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Bertsova YV, Serebryakova MV, Anashkin VA, Baykov AA, Bogachev AV. A Redox-Regulated, Heterodimeric NADH:cinnamate Reductase in Vibrio ruber. Biochemistry (Mosc) 2024; 89:241-256. [PMID: 38622093 DOI: 10.1134/s0006297924020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 04/17/2024]
Abstract
Genes of putative reductases of α,β-unsaturated carboxylic acids are abundant among anaerobic and facultatively anaerobic microorganisms, yet substrate specificity has been experimentally verified for few encoded proteins. Here, we co-produced in Escherichia coli a heterodimeric protein of the facultatively anaerobic marine bacterium Vibrio ruber (GenBank SJN56019 and SJN56021; annotated as NADPH azoreductase and urocanate reductase, respectively) with Vibrio cholerae flavin transferase. The isolated protein (named Crd) consists of the sjn56021-encoded subunit CrdB (NADH:flavin, FAD binding 2, and FMN bind domains) and an additional subunit CrdA (SJN56019, a single NADH:flavin domain) that interact via their NADH:flavin domains (Alphafold2 prediction). Each domain contains a flavin group (three FMNs and one FAD in total), one of the FMN groups being linked covalently by the flavin transferase. Crd readily reduces cinnamate, p-coumarate, caffeate, and ferulate under anaerobic conditions with NADH or methyl viologen as the electron donor, is moderately active against acrylate and practically inactive against urocanate and fumarate. Cinnamates induced Crd synthesis in V. ruber cells grown aerobically or anaerobically. The Crd-catalyzed reduction started by NADH demonstrated a time lag of several minutes, suggesting a redox regulation of the enzyme activity. The oxidized enzyme is inactive, which apparently prevents production of reactive oxygen species under aerobic conditions. Our findings identify Crd as a regulated NADH-dependent cinnamate reductase, apparently protecting V. ruber from (hydroxy)cinnamate poisoning.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Victor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Galkina SI, Golenkina EA, Fedorova NV, Ksenofontov AL, Serebryakova MV, Stadnichuk VI, Baratova LA, Sud'ina GF. Effect of Dexamethasone on Adhesion of Human Neutrophils and Concomitant Secretion. Biochemistry (Mosc) 2023; 88:2094-2106. [PMID: 38462453 DOI: 10.1134/s000629792312012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 03/12/2024]
Abstract
Neutrophils play a dual role in protecting the body. They are able to penetrate infected tissues and destroy pathogens there by releasing aggressive bactericidal substances. While into the surrounding tissues, the aggressive products secreted by neutrophils initiate development of inflammatory processes. Invasion of neutrophils into tissues is observed during the development of pneumonia in the patients with lung diseases of various etiologies, including acute respiratory distress syndrome caused by coronavirus disease. Synthetic corticosteroid hormone dexamethasone has a therapeutic effect in treatment of lung diseases, including reducing mortality in the patients with severe COVID-19. The acute (short-term) effect of dexamethasone on neutrophil adhesion to fibrinogen and concomitant secretion was studied. Dexamethasone did not affect either attachment of neutrophils to the substrate or their morphology. Production of reactive oxygen species (ROS) and nitric oxide (NO) by neutrophils during adhesion also did not change in the presence of dexamethasone. Dexamethasone stimulated release of metalloproteinases in addition to the proteins secreted by neutrophils during adhesion under control conditions, and selectively stimulated release of free amino acid hydroxylysine, a product of lysyl hydroxylase. Metalloproteinases play a key role and closely interact with lysyl hydroxylase in the processes of modification of the extracellular matrix. Therapeutic effect of dexamethasone could be associated with its ability to reorganize extracellular matrix in the tissues by changing composition of the neutrophil secretions, which could result in the improved gas exchange in the patients with severe lung diseases.
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Affiliation(s)
- Svetlana I Galkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Ekaterina A Golenkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Natalia V Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander L Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Ludmila A Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Galina F Sud'ina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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3
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Teplova AD, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3. Int J Mol Sci 2023; 24:16527. [PMID: 38003717 PMCID: PMC10671509 DOI: 10.3390/ijms242216527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.
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Affiliation(s)
- Anastasia D. Teplova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia; (A.D.T.); (A.A.P.)
| | - Artemii A. Pigidanov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia; (A.D.T.); (A.A.P.)
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (S.A.G.); (R.A.G.); (N.V.C.)
| | - Sergei A. Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (S.A.G.); (R.A.G.); (N.V.C.)
| | - Raisa A. Galiullina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (S.A.G.); (R.A.G.); (N.V.C.)
| | - Nina V. Chichkova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (S.A.G.); (R.A.G.); (N.V.C.)
| | - Andrey B. Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (S.A.G.); (R.A.G.); (N.V.C.)
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4
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Baksheeva VE, Tiulina VV, Iomdina EN, Petrov SY, Filippova OM, Kushnarevich NY, Suleiman EA, Eyraud R, Devred F, Serebryakova MV, Shebardina NG, Chistyakov DV, Senin II, Mitkevich VA, Tsvetkov PO, Zernii EY. Tear nanoDSF Denaturation Profile Is Predictive of Glaucoma. Int J Mol Sci 2023; 24:ijms24087132. [PMID: 37108298 PMCID: PMC10139145 DOI: 10.3390/ijms24087132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/07/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is a frequent blindness-causing neurodegenerative disorder characterized by optic nerve and retinal ganglion cell damage most commonly due to a chronic increase in intraocular pressure. The preservation of visual function in patients critically depends on the timeliness of detection and treatment of the disease, which is challenging due to its asymptomatic course at early stages and lack of objective diagnostic approaches. Recent studies revealed that the pathophysiology of glaucoma includes complex metabolomic and proteomic alterations in the eye liquids, including tear fluid (TF). Although TF can be collected by a non-invasive procedure and may serve as a source of the appropriate biomarkers, its multi-omics analysis is technically sophisticated and unsuitable for clinical practice. In this study, we tested a novel concept of glaucoma diagnostics based on the rapid high-performance analysis of the TF proteome by differential scanning fluorimetry (nanoDSF). An examination of the thermal denaturation of TF proteins in a cohort of 311 ophthalmic patients revealed typical profiles, with two peaks exhibiting characteristic shifts in POAG. Clustering of the profiles according to peaks maxima allowed us to identify glaucoma in 70% of cases, while the employment of artificial intelligence (machine learning) algorithms reduced the amount of false-positive diagnoses to 13.5%. The POAG-associated alterations in the core TF proteins included an increase in the concentration of serum albumin, accompanied by a decrease in lysozyme C, lipocalin-1, and lactotransferrin contents. Unexpectedly, these changes were not the only factor affecting the observed denaturation profile shifts, which considerably depended on the presence of low-molecular-weight ligands of tear proteins, such as fatty acids and iron. Overall, we recognized the TF denaturation profile as a novel biomarker of glaucoma, which integrates proteomic, lipidomic, and metallomic alterations in tears, and monitoring of which could be adapted for rapid non-invasive screening of the disease in a clinical setting.
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Affiliation(s)
- Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Veronika V Tiulina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Elena N Iomdina
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Sergey Yu Petrov
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Olga M Filippova
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Nina Yu Kushnarevich
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Elena A Suleiman
- Helmholtz National Medical Research Center of Eye Diseases, 105062 Moscow, Russia
| | - Rémi Eyraud
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023 Saint-Etienne, France
| | - François Devred
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Natalia G Shebardina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Dmitry V Chistyakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Ivan I Senin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Philipp O Tsvetkov
- Institut Neurophysiopathol, INP, Faculté des Sciences Médicales et Paramédicales, Aix Marseille Univ, CNRS, 13005 Marseille, France
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1-40 Leninskye Gory, 119992 Moscow, Russia
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5
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Zorova LD, Pevzner IB, Khailova LS, Korshunova GA, Kovaleva MA, Kovalev LI, Serebryakova MV, Silachev DN, Sudakov RV, Zorov SD, Rokitskaya TI, Popkov VA, Plotnikov EY, Antonenko YN, Zorov DB. Mitochondrial ATP Synthase and Mild Uncoupling by Butyl Ester of Rhodamine 19, C4R1. Antioxidants (Basel) 2023; 12:antiox12030646. [PMID: 36978894 PMCID: PMC10044837 DOI: 10.3390/antiox12030646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The homeostasis of the transmembrane potential of hydrogen ions in mitochondria is a prerequisite for the normal mitochondrial functioning. However, in different pathological conditions it is advisable to slightly reduce the membrane potential, while maintaining it at levels sufficient to produce ATP that will ensure the normal functioning of the cell. A number of chemical agents have been found to provide mild uncoupling; however, natural proteins residing in mitochondrial membrane can carry this mission, such as proteins from the UCP family, an adenine nucleotide translocator and a dicarboxylate carrier. In this study, we demonstrated that the butyl ester of rhodamine 19, C4R1, binds to the components of the mitochondrial ATP synthase complex due to electrostatic interaction and has a good uncoupling effect. The more hydrophobic derivative C12R1 binds poorly to mitochondria with less uncoupling activity. Mass spectrometry confirmed that C4R1 binds to the β-subunit of mitochondrial ATP synthase and based on molecular docking, a C4R1 binding model was constructed suggesting the binding site on the interface between the α- and β-subunits, close to the anionic amino acid residues of the β-subunit. The association of the uncoupling effect with binding suggests that the ATP synthase complex can provide induced uncoupling.
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Affiliation(s)
- Ljubava D. Zorova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Irina B. Pevzner
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Ljudmila S. Khailova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Galina A. Korshunova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Marina A. Kovaleva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Leonid I. Kovalev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marina V. Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Denis N. Silachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Roman V. Sudakov
- N.N. Blokhin Russian Cancer Research Center, 115478 Moscow, Russia
| | - Savva D. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatyana I. Rokitskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vasily A. Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Egor Y. Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
| | - Yuri N. Antonenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
| | - Dmitry B. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
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6
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Kordyukova LV, Moiseenko AV, Serebryakova MV, Shuklina MA, Sergeeva MV, Lioznov DA, Shanko AV. Structural and Immunoreactivity Properties of the SARS-CoV-2 Spike Protein upon the Development of an Inactivated Vaccine. Viruses 2023; 15:v15020480. [PMID: 36851694 PMCID: PMC9961907 DOI: 10.3390/v15020480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/21/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Inactivated vaccines are promising tools for tackling the COVID-19 pandemic. We applied several protocols for SARS-CoV-2 inactivation (by β-propiolactone, formaldehyde, and UV radiation) and examined the morphology of viral spikes, protein composition of the preparations, and their immunoreactivity in ELISA using two panels of sera collected from convalescents and people vaccinated by Sputnik V. Transmission electron microscopy (TEM) allowed us to distinguish wider flail-like spikes (supposedly the S-protein's pre-fusion conformation) from narrower needle-like ones (the post-fusion state). While the flails were present in all preparations studied, the needles were highly abundant in the β-propiolactone-inactivated samples only. Structural proteins S, N, and M of SARS-CoV-2 were detected via mass spectrometry. Formaldehyde and UV-inactivated samples demonstrated the highest affinity/immunoreactivity against the convalescent sera, while β-propiolactone (1:2000, 36 h) and UV-inactivated ones were more active against the sera of people vaccinated with Sputnik V. A higher concentration of β-propiolactone (1:1000, 2 h) led to a loss of antigenic affinity for both serum panels. Thus, although we did not analyze native SARS-CoV-2 for biosafety reasons, our comparative approach helped to exclude some destructive inactivation conditions and select suitable variants for future animal research. We believe that TEM is a valuable tool for inactivated COVID-19 vaccine quality control during the downstream manufacturing process.
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Affiliation(s)
- Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (L.V.K.); (A.V.S.)
| | - Andrey V. Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina A. Shuklina
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Maria V. Sergeeva
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Dmitry A. Lioznov
- WHO National Influenza Center, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia
| | - Andrei V. Shanko
- R&D Department, FORT LLC, 119435 Moscow, Russia
- Correspondence: (L.V.K.); (A.V.S.)
