- Tao Zhang
- Department
of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Marcel P. de Vries
- Department
of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University Medical Center Groningen, University of
Groningen, Hanzeplein
1, 9713 GZ, Groningen, The Netherlands
| | - Hjalmar P. Permentier
- Department
of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Rainer Bischoff
- Department
of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| |
Collapse
|
12
|
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]
|
13
|
Oliveira CR, Silva Cunha Tamashiro WM, Bueno SMA. Evaluation of OPS-agarose pseudo-affinity adsorption IgG 2a mouse monoclonal antibody. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Miroshnichenko IV, Petushkova NA, Moskaleva NE, Teryaeva NB, Zgoda VG, Ilgisonis EV, Belyaev AY. [The possibility of using PlasmaDeepDive™ MRM panel in clinical diagnostics]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:272-8. [PMID: 25978393 DOI: 10.18097/pbmc20156102272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Concentrations of 46 proteins have been determined in human blood plasma using PlasmaDeepDive™ MRM Panel ("Biognosys AG", Switzerland). 18 of them were included into the group of proteins with higher concentrations, also identified by the shotgun proteomic analysis. Based on literature data it is concluded that the PlasmaDeepDive™ MRM Panel is applicable for studies of human plasma samples for potential biomarkers of various nervous system disorders.
Collapse
Affiliation(s)
| | | | | | - N B Teryaeva
- Burdenko Institute of Neurosurgery, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - A Yu Belyaev
- Burdenko Institute of Neurosurgery, Moscow, Russia
| |
Collapse
|
16
|
Discovery and validation of an INflammatory PROtein-driven GAstric cancer Signature (INPROGAS) using antibody microarray-based oncoproteomics. Oncotarget 2015; 5:1942-54. [PMID: 24722433 PMCID: PMC4039123 DOI: 10.18632/oncotarget.1879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study aimed to improve gastric cancer (GC) diagnosis by identifying and validating an INflammatory PROtein-driven GAstric cancer Signature (hereafter INPROGAS) using low-cost affinity proteomics. The detection of 120 cytokines, 43 angiogenic factors, 41 growth factors, 40 inflammatory factors and 10 metalloproteinases was performed using commercially available human antibody microarray-based arrays. We identified 21 inflammation-related proteins (INPROGAS) with significant differences in expression between GC tissues and normal gastric mucosa in a discovery cohort of matched pairs (n=10) of tumor/normal gastric tissues. Ingenuity pathway analysis confirmed the "inflammatory response", "cellular movement" and "immune cell trafficking" as the most overrepresented biofunctions within INPROGAS. Using an expanded independent validation cohort (n = 22), INPROGAS classified gastric samples as "GC" or "non-GC" with a sensitivity of 82% (95% CI 59-94) and a specificity of 73% (95% CI 49-89). The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. Antibody microarray analyses of the GC-associated inflammatory proteome identified a 21-protein INPROGAS that accurately discriminated GC from noncancerous gastric mucosa.
Collapse
|
17
|
Buneeva OA, Gnedenko OV, Medvedeva MV, Ivanov AS, Medvedev AE. [The use of immobilized ubiquitin for biosensor analysis of the mitochondrial subinteractome]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 60:615-22. [PMID: 25552499 DOI: 10.18097/pbmc20146006615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Protein ubiquitination is considered as an important mechanism that is responsible not only for specific labeling of proteins for their subsequent degradation but also for localization of proteins in the cell and regulation of protein-protein interactions. In the context of protein-protein interactions binding of (mono/poly)ubiquitinated molecules to proteins containing specific ubiquitin binding domains appear to play the decisive role. Although formation of the ubiquitin interactome has been demonstrated for cytosol, involvement of mitochondria and associated extramitochondrial proteins into such interactions still requires detailed investigation. In this study using an optical biosensor we have demonstrated binding of proteins of mouse brain mitochondrial lysates to immobilized monomeric ubiquitin. Model purified proteins, which are known to be associated with the outer mitochondrial compartment (glyceraldehyde-3-phosphate dehydorgenase, creatine phosphokinase), interacted with immobilized ubiquitin as well as with each other. This suggests that (poly)ubiquitinated chains may be involved in protein-protein interactions between ubiquitinated and non-ubiquitinated proteins and thus may contribute to formation of (mitochondrial) ubiquitin subinteractome.
Collapse
Affiliation(s)
- O A Buneeva
- Orekhovich Institute of Biomedical Chemistry
| | | | - M V Medvedeva
- School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A S Ivanov
- Orekhovich Institute of Biomedical Chemistry
| | | |
Collapse
|
18
|
Buneeva OA, Gnedenko OV, Medvedeva MV, Ivanov AS, Medvedev AE. The use of immobilized ubiquitin for biosensor analysis of the mitochondrial subinteractome. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2014. [DOI: 10.1134/s1990750814030032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
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.
