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Tolstova AP, Makarov AA, Adzhubei AA. Structure Comparison of Beta Amyloid Peptide Aβ 1-42 Isoforms. Molecular Dynamics Modeling. J Chem Inf Model 2024; 64:918-932. [PMID: 38241093 DOI: 10.1021/acs.jcim.3c01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Beta amyloid peptide Aβ 1-42 (Aβ42) has a unique dual role in the human organism, as both the peptide with an important physiological function and one of the most toxic biological compounds provoking Alzheimer's disease (AD). There are several known Aβ42 isoforms that we discuss here that are highly neurotoxic and lead to the early onset of AD. Aβ42 is an intrinsically disordered protein with no experimentally solved structure under physiological conditions. The objective of this research was to establish the appropriate molecular dynamics (MD) methodology and model a uniform set of structures for the Aβ42 isoforms that form the core of this study. For that purpose, force field selection and verification including convergence testing for MD simulations was made. Replica exchange MD and conventional MD modeling of several Aβ42 and Aβ16 isoforms that have neurotoxic and amyloidogenic effects impacting the severity of Alzheimer's disease were carried out with the optimal force field and solvent parameters. A standardized ensemble of structures for the Aβ42 and Aβ16 isoforms covering 30-50% of the conformational ensembles extracted from the free energy minima was calculated from MD trajectories. The resulting data set of modeled structures includes Aβ42 wild type, isoD7, pS8, D7H, and H6R-Aβ42 and Aβ16 wild type, isoD7, pS8, D7H, and H6R-Aβ16. The representative structures are given in the Supporting Information; they are open for public access. In the study, we also evaluated the differences between the structures of Aβ42 isoforms and speculate on their possible relevance to the known functions. Utilizing several representative structures for a single disordered protein for docking, with their subsequent averaging by conformations, would markedly increase the reliability of docking results.
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Affiliation(s)
- Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
- Washington University School of Medicine and Health Sciences, Washington 20052, D.C., United States
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Zhitkevich A, Bayurova E, Avdoshina D, Zakirova N, Frolova G, Chowdhury S, Ivanov A, Gordeychuk I, Palefsky JM, Isaguliants M. HIV-1 Reverse Transcriptase Expression in HPV16-Infected Epidermoid Carcinoma Cells Alters E6 Expression and Cellular Metabolism, and Induces a Hybrid Epithelial/Mesenchymal Cell Phenotype. Viruses 2024; 16:193. [PMID: 38399969 PMCID: PMC10892743 DOI: 10.3390/v16020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The high incidence of epithelial malignancies in HIV-1 infected individuals is associated with co-infection with oncogenic viruses, such as high-risk human papillomaviruses (HR HPVs), mostly HPV16. The molecular mechanisms underlying the HIV-1-associated increase in epithelial malignancies are not fully understood. A collaboration between HIV-1 and HR HPVs in the malignant transformation of epithelial cells has long been anticipated. Here, we delineated the effects of HIV-1 reverse transcriptase on the in vitro and in vivo properties of HPV16-infected cervical cancer cells. A human cervical carcinoma cell line infected with HPV16 (Ca Ski) was made to express HIV-1 reverse transcriptase (RT) by lentiviral transduction. The levels of the mRNA of the E6 isoforms and of the factors characteristic to the epithelial/mesenchymal transition were assessed by real-time RT-PCR. The parameters of glycolysis and mitochondrial respiration were determined using Seahorse technology. RT expressing Ca Ski subclones were assessed for the capacity to form tumors in nude mice. RT expression increased the expression of the E6*I isoform, modulated the expression of E-CADHERIN and VIMENTIN, indicating the presence of a hybrid epithelial/mesenchymal phenotype, enhanced glycolysis, and inhibited mitochondrial respiration. In addition, the expression of RT induced phenotypic alterations impacting cell motility, clonogenic activity, and the capacity of Ca Ski cells to form tumors in nude mice. These findings suggest that HIV-RT, a multifunctional protein, affects HPV16-induced oncogenesis, which is achieved through modulation of the expression of the E6 oncoprotein. These results highlight a complex interplay between HIV antigens and HPV oncoproteins potentiating the malignant transformation of epithelial cells.