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7
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Teplova AD, Serebryakova MV, Galiullina RA, Chichkova NV, Vartapetian AB. Identification of Phytaspase Interactors via the Proximity-Dependent Biotin-Based Identification Approach. Int J Mol Sci 2021; 22:13123. [PMID: 34884925 PMCID: PMC8658550 DOI: 10.3390/ijms222313123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/22/2023] Open
Abstract
Proteolytic enzymes are instrumental in various aspects of plant development, including senescence. This may be due not only to their digestive activity, which enables protein utilization, but also to fulfilling regulatory functions. Indeed, for the largest family of plant serine proteases, subtilisin-like proteases (subtilases), several members of which have been implicated in leaf and plant senescence, both non-specific proteolysis and regulatory protein processing have been documented. Here, we strived to identify the protein partners of phytaspase, a plant subtilase involved in stress-induced programmed cell death that possesses a characteristic aspartate-specific hydrolytic activity and unusual localization dynamics. A proximity-dependent biotin identification approach in Nicotiana benthamiana leaves producing phytaspase fused to a non-specific biotin ligase TurboID was employed. Although the TurboID moiety appeared to be unstable in the apoplast environment, several intracellular candidate protein interactors of phytaspase were identified. These were mainly, though not exclusively, represented by soluble residents of the endoplasmic reticulum, namely endoplasmin, BiP, and calreticulin-3. For calreticultin-3, whose gene is characterized by an enhanced expression in senescing leaves, direct interaction with phytaspase was confirmed in an in vitro binding assay using purified proteins. In addition, an apparent alteration of post-translational modification of calreticultin-3 in phytaspase-overproducing plant cells was observed.
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Affiliation(s)
- Anastasia D. Teplova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Raisa A. Galiullina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Nina V. Chichkova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Andrey B. Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
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8
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Bertsova YV, Serebryakova MV, Baykov AA, Bogachev AV. The flavin transferase ApbE flavinylates the ferredoxin:NAD+-oxidoreductase Rnf required for N2 fixation in Azotobacter vinelandii. FEMS Microbiol Lett 2021; 368:6381689. [PMID: 34610116 DOI: 10.1093/femsle/fnab130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022] Open
Abstract
Azotobacter vinelandii, the model microbe in nitrogen fixation studies, uses the ferredoxin:NAD+-oxidoreductase Rnf to regenerate ferredoxin (flavodoxin), acting as an electron donor for nitrogenase. However, the relative contribution of Rnf to nitrogenase functioning is unknown because this bacterium contains another ferredoxin reductase, FixABCX. Furthermore, Rnf is flavinylated in the cell, but the importance and pathway of this modification reaction also remain largely unknown. We constructed A. vinelandii cells with impaired activities of FixABCX and/or putative flavin transferase ApbE. The ApbE-deficient mutant could not produce covalently flavinylated membrane proteins and demonstrated markedly decreased flavodoxin:NAD+ oxidoreductase activity and significant growth defects under diazotrophic conditions. The double ΔFix/ΔApbE mutation abolished the flavodoxin:NAD+ oxidoreductase activity and the ability of A. vinelandii to grow in the absence of a fixed nitrogen source. ApbE flavinylated a truncated RnfG subunit of Rnf1 by forming a phosphoester bond between flavin mononucleotide and a threonine residue. These findings indicate that Rnf (presumably its Rnf1 form) is the major ferredoxin-reducing enzyme in the nitrogen fixation system and that the activity of Rnf depends on its covalent flavinylation by the flavin transferase ApbE.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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9
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Schmalhausen EV, Medvedeva MV, Serebryakova MV, Chagovets VV, Muronetz VI. Products of S-nitrosylation of glyceraldehyde-3-phosphate dehydrogenase: Relation between S-nitrosylation and oxidation. Biochim Biophys Acta Gen Subj 2021; 1866:130032. [PMID: 34627945 DOI: 10.1016/j.bbagen.2021.130032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 10/06/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the major targets of NO in cells, especially in neurodegenerative diseases. S-Nitrosylation of GAPDH is accompanied by its translocation into the nucleus with subsequent apoptosis. The product of GAPDH modification by NO is considered to be S-nitrosylated GAPDH (GAPDH-SNO). However, this has not been confirmed by direct methods. METHODS Products of GAPDH modification in the presence of the NO donor diethylamine NONOate were analyzed by MALDI- and ESI- mass spectrometry methods. RESULTS The adduct between GAPDH and dimedone was detected by MALDI-MS analysis after incubation of S-nitrosylated GAPDH with dimedone, which points to the formation of cysteine-sulfenic acid (GAPDH-SOH) in the protein. Analysis of the protein hydrolysate revealed the incorporation of dimedone into the catalytic residue Cys150. An additional peak that corresponded to GAPDH-SNO was detected by ESI-MS analysis in GAPDH after the incubation with the NO donor. The content of GAPDH-SNO and GAPDH-SOH in the modified GAPDH was evaluated by different approaches and constituted 2.3 and 0.7 mol per mol GAPDH, respectively. A small fraction of GAPDH was irreversibly inactivated after NO treatment, suggesting that a minor part of the products includes cysteine-sulfinic or cysteine-sulfonic acids. CONCLUSIONS The main products of GAPDH modification by NO are GAPDH-SNO and GAPDH-SOH that is presumably formed due to the hydrolysis of GAPDH-SNO. GENERAL SIGNIFICANCE The obtained results are important for understanding the molecular mechanism of redox regulation of cell functions and the role of GAPDH in the development of neurodegenerative disorders.
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Affiliation(s)
- E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - M V Medvedeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - V V Chagovets
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology of Ministry of Healthcare of Russia, Akademika Oparina 4, Moscow 117997, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
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10
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Galkina SI, Golenkina EA, Fedorova NV, Ksenofontov AL, Serebryakova MV, Arifulin EA, Stadnichuk VI, Baratova LA, Sud'ina GF. Inhibition of Neutrophil Secretion Upon Adhesion as a Basis for the Anti-Inflammatory Effect of the Tricyclic Antidepressant Imipramine. Front Pharmacol 2021; 12:709719. [PMID: 34421605 PMCID: PMC8375473 DOI: 10.3389/fphar.2021.709719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022] Open
Abstract
Recent studies demonstrate the involvement of inflammatory processes in the development of depression and the anti-inflammatory effects of antidepressants. Infiltration and adhesion of neutrophils to nerve tissues and their aggressive secretion are considered as possible causes of inflammatory processes in depression. We studied the effect of the antidepressant imipramine on the adhesion and accompanied secretion of neutrophils under control conditions and in the presence of lipopolysaccharides (LPS). As a model of integrin-dependent neutrophil infiltration into tissues, we used integrin-dependent adhesion of neutrophils to the fibronectin-coated substrate. Imipramine inhibited neutrophil adhesion and concomitant secretion of proteins, including matrix metalloproteinase 9 (MMP-9) and neutrophil gelatinase-associated lipocalin (NGAL), which modify the extracellular matrix and basement membranes required for cell migration. Imipramine also significantly and selectively blocked the release of the free amino acid hydroxylysine, a product of lysyl hydroxylase, an enzyme that affects the organization of the extracellular matrix by modifying collagen lysine residues. In contrast, imipramine enhanced the release of ROS by neutrophils during adhesion to fibronectin and stimulated apoptosis. The anti-inflammatory effect of imipramine may be associated with the suppression of neutrophil infiltration and their adhesion to nerve tissues by inhibiting the secretion of neutrophils, which provides these processes.
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Affiliation(s)
- Svetlana I Galkina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina A Golenkina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Natalia V Fedorova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander L Ksenofontov
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Evgenii A Arifulin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Ludmila A Baratova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Galina F Sud'ina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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11
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Nůsková H, Serebryakova MV, Ferrer-Caelles A, Sachsenheimer T, Lüchtenborg C, Miller AK, Brügger B, Kordyukova LV, Teleman AA. Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins. Nat Commun 2021; 12:4590. [PMID: 34321466 PMCID: PMC8319428 DOI: 10.1038/s41467-021-24844-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/08/2021] [Indexed: 01/13/2023] Open
Abstract
Covalent attachment of C16:0 to proteins (palmitoylation) regulates protein function. Proteins are also S-acylated by other fatty acids including C18:0. Whether protein acylation with different fatty acids has different functional outcomes is not well studied. We show here that C18:0 (stearate) and C18:1 (oleate) compete with C16:0 to S-acylate Cys3 of GNAI proteins. C18:0 becomes desaturated so that C18:0 and C18:1 both cause S-oleoylation of GNAI. Exposure of cells to C16:0 or C18:0 shifts GNAI acylation towards palmitoylation or oleoylation, respectively. Oleoylation causes GNAI proteins to shift out of cell membrane detergent-resistant fractions where they potentiate EGFR signaling. Consequently, exposure of cells to C18:0 reduces recruitment of Gab1 to EGFR and reduces AKT activation. This provides a molecular mechanism for the anti-tumor effects of C18:0, uncovers a mechanistic link how metabolites affect cell signaling, and provides evidence that the identity of the fatty acid acylating a protein can have functional consequences.
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Affiliation(s)
- Hana Nůsková
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna Ferrer-Caelles
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | | | | | - Aubry K Miller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Larisa V Kordyukova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Heidelberg, Germany.
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12
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Volpina OM, Koroev DO, Serebryakova MV, Volkova TD, Kamynina AV, Bobkova NV. Proteolytic degradation patterns of the receptor for advanced glycation end products peptide fragments correlate with their neuroprotective activity in Alzheimer's disease models. Drug Dev Res 2021; 82:1217-1226. [PMID: 34060112 DOI: 10.1002/ddr.21836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 11/10/2022]
Abstract
The receptor for advanced glycation end products (RAGE) plays an essential role in Alzheimer's disease (AD). We previously demonstrated that a fragment (60-76) of RAGE improved the memory of olfactory bulbectomized (OBX) and Tg 5 × FAD mice - animal models of AD. The peptide analog (60-76) with protected N- and C-terminal groups was more active than the free peptide in Tg 5 × FAD mice. This study investigated proteolytic cleavage of the RAGE fragment (60-76) and its C- and N-terminally modified analog by blood serum using HPLC and mass spectrometry. The modified peptide was proteolyzed slower than the free peptide. Degrading the protected analog resulted in shortened fragments with memory-enhancing effects, whereas the free peptide yielded inactive fragments. After administering the different peptides to OBX mice, their performance in a spatial memory task revealed that the effective dose of the modified peptide was five times lower than that of the free peptide. HPLC and mass spectrometry analysis of the proteolytic products allowed us to clarify the differences in the neuroprotective activity conferred by administering these two peptides to AD animal models. The current study suggests that the modified RAGE fragment is more promising for the development of anti-AD therapy than its free analog.