Collapse
Affiliation(s)
- Alexis S Ivanov
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
The emerging field of chemo- and pharmacoproteomics studies the mechanisms of action of bioactive molecules in a systems pharmacology context. In contrast to traditional drug discovery, pharmacoproteomics integrates the mechanism of a drug's action, its side effects including toxicity, and the discovery of new drug targets in a single approach. Thus, it determines early favorable (e.g. multiple kinase target in cancer drugs) and unfavorable (e.g. side effects) polypharmacology. Target profiling is accomplished using either active site-labeling probes or immobilized drugs. This strategy identifies direct targets and has in fact enabled even the determination of binding curves and half maximum inhibitory concentrations of these targets. In addition, the enrichment greatly reduces the complexity of the proteome to be analyzed by quantitative MS. Complementary to these approaches, global proteomics profiling studying drug treatement-induced changes in protein expression levels and/or post-translational modification status have started to become possible mostly due to significant improvements in instrumentation. Particularly, when using multidimensional separations, a considerable proteome depth of up to 10 000 proteins can be achieved with current state-of-the-art mass spectrometers and bioinformatics tools. In summary, chemo- and pharmacoproteomics has already contributed significantly to the identification of novel drug targets and their mechanisms of action(s). Aided by further technological advancements, this interdisciplinary approach will likely be used more broadly in the future.
Collapse
Affiliation(s)
- Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
| |
Collapse
|
21
|
Medvedev AE. In macropore tryptic digestion at acidic pH and its implication for proteomics. Proteomics 2013; 13:3101-2. [PMID: 24133050 DOI: 10.1002/pmic.201300440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/04/2013] [Indexed: 11/09/2022]
Abstract
Gan et al. (Proteomics 2013, 13, 3117-3123) described a new "macropore" protocol for effective protein digestion by trypsin suitable for a wide range of pH including acidic pH. It was effective not only in experiments with solutions of a model protein (myoglobin), but also with a subfraction of rat liver cytosol. This significantly simplifies and accelerates protein digestion procedures for subsequent MS. However, further studies are needed to find limits of experimental applicability of the described protocol in proteomics.
Collapse
Affiliation(s)
- Alexei E Medvedev
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia
| |
Collapse
|
22
|
Tomohiro T, Inoguchi H, Masuda S, Hatanaka Y. Affinity-based fluorogenic labeling of ATP-binding proteins with sequential photoactivatable cross-linkers. Bioorg Med Chem Lett 2013; 23:5605-8. [PMID: 23999042 DOI: 10.1016/j.bmcl.2013.08.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/22/2013] [Accepted: 08/08/2013] [Indexed: 01/02/2023]
Abstract
A specific illumination approach has been developed for identification of adenosine triphosphate (ATP)-binding proteins. This strategy utilizes a tandem photoactivatable unit that consists of a diazirine group as a carbene precursor and an o-hydroxycinnamate moiety as a coumarin precursor. The photolysis of diazirine induces a specific cross-link on target proteins and is followed by photoactivation of coumarin generation with a concomitant release of the pre-installed affinity ligand. The ATP, installed with this cross-linker at the γ-position, successfully transferred a coumarin onto ATP-binding proteins using only UV-irradiation.
Collapse
Affiliation(s)
- Takenori Tomohiro
- Laboratory of Biorecognition Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | | | | | | |
Collapse
|
23
|
Černý M, Skalák J, Cerna H, Brzobohatý B. Advances in purification and separation of posttranslationally modified proteins. J Proteomics 2013; 92:2-27. [PMID: 23777897 DOI: 10.1016/j.jprot.2013.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 11/25/2022]
Abstract
Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene - transcript - protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
Collapse
Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Mendel University in Brno & CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
| | | | | | | |
Collapse
|
24
|
Combinatorial peptide libraries to overcome the classical affinity-enrichment methods in proteomics. Amino Acids 2013; 45:219-29. [DOI: 10.1007/s00726-013-1505-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 12/11/2022]
|
25
|
Zgoda VG, Kopylov AT, Tikhonova OV, Moisa AA, Pyndyk NV, Farafonova TE, Novikova SE, Lisitsa AV, Ponomarenko EA, Poverennaya EV, Radko SP, Khmeleva SA, Kurbatov LK, Filimonov AD, Bogolyubova NA, Ilgisonis EV, Chernobrovkin AL, Ivanov AS, Medvedev AE, Mezentsev YV, Moshkovskii SA, Naryzhny SN, Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Govorun VM, Archakov AI. Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells. J Proteome Res 2012; 12:123-34. [PMID: 23256950 DOI: 10.1021/pr300821n] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10(-18) M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2 cells. On the basis of the results of the survey, the SRM assays were drafted for 250 proteins: 41 proteins were found only in the liver tissue, 82 proteins were specifically detected in depleted plasma, and 127 proteins were mapped in both samples. The targeted analysis of HepG2 cells was carried out for 49 proteins; 41 of them were successfully registered using ordinary SRM and 5 additional proteins were registered using a combination of irreversible binding of proteins on CN-Br Sepharose 4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq and RT-PCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome analysis was performed for cytochrome b5 using analytical and preparative optical biosensor fishing followed by MS analysis of the fished proteins. All of the data on the proteome complement of the Chr 18 have been integrated into our gene-centric knowledgebase ( www.kb18.ru ).