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Affiliation(s)
- Alla Zhitkevich
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 119991 Moscow, Russia; (E.B.); (D.A.); (G.F.); (I.G.)
| | - Ekaterina Bayurova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 119991 Moscow, Russia; (E.B.); (D.A.); (G.F.); (I.G.)
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Darya Avdoshina
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 119991 Moscow, Russia; (E.B.); (D.A.); (G.F.); (I.G.)
| | - Natalia Zakirova
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia;
| | - Galina Frolova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 119991 Moscow, Russia; (E.B.); (D.A.); (G.F.); (I.G.)
| | - Sona Chowdhury
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA 94143, USA; (S.C.); (J.M.P.)
| | - Alexander Ivanov
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia;
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, 119991 Moscow, Russia;
| | - Ilya Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 119991 Moscow, Russia; (E.B.); (D.A.); (G.F.); (I.G.)
- Gamaleya National Research Center for Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Joel M. Palefsky
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, CA 94143, USA; (S.C.); (J.M.P.)
| | - Maria Isaguliants
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
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Kulovic-Sissawo A, Tocantins C, Diniz MS, Weiss E, Steiner A, Tokic S, Madreiter-Sokolowski CT, Pereira SP, Hiden U. Mitochondrial Dysfunction in Endothelial Progenitor Cells: Unraveling Insights from Vascular Endothelial Cells. BIOLOGY 2024; 13:70. [PMID: 38392289 PMCID: PMC10886154 DOI: 10.3390/biology13020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Endothelial dysfunction is associated with several lifestyle-related diseases, including cardiovascular and neurodegenerative diseases, and it contributes significantly to the global health burden. Recent research indicates a link between cardiovascular risk factors (CVRFs), excessive production of reactive oxygen species (ROS), mitochondrial impairment, and endothelial dysfunction. Circulating endothelial progenitor cells (EPCs) are recruited into the vessel wall to maintain appropriate endothelial function, repair, and angiogenesis. After attachment, EPCs differentiate into mature endothelial cells (ECs). Like ECs, EPCs are also susceptible to CVRFs, including metabolic dysfunction and chronic inflammation. Therefore, mitochondrial dysfunction of EPCs may have long-term effects on the function of the mature ECs into which EPCs differentiate, particularly in the presence of endothelial damage. However, a link between CVRFs and impaired mitochondrial function in EPCs has hardly been investigated. In this review, we aim to consolidate existing knowledge on the development of mitochondrial and endothelial dysfunction in the vascular endothelium, place it in the context of recent studies investigating the consequences of CVRFs on EPCs, and discuss the role of mitochondrial dysfunction. Thus, we aim to gain a comprehensive understanding of mechanisms involved in EPC deterioration in relation to CVRFs and address potential therapeutic interventions targeting mitochondrial health to promote endothelial function.