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Affiliation(s)
- Olga M Volpina
- Department of Molecular Neurobiology, Laboratory of Synthetic Vaccines, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (RAS), Moscow, Russia
| | - Dmitriy O Koroev
- Department of Molecular Neurobiology, Laboratory of Synthetic Vaccines, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (RAS), Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana D Volkova
- Department of Molecular Neurobiology, Laboratory of Synthetic Vaccines, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (RAS), Moscow, Russia
| | - Anna V Kamynina
- Department of Molecular Neurobiology, Laboratory of Synthetic Vaccines, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (RAS), Moscow, Russia.,Research Center for Molecular Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Natalia V Bobkova
- Laboratory of Cellular Mechanisms of Memory Pathology, Institute of Cell Biophysics (RAS), Pushchino, Russia
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13
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Gadalla MR, Morrison E, Serebryakova MV, Han X, Wolff T, Freund C, Kordyukova L, Veit M. NS1-mediated upregulation of ZDHHC22 acyltransferase in influenza a virus infected cells. Cell Microbiol 2021; 23:e13322. [PMID: 33629465 DOI: 10.1111/cmi.13322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/20/2022]
Abstract
Influenza A viruses contain two S-acylated proteins, the ion channel M2 and the glycoprotein hemagglutinin (HA). Acylation of the latter is essential for virus replication. Here we analysed the expression of each of the 23 members of the family of ZDHHC acyltransferases in human airway cells, the site of virus replication. RT-PCR revealed that every ZDHHC acyltransferase (except ZDHHC19) is expressed in A549 and Calu cells. Interestingly, expression of one ZDHHC, ZDHHC22, is upregulated in virus-infected cells; this effect is more pronounced after infection with an avian compared to a human virus strain. The viral protein NS1 triggers ZDHHC22 expression in transfected cells, whereas recombinant viruses lacking a functional NS1 gene did not cause ZDHHC22 upregulation. CRISPR/Cas9 technology was then used to knock-out the ZDHHC22 gene in A549 cells. However, acylation of M2 and HA was not reduced, as analysed for intracellular HA and M2 and the stoichiometry of S-acylation of HA incorporated into virus particles did not change according to MALDI-TOF mass spectrometry analysis. Comparative mass spectrometry of palmitoylated proteins in wt and ΔZDHHC22 cells identified 25 potential substrates of ZDHHC22 which might be involved in virus replication.
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Affiliation(s)
- Mohamed Rasheed Gadalla
- Institute of Virology, Free University Berlin, Berlin, Germany.,Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Eliot Morrison
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Xueijiao Han
- Institute of Virology, Free University Berlin, Berlin, Germany
| | - Thorsten Wolff
- Unit 17: Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Christian Freund
- Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
| | - Larisa Kordyukova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Michael Veit
- Institute of Virology, Free University Berlin, Berlin, Germany
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14
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Iomdina EN, Tikhomirova NK, Bessmertny AM, Serebryakova MV, Baksheeva VE, Zalevsky AO, Kotelin VI, Kiseleva OA, Kosakyan SM, Zamyatnin AA, Philippov PP, Zernii EY. Alterations in proteome of human sclera associated with primary open-angle glaucoma involve proteins participating in regulation of the extracellular matrix. Mol Vis 2020; 26:623-640. [PMID: 32913388 PMCID: PMC7479071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/31/2020] [Indexed: 11/14/2022] Open
Abstract
Purpose Primary open-angle glaucoma (POAG) is a common ocular disease, associated with abnormalities in aqueous humor circulation and an increase in intraocular pressure (IOP), leading to progressive optical neuropathy and loss of vision. POAG pathogenesis includes alterations of the structural properties of the sclera, especially in the optic nerve head area, contributing to the degeneration of the retinal ganglion cells. Abnormal sclera biomechanics hinder adequate compensation of IOP fluctuations, thus aggravating POAG progression. The proteomic basis of biomechanical disorders in glaucomatous sclera remains poorly understood. This study is aimed at revealing alterations in major scleral proteins, associated with POAG, at different stages of the disease and with different IOP conditions. Methods Samples of sclera were collected from 67 patients with POAG during non-penetrating deep sclerectomy and from nine individuals without POAG. Scleral proteins were extracted with a strong lysis buffer, containing a combination of an ionic detergent, a chaotropic agent, and a disulfide reducing agent, and were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The major scleral proteins were selected, subjected to in-gel digestion, and identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)/TOF mass spectrometry (MS), coupled with tandem mass spectrometry (MS/MS). The specific POAG-associated alterations of the selected proteins were analyzed with SDS-PAGE and confirmed with western blotting of the scleral extracts, using the respective antibodies. The group of POAG-associated proteins was analyzed using Gene Ontology and genome-wide association study enrichment and protein-protein interaction network prediction. Results A total of 11 proteins were identified, among which six proteins, namely, vimentin, angiopoietin-related protein 7, annexin A2, serum amyloid P component, serum albumin, and thrombospondin-4, were found to be upregulated in the sclera of patients with advanced and terminal POAG. In the early stages of the disease, thrombospondin-4 level was, on the contrary, reduced when compared with the control, whereas the concentration of vimentin varied, depending on the IOP level. Moreover, angiopoietin-related protein 7 manifested as two forms, exhibiting opposite behavior: The common 45 kDa form grew with the progression of POAG, whereas the 35 kDa (apparently non-glycosylated) form was absent in the control samples, appeared in patients with early POAG, and decreased in concentration over the course of the disease. Functional bioinformatics analysis linked the POAG-associated proteins with IOP alterations and predicted their secretion into extracellular space and their association with extracellular vesicles and a collagen-containing extracellular matrix. Conclusions POAG is accompanied by alterations of the scleral proteome, which represent a novel hallmark of the disease and can reflect pathological changes in scleral biochemistry and biomechanics. The potential mechanisms underlying these changes relate mainly to the structure of the extracellular matrix, protein glycosylation, and calcium binding, and may involve fibroblast cytoskeleton regulation, as well as oxidative and inflammatory responses.
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Affiliation(s)
- Elena N. Iomdina
- Helmholtz National Medical Research Center of Eye Diseases, Moscow, Russia
| | - Natalya K. Tikhomirova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Viktoriia E. Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arthur O. Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Olga A. Kiseleva
- Helmholtz National Medical Research Center of Eye Diseases, Moscow, Russia
| | - Sbrui M. Kosakyan
- Helmholtz National Medical Research Center of Eye Diseases, Moscow, Russia
| | - Andrey A. Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Pavel P. Philippov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeni Yu. Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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15
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Shubina MY, Arifulin EA, Sorokin DV, Sosina MA, Tikhomirova MA, Serebryakova MV, Smirnova T, Sokolov SS, Musinova YR, Sheval EV. The GAR domain integrates functions that are necessary for the proper localization of fibrillarin (FBL) inside eukaryotic cells. PeerJ 2020; 8:e9029. [PMID: 32377452 PMCID: PMC7194090 DOI: 10.7717/peerj.9029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/31/2020] [Indexed: 01/25/2023] Open
Abstract
Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from Archaea to Eukaryota. An additional N-terminal glycine–arginine-rich (GAR) domain is present in the FBL of eukaryotes. Here, we demonstrate that the GAR domain is involved in FBL functioning and integrates the functions of the nuclear localization signal and the nucleolar localization signal (NoLS). The methylation of the arginine residues in the GAR domain is necessary for nuclear import but decreases the efficiency of nucleolar retention via the NoLS. The presented data indicate that the GAR domain can be considered an evolutionary innovation that integrates several functional activities and thereby adapts FBL to the highly compartmentalized content of the eukaryotic cell.
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Affiliation(s)
- Maria Y Shubina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Sorokin
- Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Moscow, Russia
| | - Mariya A Sosina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Tikhomirova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Smirnova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Svyatoslav S Sokolov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Skobelkin State Scientific Center of Laser Medicine FMBA, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, France
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16
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Kordyukova LV, Mintaev RR, Rtishchev AA, Kunda MS, Ryzhova NN, Abramchuk SS, Serebryakova MV, Khrustalev VV, Khrustaleva TA, Poboinev VV, Markushin SG, Voronina OL. Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus. Microsc Microanal 2020; 26:297-309. [PMID: 32036809 DOI: 10.1017/s1431927620000069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Influenza A virus is a serious human pathogen that assembles enveloped virions on the plasma membrane of the host cell. The pleiomorphic morphology of influenza A virus, represented by spherical, elongated, or filamentous particles, is important for the spread of the virus in nature. Using fixative protocols for sample preparation and negative staining electron microscopy, we found that the recombinant A/WSN/33 (H1N1) (rWSN) virus, a strain considered to be strictly spherical, may produce filamentous particles when amplified in the allantoic cavity of chicken embryos. In contrast, the laboratory WSN strain and the rWSN virus amplified in Madin-Darby canine kidney cells exhibited a spherical morphology. Next-generation sequencing (NGS) suggested a rare Ser126Cys substitution in the M1 protein of rWSN, which was confirmed by the mass spectrometric analysis. No structurally relevant substitutions were found by NGS in other proteins of rWSN. Bioinformatics algorithms predicted a neutral structural effect of the Ser126Cys mutation. The mrWSN_M1_126S virus generated after the introduction of the reverse Cys126Ser substitution exhibited a similar host-dependent partially filamentous phenotype. We hypothesize that a shortage of some as-yet-undefined cellular components involved in virion budding and membrane scission may result in the appearance of filamentous particles in the case of usually "nonfilamentous" virus strains.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991Moscow, Russia
| | - Ramil R Mintaev
- Mechnikov Research Institute of Vaccine and Sera, 105064Moscow, Russia
- Federal State Budgetary Institution «Center for Strategic Planning and Management for Medical and Biological Health Risks», Ministry of Health, 119121Moscow, Russia
| | | | - Marina S Kunda
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
| | - Natalia N Ryzhova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
| | - Sergei S Abramchuk
- Department of Chemistry, Lomonosov Moscow State University, 119234Moscow, Russia
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 119991Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991Moscow, Russia
| | - Vladislav V Khrustalev
- Department of General Chemistry, Belarusian State Medical University, 220116Minsk, Belarus
| | - Tatyana A Khrustaleva
- Biochemical Group of the Multidisciplinary Diagnostic Laboratory, Institute of Physiology of the National Academy of Sciences of Belarus, 220072Minsk, Belarus
| | - Victor V Poboinev
- Department of General Chemistry, Belarusian State Medical University, 220116Minsk, Belarus
| | | | - Olga L Voronina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health, 123098Moscow, Russia
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17
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Barinova KV, Serebryakova MV, Eldarov MA, Kulikova AA, Mitkevich VA, Muronetz VI, Schmalhausen EV. S-glutathionylation of human glyceraldehyde-3-phosphate dehydrogenase and possible role of Cys152-Cys156 disulfide bridge in the active site of the protein. Biochim Biophys Acta Gen Subj 2020; 1864:129560. [PMID: 32061786 DOI: 10.1016/j.bbagen.2020.129560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND We previously showed that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is S-glutathionylated in the presence of H2O2 and GSH. S-glutathionylation was shown to result in the formation of a disulfide bridge in the active site of the protein. In the present work, the possible biological significance of the disulfide bridge was investigated. METHODS Human recombinant GAPDH with the mutation C156S (hGAPDH_C156S) was obtained to prevent the formation of the disulfide bridge. Properties of S-glutathionylated hGAPDH_C156S were studied in comparison with those of the wild-type protein hGAPDH. RESULTS S-glutathionylation of hGAPDH and hGAPDH_C156S results in the reversible inactivation of the proteins. In both cases, the modification results in corresponding mixed disulfides between the catalytic Cys152 and GSH. In the case of hGAPDH, the mixed disulfide breaks down yielding Cys152-Cys156 disulfide bridge in the active site. In hGAPDH_C156S, the mixed disulfide is stable. Differential scanning calorimetry method showed that S-glutathionylation leads to destabilization of hGAPDH molecule, but does not affect significantly hGAPDH_C156S. Reactivation of S-glutathionylated hGAPDH in the presence of GSH and glutaredoxin 1 is approximately two-fold more efficient compared to that of hGAPDH_C156S. CONCLUSIONS S-glutathionylation induces the formation of Cys152-Cys156 disulfide bond in the active site of hGAPDH, which results in structural changes of the protein molecule. Cys156 is important for reactivation of S-glutathionylated GAPDH by glutaredoxin 1. GENERAL SIGNIFICANCE The described mechanism may be important for interaction between GAPDH and other proteins and ligands, involved in cell signaling.
