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Kozin SA. Role of Interaction between Zinc and Amyloid Beta in Pathogenesis of Alzheimer’s Disease. BIOCHEMISTRY (MOSCOW) 2023; 88:S75-S87. [PMID: 37069115 DOI: 10.1134/s0006297923140055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Progression of Alzheimer's disease is accompanied by the appearance of extracellular deposits in the brain tissues of patients with characteristic supramolecular morphology (amyloid plaques) the main components of which are β-amyloid isoforms (Aβ) and biometal ions (zinc, copper, iron). For nearly 40 years and up to the present time, the vast majority of experimental data indicate critical role of formation and accumulation of amyloid plaques (cerebral amyloidogenesis) in pathogenesis of Alzheimer's disease, however, nature of the molecular agents that initiate cerebral amyloidogenesis, as well as causes of aggregation of the native Aβ molecules in vivo remained unknown for a long time. This review discusses the current level of fundamental knowledge about the molecular mechanisms of interactions of zinc ions with a number of Aβ isoforms present in amyloid plaques of the patients with Alzheimer's disease, and also shows how this knowledge made it possible to identify driving forces of the cerebral amyloidogenesis in Alzheimer's disease and made it possible to determine fundamentally new biomarkers and drug targets as part of development of innovative strategy for diagnosis and treatment of Alzheimer's disease.
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Affiliation(s)
- Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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Ershov P, Kaluzhskiy L, Mezentsev Y, Yablokov E, Gnedenko O, Ivanov A. Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. Biomedicines 2021; 9:biomedicines9080895. [PMID: 34440098 PMCID: PMC8389681 DOI: 10.3390/biomedicines9080895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
A global protein interactome ensures the maintenance of regulatory, signaling and structural processes in cells, but at the same time, aberrations in the repertoire of protein-protein interactions usually cause a disease onset. Many metabolic enzymes catalyze multistage transformation of cholesterol precursors in the cholesterol biosynthesis pathway. Cancer-associated deregulation of these enzymes through various molecular mechanisms results in pathological cholesterol accumulation (its precursors) which can be disease risk factors. This work is aimed at systematization and bioinformatic analysis of the available interactomics data on seventeen enzymes in the cholesterol pathway, encoded by HMGCR, MVK, PMVK, MVD, FDPS, FDFT1, SQLE, LSS, DHCR24, CYP51A1, TM7SF2, MSMO1, NSDHL, HSD17B7, EBP, SC5D, DHCR7 genes. The spectrum of 165 unique and 21 common protein partners that physically interact with target enzymes was selected from several interatomic resources. Among them there were 47 modifying proteins from different protein kinases/phosphatases and ubiquitin-protein ligases/deubiquitinases families. A literature search, enrichment and gene co-expression analysis showed that about a quarter of the identified protein partners was associated with cancer hallmarks and over-represented in cancer pathways. Our results allow to update the current fundamental view on protein-protein interactions and regulatory aspects of the cholesterol synthesis enzymes and annotate of their sub-interactomes in term of possible involvement in cancers that will contribute to prioritization of protein targets for future drug development.
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Ershov PV, Yablokov E, Zgoda V, Mezentsev Y, Gnedenko O, Kaluzhskiy L, Svirid A, Gilep A, Usanov SA, Ivanov A. A new insight into subinteractomes of functional antagonists: Thromboxane (CYP5A1) and prostacyclin (CYP8A1) synthases. Cell Biol Int 2021; 45:1175-1182. [PMID: 33527589 DOI: 10.1002/cbin.11564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/10/2020] [Accepted: 01/31/2021] [Indexed: 12/14/2022]
Abstract
The current article aims to summarize all possible spectrum of protein-protein interactions for thromboxane A synthase (CYP5A1) and prostacyclin synthase (CYP8A1). These enzymes metabolize the same substrate (prostaglandin H2 ) and can participate in cardiovascular, inflammatory, immune processes, and apoptosis modulation, as well as significantly influence the risk of cancers. Binary protein-protein and multiprotein complexes are of great importance in enzyme-regulating and signal-transduction pathways. However, protein partners of CYP5A1 and CYP8A1 are not yet fully identified, although both synthases are considered as prospective drug targets. At least 36 novel protein partners of CYP5A1 and CYP8A1 were revealed from different tissue types using an approach based on affinity isolation and mass spectrometry. Enrichment analysis showed that these proteins have different molecular functions: folding (refolding), unfolded protein and chaperon binding, protein transport (export/import), posttranslational modification, protein domain-specific binding, antioxidant activity, and glutathione homeostasis. A significant part of them, belonging to molecular chaperones, were common partners for CYP5A1 and CYP8A1, while other proteins were unique with the tissue-dependent distribution. New aspects of CYP5A1 and CYP8A1 interactomics and hetero-complex formation with different protein partners, including cytochrome P450s are discussed.