Collapse
Affiliation(s)
- Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Russia
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Buneeva OA, Kopylov AT, Tikhonova OV, Zgoda VG, Medvedev AE, Archakov AI. Effect of affinity Sorbent on proteomic profiling of isatin-binding proteins of mouse brain. BIOCHEMISTRY (MOSCOW) 2012; 77:1326-38. [DOI: 10.1134/s0006297912110120] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
27
|
Use of biotinylated ubiquitin for analysis of rat brain mitochondrial proteome and interactome. Int J Mol Sci 2012; 13:11593-11609. [PMID: 23109873 PMCID: PMC3472765 DOI: 10.3390/ijms130911593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/22/2012] [Accepted: 09/03/2012] [Indexed: 11/16/2022] Open
Abstract
Applicability of in vitro biotinylated ubiquitin for evaluation of endogenous ubiquitin conjugation and analysis of ubiquitin-associated protein-protein interactions has been investigated. Incubation of rat brain mitochondria with biotinylated ubiquitin followed by affinity chromatography on avidin-agarose, intensive washing, tryptic digestion of proteins bound to the affinity sorbent and their mass spectrometry analysis resulted in reliable identification of 50 proteins belonging to mitochondrial and extramitochondrial compartments. Since all these proteins were bound to avidin-agarose only after preincubation of the mitochondrial fraction with biotinylated ubiquitin, they could therefore be referred to as specifically bound proteins. A search for specific ubiquitination signature masses revealed several extramitochondrial and intramitochondrial ubiquitinated proteins representing about 20% of total number of proteins bound to avidin-agarose. The interactome analysis suggests that the identified non-ubiquitinated proteins obviously form tight complexes either with ubiquitinated proteins or with their partners and/or mitochondrial membrane components. Results of the present study demonstrate that the use of biotinylated ubiquitin may be considered as the method of choice for in vitro evaluation of endogenous ubiquitin-conjugating machinery in particular subcellular organelles and changes in ubiquitin/organelle associated interactomes. This may be useful for evaluation of changes in interactomes induced by protein ubiquitination under norm and various brain pathologies.
Collapse
|
28
|
Fedchenko V, Buneeva O, Kopylov A, Kaloshin A, Axenova L, Zgoda V, Medvedev A. Mass spectrometry detection of monomeric renalase in human urine. ACTA ACUST UNITED AC 2012; 58:599-607. [DOI: 10.18097/pbmc20125805599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Renalase is a recently discovered secretory protein, which is suggested to play a role (which still remains elusive) in regulation of blood pressure. Earlier it was purified from urine of healthy volunteers by means of ammonium sulfate fractionation and subsequent affinity chromatography (Xu et al. (2005) J. Clin. Invest., 115, 1275). The resultant purified preparation of renalase contained 2 proteins with molecular masses of 35 and 67-75 kDa. The authors believed that the latter represents a dimerization (aggregation) product of the 35 kDa protein. In this study we have detected relanase in urinary samples of 2 of 6 volunteers only after immunoaffinity enrichment of urinary samples subjected to ammonium sulfate precipitation. Electrophoresis of the purified preparation also demonstrated the presence of 2 proteins with molecular masses of 35 and 66 kDa, respectively. Mass spectrometry analysis of these proteins identified 35 and 66 kDa proteins as renalase and serum albumin, respectively. Thus, our results do not support suggestion on formation of renalase dimers and they indicate that urinary renalase excretion significantly varies in humans.
Collapse
Affiliation(s)
- V.I. Fedchenko
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - O.A. Buneeva
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.T. Kopylov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.A. Kaloshin
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - L.N. Axenova
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - V.G. Zgoda
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| | - A.E. Medvedev
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences
| |
Collapse
|