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Affiliation(s)
- K V Barinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M A Eldarov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky prosp. 33-2, Moscow 119071, Russia
| | - A A Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia
| | - V A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow 119991, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
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18
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Bertsova YV, Serebryakova MV, Anashkin VA, Baykov AA, Bogachev AV. Mutational analysis of the flavinylation and binding motifs in two protein targets of the flavin transferase ApbE. FEMS Microbiol Lett 2019; 366:5675630. [DOI: 10.1093/femsle/fnz252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
Many flavoproteins belonging to three domain types contain an FMN residue linked through a phosphoester bond to a threonine or serine residue found in a conserved seven-residue motif. The flavinylation reaction is catalyzed by a specific enzyme, ApbE, which uses FAD as a substrate. To determine the structural requirements of the flavinylation reaction, we examined the effects of single substitutions in the flavinylation motif of Klebsiella pneumoniae cytoplasmic fumarate reductase on its modification by its own ApbE in recombinant Escherichia coli cells. The replacement of the flavin acceptor threonine with alanine completely abolished the modification reaction, whereas the replacements of conserved aspartate and serine had only minor effects. Effects of other substitutions, including replacing the acceptor threonine with serine, (a 10–55% decrease in the flavinylation degree) pinpointed important glycine and alanine residues and suggested an excessive capacity of the ApbE-based flavinylation system in vivo. Consistent with this deduction, drastic replacements of conserved leucine and threonine residues in the binding pocket that accommodates FMN residue still allowed appreciable flavinylation of the NqrC subunit of Vibrio harveyi Na+-translocating NADH:quinone oxidoreductase, despite a profound weakening of the isoalloxazine ring binding and an increase in its exposure to solvent.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Victor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
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19
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Kordyukova LV, Serebryakova MV, Khrustalev VV, Veit M. Differential S-Acylation of Enveloped Viruses. Protein Pept Lett 2019; 26:588-600. [PMID: 31161979 DOI: 10.2174/0929866526666190603082521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022]
Abstract
Post-translational modifications often regulate protein functioning. Covalent attachment of long chain fatty acids to cysteine residues via a thioester linkage (known as protein palmitoylation or S-acylation) affects protein trafficking, protein-protein and protein-membrane interactions. This post-translational modification is coupled to membrane fusion or virus assembly and may affect viral replication in vitro and thus also virus pathogenesis in vivo. In this review we outline modern methods to study S-acylation of viral proteins and to characterize palmitoylproteomes of virus infected cells. The palmitoylation site predictor CSS-palm is critically tested against the Class I enveloped virus proteins. We further focus on identifying the S-acylation sites directly within acyl-peptides and the specific fatty acid (e.g, palmitate, stearate) bound to them using MALDI-TOF MS-based approaches. The fatty acid heterogeneity/ selectivity issue attracts now more attention since the recently published 3D-structures of two DHHC-acyl-transferases gave a hint how this might be achieved.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Vladislav V Khrustalev
- Department of General Chemistry, Belarusian State Medical University, Minsk 220116, Belarus
| | - Michael Veit
- Institut für Virologie, Vet.-Med. Faculty, Free University Berlin, Berlin 14163, Germany
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20
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Pletnev PI, Nesterchuk MV, Rubtsova MP, Serebryakova MV, Dmitrieva K, Osterman IA, Bogdanov AA, Sergiev PV. Oligoglutamylation of E. coli ribosomal protein S6 is under growth phase control. Biochimie 2019; 167:61-67. [PMID: 31520657 DOI: 10.1016/j.biochi.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
Ribosomal protein S6 in Escherichia coli is modified by ATP-dependent glutamate ligase RimK. Up to four glutamate residues are added to the C-terminus of S6 protein. In this work we demonstrated that unlike the majority of ribosome modifications in E. coli, oligoglutamylation of S6 protein is regulated and happens only in the stationary phase of bacterial culture. Only S6 protein incorporated into assembled small ribosomal subunits, but not newly made free S6 protein is a substrate for RimK protein. Overexpression of the rimK gene leads to the modification of S6 protein even in the exponential phase of bacterial culture. Thus, it is unlikely that any stationary phase specific factor is needed for the modification. We propose a model that S6 modification is regulated solely via the rate of ribosome biosynthesis at limiting concentration of RimK enzyme.
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Affiliation(s)
- Philipp I Pletnev
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | | | - Maria P Rubtsova
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Ksenia Dmitrieva
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia; Skolkovo Institute for Science and Technology, Moscow, 143025, Russia.
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21
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Makarov VA, Tikhomirova NK, Savvateeva LV, Petushkova AI, Serebryakova MV, Baksheeva VE, Gorokhovets NV, Zernii EY, Zamyatnin AA. Novel applications of modification of thiol enzymes and redox-regulated proteins using S-methyl methanethiosulfonate (MMTS). Biochim Biophys Acta Proteins Proteom 2019; 1867:140259. [PMID: 31376523 DOI: 10.1016/j.bbapap.2019.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
S-Methyl methanethiosulfonate (MMTS) is used in experimental biochemistry for alkylating thiol groups of protein cysteines. Its applications include mainly trapping of natural thiol-disulfide states of redox-sensitive proteins and proteins which have undergone S-nitrosylation. The reagent can also be employed as an inhibitor of enzymatic activity, since nucleophilic cysteine thiolates are commonly present at active sites of various enzymes. The advantage of using MMTS for this purpose is the reversibility of the formation of methylthio mixed disulfides, compared to irreversible alkylation using conventional agents. Additional benefits include good accessibility of MMTS to buried protein cysteines due to its small size and the simplicity of the protection and deprotection procedures. In this study we report examples of MMTS application in experiments involving oxidoreductase (glyceraldehyde-3-phosphate dehydrogenase, GAPDH), redox-regulated protein (recoverin) and cysteine protease (triticain-α). We demonstrate that on the one hand MMTS can modify functional cysteines in the thiol enzyme GAPDH, thereby preventing thiol oxidation and reversibly inhibiting the enzyme, while on the other hand it can protect the redox-sensitive thiol group of recoverin from oxidation and such modification produces no impact on the activity of the protein. Furthermore, using the example of the papain-like enzyme triticain-α, we report a novel application of MMTS as a protector of the primary structure of active cysteine protease during long-term purification and refolding procedures. Based on the data, we propose new lines of MMTS employment in research, pharmaceuticals and biotechnology for reversible switching off of undesirable activity and antioxidant protection of proteins with functional thiol groups.
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Affiliation(s)
- Vladimir A Makarov
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia
| | - Natalia K Tikhomirova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Lyudmila V Savvateeva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia
| | - Anastasiia I Petushkova
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Viktoriia E Baksheeva
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Neonila V Gorokhovets
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia
| | - Evgeni Yu Zernii
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia; Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia; Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia.
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22
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Kasheverov IE, Oparin PB, Zhmak MN, Egorova NS, Ivanov IA, Gigolaev AM, Nekrasova OV, Serebryakova MV, Kudryavtsev DS, Prokopev NA, Hoang AN, Tsetlin VI, Vassilevski AA, Utkin YN. Scorpion toxins interact with nicotinic acetylcholine receptors. FEBS Lett 2019; 593:2779-2789. [PMID: 31276191 DOI: 10.1002/1873-3468.13530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/30/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022]
Abstract
Neurotoxins are among the main components of scorpion and snake venoms. Scorpion neurotoxins affect voltage-gated ion channels, while most snake neurotoxins target ligand-gated ion channels, mainly nicotinic acetylcholine receptors (nAChRs). We report that scorpion venoms inhibit α-bungarotoxin binding to both muscle-type nAChR from Torpedo californica and neuronal human α7 nAChR. Toxins inhibiting nAChRs were identified as OSK-1 (α-KTx family) from Orthochirus scrobiculosus and HelaTx1 (κ-KTx family) from Heterometrus laoticus, both being blockers of voltage-gated potassium channels. With an IC50 of 1.6 μm, OSK1 inhibits acetylcholine-induced current through mouse muscle-type nAChR heterologously expressed in Xenopus oocytes. Other well-characterized scorpion toxins from these families also bind to Torpedo nAChR with micromolar affinities. Our results indicate that scorpion neurotoxins present target promiscuity.
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Affiliation(s)
- Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Peter B Oparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim N Zhmak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Natalya S Egorova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrei M Gigolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Oksana V Nekrasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Denis S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikita A Prokopev
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, Russia
| | - Anh N Hoang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Vassilevski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Oblast, Russia
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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23
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Smirnova VV, Shestakova ED, Bikmetov DV, Chugunova AA, Osterman IA, Serebryakova MV, Sergeeva OV, Zatsepin TS, Shatsky IN, Terenin IM. eIF4G2 balances its own mRNA translation via a PCBP2-based feedback loop. RNA 2019; 25:757-767. [PMID: 31010886 PMCID: PMC6573783 DOI: 10.1261/rna.065623.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Poly(rC)-binding protein 2 (PCBP2, hnRNP E2) is one of the most abundant RNA-binding proteins in mammalian cells. In humans, it exists in seven isoforms, which are assumed to play similar roles in cells. The protein is shown to bind 3'-untranslated regions (3'-UTRs) of many mRNAs and regulate their translation and/or stability, but nothing is known about the functional consequences of PCBP2 binding to 5'-UTRs. Here we show that the PCBP2 isoform f interacts with the 5'-UTRs of mRNAs encoding eIF4G2 (a translation initiation factor with a yet unknown mechanism of action, also known as DAP5) and Cyclin I, and inhibits their translation in vitro and in cultured cells, while the PCBP2 isoform e only affects Cyclin I translation. Furthermore, eIF4G2 participates in a cap-dependent translation of the PCBP2 mRNA. Thus, PCBP2 and eIF4G2 seem to regulate one another's expression via a novel type of feedback loop formed by the translation initiation factor and the RNA-binding protein.
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Affiliation(s)
- Victoria V Smirnova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ekaterina D Shestakova
- Department of Biochemistry, School of Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow, 119234, Russian Federation
| | - Dmitry V Bikmetov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia
| | - Anastasia A Chugunova
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ilya A Osterman
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Olga V Sergeeva
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Timofey S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region 143026, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russian Federation
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24
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Kravchuk OI, Lyupina YV, Erokhov PA, Finoshin AD, Adameyko KI, Mishyna MY, Moiseenko AV, Sokolova OS, Orlova OV, Beljelarskaya SN, Serebryakova MV, Indeykina MI, Bugrova AE, Kononikhin AS, Mikhailov VS. Characterization of the 20S proteasome of the lepidopteran, Spodoptera frugiperda. Biochim Biophys Acta Proteins Proteom 2019; 1867:840-853. [PMID: 31228587 DOI: 10.1016/j.bbapap.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/05/2019] [Accepted: 06/17/2019] [Indexed: 02/08/2023]
Abstract
Multiple complexes of 20S proteasomes with accessory factors play an essential role in proteolysis in eukaryotic cells. In this report, several forms of 20S proteasomes from extracts of Spodoptera frugiperda (Sf9) cells were separated using electrophoresis in a native polyacrylamide gel and examined for proteolytic activity in the gel and by Western blotting. Distinct proteasome bands isolated from the gel were subjected to liquid chromatography-tandem mass spectrometry and identified as free core particles (CP) and complexes of CP with one or two dimers of assembly chaperones PAC1-PAC2 and activators PA28γ or PA200. In contrast to the activators PA28γ and PA200 that regulate the access of protein substrates to the internal proteolytic chamber of CP in an ATP-independent manner, the 19S regulatory particle (RP) in 26S proteasomes performs stepwise substrate unfolding and opens the chamber gate in an ATP-dependent manner. Electron microscopic analysis suggested that spontaneous dissociation of RP in isolated 26S proteasomes leaves CPs with different gate sizes related presumably to different stages in the gate opening. The primary structure of 20S proteasome subunits in Sf9 cells was determined by a search of databases and by sequencing. The protein sequences were confirmed by mass spectrometry and verified by 2D gel electrophoresis. The relative rates of sequence divergence in the evolution of 20S proteasome subunits, the assembly chaperones and activators were determined by using bioinformatics. The data confirmed the conservation of regular CP subunits and PA28γ, a more accelerated evolution of PAC2 and PA200, and especially high divergence rates of PAC1.