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Affiliation(s)
- Pavel V Ershov
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia.,Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, The Federal Medical Biological Agency, Moscow, Russia
| | - Evgeniy Yablokov
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
| | - Victor Zgoda
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
| | - Yuri Mezentsev
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
| | - Oksana Gnedenko
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
| | - Leonid Kaluzhskiy
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
| | - Andrey Svirid
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Alexis Ivanov
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Moscow, Russia
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzgskiy LA, Ivanov AS, Gnuchev NV, Mitkevich VA, Makarov AA, Kozin SA. Direct Molecular Fishing of Zinc-Dependent Protein Partners of Amyloid-beta 1–16 with the Taiwan (D7H) Mutation and Phosphorylated Ser8 Residue. Mol Biol 2021. [DOI: 10.1134/s0026893320060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ershov PV, Veselovsky AV, Mezentsev YV, Yablokov EO, Kaluzhskiy LA, Tumilovich AM, Kavaleuski AA, Gilep AA, Moskovkina TV, Medvedev AE, Ivanov AS. Mechanism of the Affinity-Enhancing Effect of Isatin on Human Ferrochelatase and Adrenodoxin Reductase Complex Formation: Implication for Protein Interactome Regulation. Int J Mol Sci 2020; 21:E7605. [PMID: 33066693 PMCID: PMC7593955 DOI: 10.3390/ijms21207605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/04/2023] Open
Abstract
Isatin (indole-2, 3-dione) is a non-peptide endogenous bioregulator exhibiting a wide spectrum of biological activity, realized in the cell via interactions with numerous isatin-binding proteins, their complexes, and (sub) interactomes. There is increasing evidence that isatin may be involved in the regulation of complex formations by modulating the affinity of the interacting protein partners. Recently, using Surface Plasmon Resonance (SPR) analysis, we have found that isatin in a concentration dependent manner increased interaction between two human mitochondrial proteins, ferrochelatase (FECH), and adrenodoxine reductase (ADR). In this study, we have investigated the affinity-enhancing effect of isatin on the FECH/ADR interaction. The SPR analysis has shown that FECH forms not only homodimers, but also FECH/ADR heterodimers. The affinity-enhancing effect of isatin on the FECH/ADR interaction was highly specific and was not reproduced by structural analogues of isatin. Bioinformatic analysis performed using three dimensional (3D) models of the interacting proteins and in silico molecular docking revealed the most probable mechanism involving FECH/isatin/ADR ternary complex formation. In this complex, isatin is targeted to the interface of interacting FECH and ADR monomers, forming hydrogen bonds with both FECH and ADR. This is a new regulatory mechanism by which isatin can modulate protein-protein interactions (PPI).
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Affiliation(s)
- Pavel V. Ershov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Alexander V. Veselovsky
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Yuri V. Mezentsev
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Evgeniy O. Yablokov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Leonid A. Kaluzhskiy
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Anastasiya M. Tumilovich
- Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus; (A.M.T.); (A.A.K.); (A.A.G.)
| | - Anton A. Kavaleuski
- Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus; (A.M.T.); (A.A.K.); (A.A.G.)
| | - Andrei A. Gilep
- Institute of Bioorganic Chemistry NASB, 5 Building 2, V.F. Kuprevich Street, 220141 Minsk, Belarus; (A.M.T.); (A.A.K.); (A.A.G.)
| | - Taisiya V. Moskovkina
- Far East Federal University, FEFU Campus, 10 Ajax Bay, Russky Island, 690922 Vladivostok, Russia;
| | - Alexei E. Medvedev
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
| | - Alexis S. Ivanov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 140006 Moscow, Russia; (A.V.V.); (Y.V.M.); (E.O.Y.); (L.A.K.); (A.E.M.); (A.S.I.)
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Zhang Z, Yang D, Wang J, Huo J, Zhang J. Studies on the interactions between nicosulfuron and degradation enzymes. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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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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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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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhsky LA, Florinskaya AV, Buneeva OA, Medvedev AE, Ivanov AS. Effect of Bioregulator Isatin on Protein–Protein Interactions Involving Isatin-Binding Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018010053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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