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Affiliation(s)
- Oksana I Kravchuk
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Yulia V Lyupina
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Pavel A Erokhov
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Alexander D Finoshin
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Kim I Adameyko
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia
| | - Maryia Yu Mishyna
- M.V. Lomonosov Moscow State University, Faculty of Biology, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Andrey V Moiseenko
- M.V. Lomonosov Moscow State University, Faculty of Biology, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Olga S Sokolova
- M.V. Lomonosov Moscow State University, Faculty of Biology, 1-12 Leninskie Gory, Moscow 119991, Russia
| | - Olga V Orlova
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119334, Russia
| | - Svetlana N Beljelarskaya
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova str., Moscow 119334, Russia
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology MSU, 1c40 Leniniskie Gory, Moscow 119234, Russia
| | - Maria I Indeykina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina str., Moscow 119334, Russia
| | - Anna E Bugrova
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina str., Moscow 119334, Russia
| | - Alexey S Kononikhin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina str., Moscow 119334, Russia; Skolkovo Institute of Science and Technology, 3 Ulitsa Nobelya, Moscow region, Skolkovo 121205, Russia
| | - Victor S Mikhailov
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova str., Moscow 119334, Russia.
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25
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Ksenofontov AL, Fedorova NV, Badun GA, Serebryakova MV, Nikitin NA, Evtushenko EA, Chernysheva MG, Bogacheva EN, Dobrov EN, Baratova LA, Atabekov JG, Karpova OV. Surface characterization of the thermal remodeling helical plant virus. PLoS One 2019; 14:e0216905. [PMID: 31150411 PMCID: PMC6544241 DOI: 10.1371/journal.pone.0216905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/30/2019] [Indexed: 01/19/2023] Open
Abstract
Previously, we have reported that spherical particles (SPs) are formed by the thermal remodeling of rigid helical virions of native tobacco mosaic virus (TMV) at 94°C. SPs have remarkable features: stability, unique adsorption properties and immunostimulation potential. Here we performed a comparative study of the amino acid composition of the SPs and virions surface to characterize their properties and take an important step to understanding the structure of SPs. The results of tritium planigraphy showed that thermal transformation of TMV leads to a significant increase in tritium label incorporation into the following sites of SPs protein: 41-71 а.a. and 93-122 a.a. At the same time, there was a decrease in tritium label incorporation into the N- and C- terminal region (1-15 a.a., 142-158 a.a). The use of complementary physico-chemical methods allowed us to carry out a detailed structural analysis of the surface and to determine the most likely surface areas of SPs. The obtained data make it possible to consider viral protein thermal rearrangements, and to open new opportunities for biologically active complex design using information about SPs surface amino acid composition and methods of non-specific adsorption and bioconjugation.
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Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Gennady A. Badun
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nikolai A. Nikitin
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Elena N. Bogacheva
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Joseph G. Atabekov
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga V. Karpova
- Department of Virology, Lomonosov Moscow State University, Moscow, Russia
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26
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Zernii EY, Nazipova AA, Nemashkalova EL, Kazakov AS, Gancharova OS, Serebryakova MV, Tikhomirova NK, Baksheeva VE, Vladimirov VI, Zinchenko DV, Philippov PP, Senin II, Permyakov SE. Light-Induced Thiol Oxidation of Recoverin Affects Rhodopsin Desensitization. Front Mol Neurosci 2019; 11:474. [PMID: 30666186 PMCID: PMC6330308 DOI: 10.3389/fnmol.2018.00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/05/2018] [Indexed: 02/03/2023] Open
Abstract
The excessive light illumination of mammalian retina is known to induce oxidative stress and photoreceptor cell death linked to progression of age-related macular degeneration. The photochemical damage of photoreceptors is suggested to occur via two apoptotic pathways that involve either excessive rhodopsin activation or constitutive phototransduction, depending on the light intensity. Both pathways are dramatically activated in the absence of rhodopsin desensitization by GRK1. Previously, we have shown that moderate illumination (halogen lamp, 1,500 lx, 1–5 h) of mammalian eyes provokes disulfide dimerization of recoverin, a calcium-dependent regulator of GRK1. Here, we demonstrate under in vivo conditions that both moderate long-term (metal halide lamp, 2,500 lx, 14 h, rat model) and intense short-term (halogen lamp, 30,000 lx for 3 h, rabbit model) illumination of the mammalian retina are accompanied by accumulation of disulfide dimer of recoverin. Furthermore, in the second case we reveal alternatively oxidized derivatives of the protein, apparently including its monomer with sulfinic group. Histological data indicate that thiol oxidation of recoverin precedes apoptosis of photoreceptors. Both disulfide dimer and oxidized monomer (or oxidation mimicking C39D mutant) of recoverin exhibit lowered α-helical content and thermal stability of their apo-forms, as well as increased Ca2+ affinity. Meanwhile, the oxidized monomer and C39D mutant of recoverin demonstrate impaired ability to bind photoreceptor membranes and regulate GRK1, whereas disulfide dimer exhibits notably improved membrane binding and GRK1 inhibition in absence of Ca2+. The latter effect is expected to slow down rhodopsin desensitization in the light, thereby favoring support of the light-induced oxidative stress, ultimately leading to photoreceptor apoptosis. Overall, the intensity and duration of illumination of the retina affect thiol oxidation of recoverin likely contributing to propagation of the oxidative stress and photoreceptor damage.
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Affiliation(s)
- Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aliya A Nazipova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | | | - Alexey S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Olga S Gancharova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalya K Tikhomirova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vasiliy I Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Russia
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Russia
| | - Pavel P Philippov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan I Senin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
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Elpidina EN, Semashko TA, Smirnova YA, Dvoryakova EA, Dunaevsky YE, Belozersky MA, Serebryakova MV, Klyachko EV, Abd El-Latif AO, Oppert B, Filippova IY. Direct detection of cysteine peptidases for MALDI-TOF MS analysis using fluorogenic substrates. Anal Biochem 2018; 567:45-50. [PMID: 30528915 DOI: 10.1016/j.ab.2018.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/19/2018] [Accepted: 12/03/2018] [Indexed: 01/12/2023]
Abstract
A method is described for the direct detection of unstable cysteine peptidase activity in polyacrylamide gels after native electrophoresis using new selective fluorogenic peptide substrates, pyroglutamyl-phenylalanyl-alanyl-4-amino-7-methylcoumaride (Glp-Phe-Ala-AMC) and pyroglutamyl-phenylalanyl-alanyl-4-amino-7-trifluoromethyl-coumaride (Glp-Phe-Ala-AFC). The detection limit of the model enzyme papain was 17 pmol (0.29 μg) for Glp-Phe-Ala-AMC and 43 pmol (0.74 μg) for Glp-Phe-Ala-AFC, with increased sensitivity and selectivity compared to the traditional method of protein determination with Coomassie G-250 staining or detection of activity using chromogenic substrates. Using this method, we easily identified the target digestive peptidases of Tenebrio molitor larvae by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis. The method offers simplicity, high sensitivity, and selectivity compared to traditional methods for improved identification of unstable cysteine peptidases in multi-component biological samples.
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Affiliation(s)
- Elena N Elpidina
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Tatiana A Semashko
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
| | - Yulia A Smirnova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Elena A Dvoryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Yakov E Dunaevsky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Mikhail A Belozersky
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Marina V Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Elena V Klyachko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Ashraf O Abd El-Latif
- Department of Plant Protection, Faculty of Agriculture, Sohag University, Sohag, Egypt
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, KS, 66502, USA.
| | - Irina Y Filippova
- Department of Chemistry, Moscow State University, Moscow, 119991, Russia
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Podolskaya EP, Serebryakova MV, Krasnov KA, Grachev SA, Gzgzyan AM, Sukhodolov NG. Application of Langmuir–Blodgett technology for the analysis of saturated fatty acids using the MALDI-TOF mass spectrometry. Mendeleev Communications 2018. [DOI: 10.1016/j.mencom.2018.05.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Beloshistov RE, Dreizler K, Galiullina RA, Tuzhikov AI, Serebryakova MV, Reichardt S, Shaw J, Taliansky ME, Pfannstiel J, Chichkova NV, Stintzi A, Schaller A, Vartapetian AB. Phytaspase-mediated precursor processing and maturation of the wound hormone systemin. New Phytol 2018; 218:1167-1178. [PMID: 28407256 DOI: 10.1111/nph.14568] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/21/2017] [Indexed: 05/24/2023]
Abstract
Peptide hormones are implicated in many important aspects of plant life and are usually synthesized as precursor proteins. In contrast to animals, data for plant peptide hormone maturation are scarce and the specificity of processing enzyme(s) is largely unknown. Here we tested a hypothesis that processing of prosystemin, a precursor of tomato (Solanum lycopersicum) wound hormone systemin, is performed by phytaspases, aspartate-specific proteases of the subtilase family. Following the purification of phytaspase from tomato leaves, two tomato phytaspase genes were identified, the cDNAs were cloned and the recombinant enzymes were obtained after transient expression in Nicotiana benthamiana. The newly identified tomato phytaspases hydrolyzed prosystemin at two aspartate residues flanking the systemin sequence. Site-directed mutagenesis of the phytaspase cleavage sites in prosystemin abrogated not only the phytaspase-mediated processing of the prohormone in vitro, but also the ability of prosystemin to trigger the systemic wound response in vivo. The data show that the prohormone prosystemin requires processing for signal biogenesis and biological activity. The identification of phytaspases as the proteases involved in prosystemin maturation provides insight into the mechanisms of wound signaling in tomato. Our data also suggest a novel role for cell death-related proteases in mediating defense signaling in plants.
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Affiliation(s)
- Roman E Beloshistov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Konrad Dreizler
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Raisa A Galiullina
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Alexander I Tuzhikov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Sven Reichardt
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Jane Shaw
- The James Hutton Institute, Dundee, DD2 5DA, UK
| | | | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Unit, University of Hohenheim, Stuttgart, 70593, Germany
| | - Nina V Chichkova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Annick Stintzi
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Andreas Schaller
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Andrey B Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
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30
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Sergeeva OV, Bredikhin DO, Nesterchuk MV, Serebryakova MV, Sergiev PV, Dontsova OA. Possible Role of Escherichia coli Protein YbgI. Biochemistry (Mosc) 2018; 83:270-280. [PMID: 29625546 DOI: 10.1134/s0006297918030070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteins containing the NIF3 domain are highly conserved and are found in bacteria, eukaryotes, and archaea. YbgI is an Escherichia coli protein whose gene is conserved among bacteria. The structure of YbgI is known; however, the function of this protein in cells remains obscure. Our studies of E. coli cells with deleted ybgI gene suggest that YbgI is involved in formation of the bacterial cell wall.
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Affiliation(s)
- O V Sergeeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Moscow Region, Russia.
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31
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Barinova KV, Serebryakova MV, Muronetz VI, Schmalhausen EV. S-glutathionylation of glyceraldehyde-3-phosphate dehydrogenase induces formation of C150-C154 intrasubunit disulfide bond in the active site of the enzyme. Biochim Biophys Acta Gen Subj 2017; 1861:3167-3177. [PMID: 28935607 DOI: 10.1016/j.bbagen.2017.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a glycolytic protein involved in numerous non-glycolytic functions. S-glutathionylated GAPDH was revealed in plant and animal tissues. The role of GAPDH S-glutathionylation is not fully understood. METHODS Rabbit muscle GAPDH was S-glutathionylated in the presence of H2O2 and reduced glutathione (GSH). The modified protein was assayed by MALDI-MS analysis, differential scanning calorimetry, dynamic light scattering, and ultracentrifugation. RESULTS Incubation of GAPDH in the presence of H2O2 together with GSH resulted in the complete inactivation of the enzyme. In contrast to irreversible oxidation of GAPDH by H2O2, this modification could be reversed in the excess of GSH or dithiothreitol. By data of MALDI-MS analysis, the modified protein contained both mixed disulfide between Cys150 and GSH and the intrasubunit disulfide bond between Cys150 and Cys154 (different subunits of tetrameric GAPDH may contain different products). S-glutathionylation results in loosening of the tertiary structure of GAPDH, decreases its affinity to NAD+ and thermal stability. CONCLUSIONS The mixed disulfide between Cys150 and GSH is an intermediate product of S-glutathionylation: its subsequent reaction with Cys154 results in the intrasubunit disulfide bond in the active site of GAPDH. The mixed disulfide and the C150-C154 disulfide bond protect GAPDH from irreversible oxidation and can be reduced in the excess of thiols. Conformational changes that were observed in S-glutathionylated GAPDH may affect interactions between GAPDH and other proteins (ligands), suggesting the role of S-glutathionylation in the redox signaling. GENERAL SIGNIFICANCE The manuscript considers one of the possible mechanisms of redox regulation of cell functions.
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Affiliation(s)
- K V Barinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
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32
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Ksenofontov AL, Dobrov EN, Fedorova NV, Serebryakova MV, Prusov AN, Baratova LA, Paalme V, Järvekülg L, Shtykova EV. Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles. J Biomol Struct Dyn 2017; 36:1728-1738. [DOI: 10.1080/07391102.2017.1333457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Andrei N. Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Viiu Paalme
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Lilian Järvekülg
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Eleonora V. Shtykova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences , Moscow, Russia
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33
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Katrukha IA, Kogan AE, Vylegzhanina AV, Serebryakova MV, Koshkina EV, Bereznikova AV, Katrukha AG. Thrombin-Mediated Degradation of Human Cardiac Troponin T. Clin Chem 2017; 63:1094-1100. [PMID: 28428352 DOI: 10.1373/clinchem.2016.266635] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Cardiac troponin T (cTnT) is an acknowledged biomarker of acute myocardial infarction (AMI) that is known to be prone to proteolytic degradation in serum. Such degradation is usually explained by the action of μ-calpain, although there could be other candidates for that role. In the current study, we explored the hypothesis that thrombin-mediated cTnT cleavage occurs as a result of the serum sample preparation. METHODS cTnT degradation was studied by using immunoblotting and mass spectrometry (MS) analysis. RESULTS The comparison of cTnT isolated from AMI heparin plasma and serum samples showed that cTnT in the plasma samples was mainly present as the full-sized molecule (approximately 35 kDa), while in serum samples it was present as a 29-kDa fragment. The incubation of recombinant cTnT, or native ternary cardiac troponin complex with thrombin or in normal human serum (NHS), resulted in the formation of a 29-kDa product that was similar to that detected in AMI serum samples. No cTnT degradation was observed when thrombin or NHS was pretreated with hirudin, a specific inhibitor of thrombin, or during incubation of troponin in normal heparin plasma. When the products of thrombin-mediated cTnT proteolysis were analyzed by MS, 2 fragments consisting of amino acid residues (aar) 2-68 and 69-288 were identified, which suggests that thrombin cleaves cTnT between R68 and S69. CONCLUSIONS The results of this study suggest that the 29-kDa fragment of cTnT in AMI serum samples mainly appears due to the cleavage by thrombin during serum sample preparation.
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Affiliation(s)
- Ivan A Katrukha
- HyTest Ltd., Turku, Finland; .,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexander E Kogan
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | | | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | | | - Anastasia V Bereznikova
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
| | - Alexey G Katrukha
- HyTest Ltd., Turku, Finland.,Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia
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Komarova TV, Sheshukova EV, Kosobokova EN, Serebryakova MV, Kosorukov VS, Tashlitsky VN, Dorokhov YL. Trastuzumab and Pertuzumab Plant Biosimilars: Modification of Asn297-linked Glycan of the mAbs Produced in a Plant with Fucosyltransferase and Xylosyltransferase Gene Knockouts. Biochemistry (Mosc) 2017; 82:510-520. [PMID: 28371609 DOI: 10.1134/s0006297917040137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Plant biosimilars of anticancer therapeutic antibodies are of interest not only because of the prospects of their practical use, but also as an instrument and object for study of plant protein glycosylation. In this work, we first designed a pertuzumab plant biosimilar (PPB) and investigated the composition of its Asn297-linked glycan in comparison with trastuzumab plant biosimilar (TPB). Both biosimilars were produced in wild-type (WT) Nicotiana benthamiana plant (PPB-WT and TPB-WT) and transgenic ΔXTFT N. benthamiana plant with XT and FT genes knockout (PPB-ΔXTFT and TPB-ΔXTFT). Western blot analysis with anti-α1,3-fucose and anti-xylose antibodies, as well as a test with peptide-N-glycosidase F, confirmed the absence of α1,3-fucose and xylose in the Asn297-linked glycan of PPB-ΔXTFT and TPB-ΔXTFT. Peptide analysis followed by the identification of glycomodified peptides using MALDI-TOF/TOF showed that PPB-WT and TPB-WT Asn297-linked glycans are mainly of complex type GnGnXF. The core of PPB-WT and TPB-WT Asn297-linked GnGn-type glycan contains α1,3-fucose and β1,2-xylose, which, along with the absence of terminal galactose and sialic acid, distinguishes these plant biosimilars from human IgG. Analysis of TPB-ΔXTFT total carbohydrate content indicates the possibility of changing the composition of the carbohydrate profile not only of the Fc, but also of the Fab portion of an antibody produced in transgenic ΔXTFT N. benthamiana plants. Nevertheless, study of the antigen-binding capacity of the biosimilars showed that absence of xylose and fucose residues in the Asn297-linked glycans does not affect the ability of the glycomodified antibodies to interact with HER2/neu positive cancer cells.
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Affiliation(s)
- T V Komarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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Zernii EY, Gancharova OS, Ishutina IE, Baksheeva VE, Golovastova MO, Kabanova EI, Savchenko MS, Serebryakova MV, Sotnikova LF, Zamyatnin AA, Philippov PP, Senin II. [Mechanisms of perioperative corneal abrasions: alterations in tear film proteome]. Biomed Khim 2017; 62:683-690. [PMID: 28026813 DOI: 10.18097/pbmc20166206683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Perioperative corneal abrasion is an ophthalmic complication commonly found in patients underwent general anesthesia. In this study, correlations between development of corneal injury and proteomic changes in tear film during general anesthesia were examined using an animal (rabbit) model. Being started after 1-h anesthesia, the process of accumulation of pathological changes in the cornea unequivocally led clinically significant abrasions following 3-6 h of the narcosis. The corneal damage was associated with alterations in profiles of major proteins of the tear film. Analysis of the tear proteome pointed to depression of lachrymal glands function, and suggested serotransferrin, serum albumin and annexin A1 as potential tear markers of the complication. The tear film alterations included fast drop of total antioxidant activity and activity of superoxide dismutase, and decrease in interleukin-4 and increase in interleukin-6 content indicating development of oxidative and pro-inflammatory responses. These findings suggest antioxidant and anti-inflammatory therapy as prospective approach for prevention/treatment of perioperative corneal abrasions. The observed anesthesia-induced effects should be considered in any study of ocular surface diseases employing anesthetized animals.
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Affiliation(s)
- E Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - O S Gancharova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I E Ishutina
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - V E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - M O Golovastova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E I Kabanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - M S Savchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - L F Sotnikova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, Russia
| | - A A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | - P P Philippov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I I Senin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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36
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Andreeva AM, Serebryakova MV, Lamash NE. Oligomeric protein complexes of apolipoproteins stabilize the internal fluid environment of organism in redfins of the Tribolodon genus [Pisces; Cypriniformes, Cyprinidae]. Comp Biochem Physiol Part D Genomics Proteomics 2017; 22:90-97. [PMID: 28288366 DOI: 10.1016/j.cbd.2017.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/21/2017] [Accepted: 02/24/2017] [Indexed: 01/25/2023]
Abstract
One of the most important functions of plasma proteins in vertebrates is their participation in osmotic homeostasis in the organism. Modern concepts about plasma proteins and their capillary filtration are based on a model of large monomeric proteins that are able to penetrate the interstitial space. At the same time, it was revealed that a considerable amount of oligomeric complexes are present in the low-molecular-weight (LM) protein fraction in the extracellular fluids of fishes. The functions of these complexes are unknown. In the present study, we investigated the LM-fraction proteins in the plasma and interstitial fluid (IF) of redfins of the genus Tribolodon. This fish alternatively spends parts of its life cycle in saline and fresh waters. We identified the protein Wap65, serpins and apolipoproteins in this fraction. By combining the methods of 2D-E under native and denaturing conditions with MALDI, we demonstrated that only apolipoproteins formed complexes. We showed that serum apolipoproteins (АроА-I, Аро-14) were present in the form of homooligomeric complexes that were dissociated with the release of monomeric forms of proteins in the course of capillary filtration to IF. Dissociation of homooligomers is not directly correlated with the change in salinity but is correlated with seasonal dynamics. We found that there was a significant decrease in the total protein concentration in IF relative to plasma. Therefore, we suggested that dissociation of homooligomeric complexes from various apolipoproteins supports the isoosmoticity of extracellular fluids relative to capillary wall stabilization through a fluid medium in fish.
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Affiliation(s)
- Alla M Andreeva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Nekouzskii raion, Yaroslavl oblast, Russia.
| | - Marina V Serebryakova
- Lomonosov Moscow State University, A. N. Belozersky Institute of Physico-Chemical Biology, Moscow 119992, Leninskye gory, house 1, building 40, Russia
| | - Nina E Lamash
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Nekouzskii raion, Yaroslavl oblast, Russia; A.V. Zhirmunsky Institute of Marine Biology, National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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Barinova KV, Kuravsky ML, Arutyunyan AM, Serebryakova MV, Schmalhausen EV, Muronetz VI. Dimerization of Tyr136Cys alpha-synuclein prevents amyloid transformation of wild type alpha-synuclein. Int J Biol Macromol 2016; 96:35-43. [PMID: 27939273 DOI: 10.1016/j.ijbiomac.2016.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
Expression of human alpha-synuclein in E. coli cells is known to result in a mixture of the wild type alpha-synuclein and the protein containing Tyr136Cys substitution due to the translational error. The amount of Cys136 alpha-synuclein (Cys136-AS) may reach approximately 50% of the recombinant protein. The wild-type and Cys136-containing fractions of alpha-synuclein were separated using thiol-Sepharose, and their properties were investigated. In the absence of reducing agents, Cys136-AS forms dimers due to the disulfide bonding. Both wild-type and Cys136 alpha-synuclein preparations are prone to aggregate during prolonged incubation under shaking at pH 4 and 37°C, but only the wild-type alpha-synuclein produces amyloid aggregates. The aggregates produced by either monomeric or dimeric Cys136-AS do not exhibit amyloid properties according to the test with Thioflavin T. Moreover, an admixture of dimeric Cys136-AS prevents the amyloid transformation of the wild-type alpha-synuclein. CD spectroscopy analysis revealed an enhanced content of alpha-helical structures in the aggregates produced by dimeric Cys136-AS. The admixture of Cys136-AS in preparations of human recombinant alpha-synuclein can be a source of erroneous interpretation of experiments on amyloid transformation of this protein.
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Affiliation(s)
- K V Barinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - M L Kuravsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - A M Arutyunyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - M V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Osterman IA, Komarova ES, Shiryaev DI, Korniltsev IA, Khven IM, Lukyanov DA, Tashlitsky VN, Serebryakova MV, Efremenkova OV, Ivanenkov YA, Bogdanov AA, Sergiev PV, Dontsova OA. Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors. Antimicrob Agents Chemother 2016; 60:7481-7489. [PMID: 27736765 PMCID: PMC5119032 DOI: 10.1128/aac.02117-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter. The gene of the far-red fluorescent protein, katushka2S, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
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Affiliation(s)
- Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry I Shiryaev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Ilya A Korniltsev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Irina M Khven
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry A Lukyanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Vadim N Tashlitsky
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Olga V Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Yan A Ivanenkov
- Moscow Institute of Physics and Technology (State University), Moscow Region, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga A Dontsova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Prostova MA, Gmyl AP, Bakhmutov DV, Shishova AA, Khitrina EV, Kolesnikova MS, Serebryakova MV, Isaeva OV, Agol VI. Mutational robustness and resilience of a replicative cis-element of RNA virus: Promiscuity, limitations, relevance. RNA Biol 2016; 12:1338-54. [PMID: 26488412 DOI: 10.1080/15476286.2015.1100794] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Since replication of RNA-viruses is generally a low-fidelity process, it would be advantageous, if specific interactions of their genomic cis-elements with dedicated ligands are relatively tolerant to mutations. The specificity/promiscuity trade-off of such interactions was addressed here by investigating structural requirements of the oriL (also known as the clover leaf-like element), of poliovirus RNA, a replicative cis-element containing a conserved essential tetraloop functionally interacting with the viral protein 3CD. The sequence of this tetraloop and 2 adjacent base-pairs was randomized in the viral genome, and viable viruses were selected in susceptible cells. Strikingly, each position of this octanucleotide in 62 investigated viable viruses could be occupied by any nucleotide (with the exception of one position, which lacked U), though with certain sequence preferences, confirmed by engineering mutant viral genomes whose phenotypic properties were found to correlate with the strength of the cis-element/ligand interaction. The results were compatible with a hypothesis that functional recognition by 3CD requires that this tetraloop should stably or temporarily adopt a YNMG-like (Y=U/C, N=any nucleotide, M=A/C) fold. The fitness of "weak" viruses could be increased by compensatory mutations "improving" the tetraloops. Otherwise, the recognition of "bad" tetraloops might be facilitated by alterations in the 3CD protein. The virus appeared to tolerate mutations in its cis-element relaying on either robustness (spatial structure degeneracy) or resilience (a combination of dynamic RNA folding, low-fidelity replication modifying the cis-element or its ligand, and negative selection). These mechanisms (especially resilience involving metastable low-fit intermediates) can also contribute to the viral evolvability.
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Affiliation(s)
- Maria A Prostova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Anatoly P Gmyl
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,b M V Lomonosov Moscow State University ; Moscow Russia
| | - Denis V Bakhmutov
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,c Deceased
| | - Anna A Shishova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Elena V Khitrina
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Marina S Kolesnikova
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | | | - Olga V Isaeva
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia
| | - Vadim I Agol
- a M P Chumakov Institute of Poliomyelitis and Viral Encephalitides ; Moscow Russia.,b M V Lomonosov Moscow State University ; Moscow Russia
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Tereshchenkova VF, Goptar IA, Kulemzina IA, Zhuzhikov DP, Serebryakova MV, Belozersky MA, Dunaevsky YE, Oppert B, Filippova IY, Elpidina EN. Dipeptidyl peptidase 4 - An important digestive peptidase in Tenebrio molitor larvae. Insect Biochem Mol Biol 2016; 76:38-48. [PMID: 27395781 DOI: 10.1016/j.ibmb.2016.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 06/28/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Dipeptidyl peptidase 4 (DPP 4) is a proline specific serine peptidase that plays an important role in different regulatory processes in mammals. In this report, we isolated and characterized a unique secreted digestive DPP 4 from the anterior midgut of a stored product pest, Tenebrio molitor larvae (TmDPP 4), with a biological function different than that of the well-studied mammalian DPP 4. The sequence of the purified enzyme was confirmed by mass-spectrometry, and was identical to the translated RNA sequence found in a gut EST database. The purified peptidase was characterized according to its localization in the midgut, and substrate specificity and inhibitor sensitivity were compared with those of human recombinant DPP 4 (rhDPP 4). The T. molitor enzyme was localized mainly in the anterior midgut of the larvae, and 81% of the activity was found in the fraction of soluble gut contents, while human DPP 4 is a membrane enzyme. TmDPP 4 was stable in the pH range 5.0-9.0, with an optimum activity at pH 7.9, similar to human DPP 4. Only specific inhibitors of serine peptidases, diisopropyl fluorophosphate and phenylmethylsulfonyl fluoride, suppressed TmDPP 4 activity, and the specific dipeptidyl peptidase inhibitor vildagliptin was most potent. The highest rate of TmDPP 4 hydrolysis was found for the synthetic substrate Arg-Pro-pNA, while Ala-Pro-pNA was a better substrate for rhDPP 4. Related to its function in the insect midgut, TmDPP 4 efficiently hydrolyzed the wheat storage proteins gliadins, which are major dietary proteins of T. molitor.
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Affiliation(s)
| | - Irina A Goptar
- Chemical Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina A Kulemzina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry P Zhuzhikov
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail A Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Yakov E Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA.
| | - Irina Yu Filippova
- Chemical Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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41
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Vulfius CA, Spirova EN, Serebryakova MV, Shelukhina IV, Kudryavtsev DS, Kryukova EV, Starkov VG, Kopylova NV, Zhmak MN, Ivanov IA, Kudryashova KS, Andreeva TV, Tsetlin VI, Utkin YN. Peptides from puff adder Bitis arietans venom, novel inhibitors of nicotinic acetylcholine receptors. Toxicon 2016; 121:70-76. [PMID: 27576061 DOI: 10.1016/j.toxicon.2016.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 07/19/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022]
Abstract
Phospholipase A2 (named bitanarin) possessing capability to block nicotinic acetylcholine receptors (nAChRs) was isolated earlier (Vulfius et al., 2011) from puff adder Bitis arietans venom. Further studies indicated that low molecular weight fractions of puff adder venom inhibit nAChRs as well. In this paper, we report on isolation from this venom and characterization of three novel peptides called baptides 1, 2 and 3 that reversibly block nAChRs. To isolate the peptides, the venom of B. arietans was fractionated by gel-filtration and reversed phase chromatography. The amino acid sequences of peptides were established by de novo sequencing using MALDI mass spectrometry. Baptide 1 comprised 7, baptides 2 and 3-10 amino acid residues, the latter being acetylated at the N-terminus. This is the first indication for the presence of such post-translational modification in snake venom proteins. None of the peptides contain cysteine residues. For biological activity studies the peptides were prepared by solid phase peptide synthesis. Baptide 3 and 2 blocked acetylcholine-elicited currents in isolated Lymnaea stagnalis neurons with IC50 of about 50 μM and 250 μM, respectively. In addition baptide 2 blocked acetylcholine-induced currents in muscle nAChR heterologously expressed in Xenopus oocytes with IC50 of about 3 μM. The peptides did not compete with radioactive α-bungarotoxin for binding to Torpedo and α7 nAChRs at concentration up to 200 μM that suggests non-competitive mode of inhibition. Calcium imaging studies on α7 and muscle nAChRs heterologously expressed in mouse neuroblastoma Neuro2a cells showed that on α7 receptor baptide 2 inhibited acetylcholine-induced increasing intracellular calcium concentration with IC50 of 20.6 ± 3.93 μM. On both α7 and muscle nAChRs the suppression of maximal response to acetylcholine by about 50% was observed at baptide 2 concentration of 25 μM, the value being close to IC50 on α7 nAChR. These data are in accord with non-competitive inhibition as follows from α-bungarotoxin binding experiments. The described peptides are the shortest peptides without disulfide bridges isolated from animal venom and capable to inhibit nAChR by non-competitive way.
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Affiliation(s)
- Catherine A Vulfius
- Institute of Cell Biophysics, Russian Academy of Sciences, Ul. Institutskaya 3, Pushchino Moscow Region, 142290, Russia
| | - Ekaterina N Spirova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Marina V Serebryakova
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Irina V Shelukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Denis S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Elena V Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Vladislav G Starkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Nina V Kopylova
- Moscow State Pedagogical University, Ul. M. Pirogovskaya 1/1, Moscow, 119991, Russia
| | - Maxim N Zhmak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia; OOO Syneuro, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ksenia S Kudryashova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Tatyana V Andreeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Yuri N Utkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia.
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42
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Muranova LK, Perfilov MM, Serebryakova MV, Gusev NB. Effect of methylglyoxal modification on the structure and properties of human small heat shock protein HspB6 (Hsp20). Cell Stress Chaperones 2016; 21:617-29. [PMID: 27061807 PMCID: PMC4907992 DOI: 10.1007/s12192-016-0686-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/06/2016] [Accepted: 03/26/2016] [Indexed: 01/01/2023] Open
Abstract
Human small heat shock protein HspB6 (Hsp20) was modified by metabolic α-dicarbonyl compound methylglyoxal (MGO). At low MGO/HspB6 molar ratio, Arg13, Arg14, Arg27, and Arg102 were the primary sites of MGO modification. At high MGO/HspB6 ratio, practically, all Arg and Lys residues of HspB6 were modified. Both mild and extensive MGO modification decreased susceptibility of HspB6 to trypsinolysis and prevented its heat-induced aggregation. Modification by MGO was accompanied by formation of small quantities of chemically crosslinked dimers and did not dramatically affect quaternary structure of HspB6. Mild modification by MGO did not affect whereas extensive modification decreased interaction of HspB6 with HspB1. Phosphorylation of HspB6 by cyclic adenosine monophosphate (cAMP)-dependent protein kinase was inhibited after mild modification and completely prevented after extensive modification by MGO. Chaperone-like activity of HspB6 measured with subfragment 1 of skeletal myosin was enhanced after MGO modifications. It is concluded that Arg residues located in the N-terminal domain of HspB6 are easily accessible to MGO modification and that even mild modification by MGO affects susceptibility to trypsinolysis, phosphorylation by cAMP-dependent protein kinase, and chaperone-like activity of HspB6.
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Affiliation(s)
- Lydia K Muranova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, 119991, Russian Federation
| | - Maxim M Perfilov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, 119991, Russian Federation
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russian Federation
| | - Nikolai B Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, 119991, Russian Federation.
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Lyupina YV, Zatsepina OG, Serebryakova MV, Erokhov PA, Abaturova SB, Kravchuk OI, Orlova OV, Beljelarskaya SN, Lavrov AI, Sokolova OS, Mikhailov VS. Proteomics of the 26S proteasome in Spodoptera frugiperda cells infected with the nucleopolyhedrovirus, AcMNPV. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2016; 1864:738-746. [DOI: 10.1016/j.bbapap.2016.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/04/2016] [Accepted: 02/29/2016] [Indexed: 01/13/2023]
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Baksheeva VE, Nazipova AA, Zinchenko DV, Serebryakova MV, Senin II, Permyakov SE, Philippov PP, Li Y, Zamyatnin AA, Zernii EY, Aliev G. Ca2+ -myristoyl switch in neuronal calcium sensor-1: a role of C-terminal segment. CNS Neurol Disord Drug Targets 2016; 14:437-51. [PMID: 25714968 DOI: 10.2174/1871527314666150225143403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 11/22/2022]
Abstract
NCS1 (neuronal calcium sensor-1) is a Ca(2+)-myristoyl switch protein of the NCS protein family involved in synaptic plasticity and neurotransmission via Ca(2+)-dependent regulation of dopamine D2 receptor and associated Gprotein coupled receptor kinase (GRK)-2. Overexpression of NCS1 in synaptic terminals results in accumulation of membrane-bound protein and its redundant regulatory activity associated with neurological disorders. Here, we have demonstrated that bovine photoreceptors contain NCS1 that is capable of a partially irreversible interaction with isolated photoreceptor membranes and implicated in Ca(2+)-dependent binding and regulation of GRK1 in vitro. Using NCS1- recoverin C-terminal chimeric construct (NR), it was found that the Ca(2+)-myristoyl switch of NCS1 is affected by its C-terminal segment downstream the fourth EF-loop of the protein, which is variable within the NCS family. NR retains structural stability and sensitivity to Ca(2+), but interacts with photoreceptor membranes with lower affinity in a Ca(2+)- dependent fully reversible manner and displays altered GRK1 modulation. These data combined with fluorescent probing of surface hydrophobicity of NCS1, NR and recoverin suggest that the C-terminal segment of NCS1 regulates reuptake of myristoyl group under Ca(2+)-free conditions and participates in organization of the target-binding pocket of the protein. We point out a putative role of NCS1 in photoreceptors as a modulator of GRK activity and propose targeting of the C-terminal segment of NCS1 as an appropriate way for selective suppression of excessive membrane accumulation and aberrant activity of the protein in neurons associated with central nervous system dysfunctions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Evgeni Y Zernii
- A.N. Belozersky Institute of Physico-Chemical Biology MSU, 119992 Leninskye gory 1, b. 40, Moscow, Russia.
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45
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Galiullina RA, Kasperkiewicz P, Chichkova NV, Szalek A, Serebryakova MV, Poreba M, Drag M, Vartapetian AB. Substrate Specificity and Possible Heterologous Targets of Phytaspase, a Plant Cell Death Protease. J Biol Chem 2015; 290:24806-15. [PMID: 26283788 DOI: 10.1074/jbc.m115.675819] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 12/17/2022] Open
Abstract
Plants lack aspartate-specific cell death proteases homologous to animal caspases. Instead, a subtilisin-like serine-dependent plant protease named phytaspase shown to be involved in the accomplishment of programmed death of plant cells is able to hydrolyze a number of peptide-based caspase substrates. Here, we determined the substrate specificity of rice (Oryza sativa) phytaspase by using the positional scanning substrate combinatorial library approach. Phytaspase was shown to display an absolute specificity of hydrolysis after an aspartic acid residue. The preceding amino acid residues, however, significantly influence the efficiency of hydrolysis. Efficient phytaspase substrates demonstrated a remarkable preference for an aromatic amino acid residue in the P3 position. The deduced optimum phytaspase recognition motif has the sequence IWLD and is strikingly hydrophobic. The established pattern was confirmed through synthesis and kinetic analysis of cleavage of a set of optimized peptide substrates. An amino acid motif similar to the phytaspase cleavage site is shared by the human gastrointestinal peptide hormones gastrin and cholecystokinin. In agreement with the established enzyme specificity, phytaspase was shown to hydrolyze gastrin-1 and cholecystokinin at the predicted sites in vitro, thus destroying the active moieties of the hormones.
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Affiliation(s)
- Raisa A Galiullina
- From the Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia and
| | - Paulina Kasperkiewicz
- Division of Bioorganic Chemistry, Department of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Nina V Chichkova
- From the Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia and
| | - Aleksandra Szalek
- Division of Bioorganic Chemistry, Department of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marina V Serebryakova
- From the Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia and
| | - Marcin Poreba
- Division of Bioorganic Chemistry, Department of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Drag
- Division of Bioorganic Chemistry, Department of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrey B Vartapetian
- From the Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia and
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46
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Zernii EY, Nazipova AA, Gancharova OS, Kazakov AS, Serebryakova MV, Zinchenko DV, Tikhomirova NK, Senin II, Philippov PP, Permyakov EA, Permyakov SE. Light-induced disulfide dimerization of recoverin under ex vivo and in vivo conditions. Free Radic Biol Med 2015; 83:283-95. [PMID: 25772009 DOI: 10.1016/j.freeradbiomed.2015.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/10/2015] [Accepted: 03/02/2015] [Indexed: 12/13/2022]
Abstract
Despite vast knowledge of the molecular mechanisms underlying photochemical damage of photoreceptors, linked to progression of age-related macular degeneration, information on specific protein targets of the light-induced oxidative stress is scarce. Here, we demonstrate that prolonged intense illumination (halogen bulb, 1500 lx, 1-5 h) of mammalian eyes under ex vivo (cow) or in vivo (rabbit) conditions induces disulfide dimerization of recoverin, a Ca(2+)-dependent inhibitor of rhodopsin kinase. Western blotting and mass spectrometry analysis of retinal extracts reveals illumination time-dependent accumulation of disulfide homodimers of recoverin and its higher order disulfide cross-linked species, including a minor fraction of mixed disulfides with intracellular proteins (tubulins, etc.). Meanwhile, monomeric bovine recoverin remains mostly reduced. These effects are accompanied by accumulation of disulfide homodimers of visual arrestin. Histological studies demonstrate that the light-induced oxidation of recoverin and arrestin occurs in intact retina (illumination for 2 h), while illumination for 5 h is associated with damage of the photoreceptor layer. A comparison of ex vivo levels of disulfide homodimers of bovine recoverin with redox dependence of its in vitro thiol-disulfide equilibrium (glutathione redox pair) gives the lowest estimate of redox potential in rod outer segments under illumination from -160 to -155 mV. Chemical crosslinking and dynamic light scattering data demonstrate an increased propensity of disulfide dimer of bovine recoverin to multimerization/aggregation. Overall, the oxidative stress caused by the prolonged intense illumination of retina might affect rhodopsin desensitization via concerted disulfide dimerization of recoverin and arrestin. The developed herein models of eye illumination are useful for studies of the light-induced thiol oxidation of visual proteins.
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Affiliation(s)
- Evgeni Yu Zernii
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia.
| | - Aliya A Nazipova
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Olga S Gancharova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Alexey S Kazakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Marina V Serebryakova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Dmitry V Zinchenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia
| | - Natalya K Tikhomirova
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Ivan I Senin
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Pavel P Philippov
- Department of Cell Signaling, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992 Russia
| | - Eugene A Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290 Russia
| | - Sergei E Permyakov
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290 Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290 Russia
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47
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Galkina SI, Fedorova NV, Serebryakova MV, Arifulin EA, Stadnichuk VI, Gaponova TV, Baratova LA, Sud'ina GF. Inhibition of the GTPase dynamin or actin depolymerisation initiates outward plasma membrane tubulation/vesiculation (cytoneme formation) in neutrophils. Biol Cell 2015; 107:144-58. [DOI: 10.1111/boc.201400063] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Svetlana I. Galkina
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Natalia V. Fedorova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Marina V. Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Evgenii A. Arifulin
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | | | - Tatjana V. Gaponova
- FGBU Hematology Research Center; Russian Federation Ministry of Public Health; Moscow 125167 Russia
| | - Ludmila A. Baratova
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
| | - Galina F. Sud'ina
- A. N. Belozersky Institute of Physico-Chemical Biology; Lomonosov Moscow State University; Moscow 119991 Russia
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48
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Andreeva AM, Lamas NE, Serebryakova MV, Ryabtseva IP, Bolshakov VV. Reorganization of low-molecular-weight fraction of plasma proteins in the annual cycle of cyprinidae. Biochemistry (Mosc) 2015; 80:208-18. [PMID: 25756535 DOI: 10.1134/s0006297915020078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Reorganization of the low-molecular-weight fraction of cyprinid plasma was analyzed using various electrophoretic techniques (disc electrophoresis, electrophoresis in polyacrylamide concentration gradient, in polyacrylamide with urea, and in SDS-polyacrylamide). The study revealed coordinated changes in the low-molecular-weight protein fractions with seasonal dynamics and related reproductive rhythms of fishes. We used cultured species of the Cyprinidae family with sequenced genomes for the detection of these interrelations in fresh-water and anadromous cyprinid species. The common features of organization of fish low-molecular-weight plasma protein fractions made it possible to make reliable identification of their proteins. MALDI mass-spectrometry analysis revealed the presence of the same proteins (hemopexin, apolipoproteins, and serpins) in the low-molecular-weight plasma fraction in wild species and cultured species with sequenced genomes (carp, zebrafish). It is found that the proteins of the first two classes are organized as complexes made of protein oligomers. Stoichiometry of these complexes changes in concordance with the seasonal and reproductive rhythms.
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Affiliation(s)
- A M Andreeva
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia.
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49
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Savvateeva LV, Gorokhovets NV, Makarov VA, Serebryakova MV, Solovyev AG, Morozov SY, Reddy VP, Zernii EY, Zamyatnin AA, Aliev G. Glutenase and collagenase activities of wheat cysteine protease Triticain-α: feasibility for enzymatic therapy assays. Int J Biochem Cell Biol 2015; 62:115-24. [PMID: 25765959 DOI: 10.1016/j.biocel.2015.03.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/24/2015] [Accepted: 03/02/2015] [Indexed: 12/27/2022]
Abstract
Insufficient and/or improper protein degradation is associated with the development of various human pathologies. Enzymatic therapy with proteolytic enzymes aimed to improve insufficient proteolytic activity was suggested as a treatment of protease deficiency-induced disorders. Since in many cases human degradome is incapable of degrading the entire target protein(s), other organisms can be used as a source of proteases exhibiting activities distinct from human enzymes, and plants are perspective candidates for this source. In this study recombinant wheat cysteine protease Triticain-α was shown to refold in vitro into an autocatalytically activated proteolytic enzyme possessing glutenase and collagenase activities at acidic (or close to neutral) pH levels at the temperature of human body. Mass-spectrometry analysis of the products of Triticain-α-catalyzed gluten hydrolysis revealed multiple cleavage sites within the sequences of gliadin toxic peptides, in particular, in the major toxic 33-mer α-gliadin-derived peptide initiating inflammatory responses to gluten in celiac disease (CD) patients. Triticain-α was found to be relatively stable in the conditions simulating stomach environment. We conclude that Triticain-α can be exploited as a basic compound for development of (i) pharmaceuticals for oral administration aimed at release of the active enzyme into the gastric lumen for CD treatment, and (ii) topically active pharmaceuticals for wound debridement applications.
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Affiliation(s)
- Lyudmila V Savvateeva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russia
| | - Neonila V Gorokhovets
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russia
| | - Vladimir A Makarov
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia
| | - Andrey G Solovyev
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia
| | - Sergey Yu Morozov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia
| | - V Prakash Reddy
- Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Evgeni Yu Zernii
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119991, Moscow, Russia; Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia.
| | - Gjumrakch Aliev
- "GALLY" International Biomedical Research Consulting LLC, San Antonio, TX, 78229, USA; School of Health Science and Healthcare Administration, The University of Atlanta, Johns Creek, GA, 30097, USA.
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50
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Brett K, Kordyukova LV, Serebryakova MV, Mintaev RR, Alexeevski AV, Veit M. Site-specific S-acylation of influenza virus hemagglutinin: the location of the acylation site relative to the membrane border is the decisive factor for attachment of stearate. J Biol Chem 2014; 289:34978-89. [PMID: 25349209 DOI: 10.1074/jbc.m114.586180] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
S-Acylation of hemagglutinin (HA), the main glycoprotein of influenza viruses, is an essential modification required for virus replication. Using mass spectrometry, we have previously demonstrated specific attachment of acyl chains to individual acylation sites. Whereas the two cysteines in the cytoplasmic tail of HA contain only palmitate, stearate is exclusively attached to a cysteine positioned at the end of the transmembrane region (TMR). Here we analyzed recombinant viruses containing HA with exchange of conserved amino acids adjacent to acylation sites or with a TMR cysteine shifted to a cytoplasmic location to identify the molecular signal that determines preferential attachment of stearate. We first developed a new protocol for sample preparation that requires less material and might thus also be suitable to analyze cellular proteins. We observed cell type-specific differences in the fatty acid pattern of HA: more stearate was attached if human viruses were grown in mammalian compared with avian cells. No underacylated peptides were detected in the mass spectra, and even mutations that prevented generation of infectious virus particles did not abolish acylation of expressed HA as demonstrated by metabolic labeling experiments with [(3)H]palmitate. Exchange of conserved amino acids in the vicinity of an acylation site had a moderate effect on the stearate content. In contrast, shifting the TMR cysteine to a cytoplasmic location virtually eliminated attachment of stearate. Thus, the location of an acylation site relative to the transmembrane span is the main signal for stearate attachment, but the sequence context and the cell type modulate the fatty acid pattern.
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Affiliation(s)
- Katharina Brett
- From the Institut für Virologie, Free University Berlin, 14163 Berlin, Germany
| | - Larisa V Kordyukova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marina V Serebryakova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ramil R Mintaev
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, I. I. Mechnikov Research Institute of Vaccines and Sera, Russian Academy of Medical Sciences, 105064 Moscow, Russia, and
| | - Andrei V Alexeevski
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Michael Veit
- From the Institut für Virologie, Free University Berlin, 14163 Berlin, Germany,
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