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Affiliation(s)
- Azra Kulovic-Sissawo
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Carolina Tocantins
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Mariana S Diniz
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Doctoral Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3004-531 Coimbra, Portugal
| | - Elisa Weiss
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Andreas Steiner
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
| | - Silvija Tokic
- Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - Corina T Madreiter-Sokolowski
- Division of Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Susana P Pereira
- CNC-UC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, 3004-504 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3000-504 Coimbra, Portugal
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, 4200-450 Porto, Portugal
| | - Ursula Hiden
- Perinatal Research Laboratory, Department of Obstetrics and Gynaecology, Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Auenbruggerplatz 14, 8036 Graz, Austria
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Guo W, Hassan LA, Chu YH, Yang XP, Wang SX, Zhu HX, Li Y. Mapping trends and hotspots of mitochondrial dysfunction in Alzheimer's disease from 2013 to 2022: a bibliometric analysis of global research. Front Neurosci 2023; 17:1199625. [PMID: 37434768 PMCID: PMC10330782 DOI: 10.3389/fnins.2023.1199625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
Objective Alzheimer's disease (AD), a prevalent neurodegenerative affliction that predominantly affects the elderly population, imposes a substantial burden on not only patients but also their families and society at large. Mitochondrial dysfunction plays an important role in its pathogenesis. In this study, we conducted a bibliometric analysis of research on mitochondrial dysfunction and AD over the past 10 years, with the aim of summarizing current research hotspots and trends in this field. Methods On February 12, 2023, we searched for publications about mitochondrial dysfunction and AD in the Web of Science Core Collection database from 2013 to 2022. VOSview software, CiteSpace, SCImago, and RStudio were used to analyze and visualize countries, institutions, journals, keywords, and references. Results The number of publications on mitochondrial dysfunction and AD were on the rise until 2021 and decreased slightly in 2022. The United States ranks first in the number of publications, H-index, and intensity of international cooperation in this research. In terms of institutions, Texas Tech University in the United States has the most publications. The Journal of Alzheimer's Disease has the most publications in this field of research, while Oxidative Medicine and Cellular Longevity have the highest number of citations. Mitochondrial dysfunction is still an important direction of current research. Autophagy, mitochondrial autophagy, and neuroinflammation are new hotspots. The article from Lin MT is the most cited by analyzing references. Conclusion Research on mitochondrial dysfunction in AD is gaining significant momentum as it provides a crucial research avenue for the treatment of this debilitating condition. This study sheds light on the present research trajectory concerning the molecular mechanisms underlying mitochondrial dysfunction in AD.
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Affiliation(s)
- Wang Guo
- Clinical Medical School, Dali University, Dali, China
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Liban Abdulle Hassan
- Clinical Medical School, Dali University, Dali, China
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Yu-hao Chu
- Clinical Medical School, Dali University, Dali, China
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Xue-ping Yang
- Clinical Medical School, Dali University, Dali, China
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Sheng-xue Wang
- Clinical Medical School, Dali University, Dali, China
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Han-xiao Zhu
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
| | - Yun Li
- Department of Neurology, The First Affiliated Hospital of Dali University, Dali, China
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Petrovskaya A, Tverskoi A, Medvedeva A, Nazarova M. Is blood-brain barrier a probable mediator of non-invasive brain stimulation effects on Alzheimer's disease? Commun Biol 2023; 6:416. [PMID: 37059824 PMCID: PMC10104838 DOI: 10.1038/s42003-023-04717-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/16/2023] [Indexed: 04/16/2023] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease with no existing treatment leading to full recovery. The blood-brain barrier (BBB) breakdown usually precedes the advent of first symptoms in AD and accompanies the progression of the disease. At the same time deliberate BBB opening may be beneficial for drug delivery in AD. Non-invasive brain stimulation (NIBS) techniques, primarily transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS), have shown multiple evidence of being able to alleviate symptoms of AD. Currently, TMS/tDCS mechanisms are mostly investigated in terms of their neuronal effects, while their possible non-neuronal effects, including mitigation of the BBB disruption, are less studied. We argue that studies of TMS/tDCS effects on the BBB in AD are necessary to boost the effectiveness of neuromodulation in AD. Moreover, such studies are important considering the safety issues of TMS/tDCS use in the advanced AD stages when the BBB is usually dramatically deteriorated. Here, we elucidate the evidence of NIBS-induced BBB opening and closing in various models from in vitro to humans, and highlight its importance in AD.
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Affiliation(s)
- Aleksandra Petrovskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Artem Tverskoi
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Angela Medvedeva
- Department of Chemistry, Rice University, Houston, TX, 77005, US
| | - Maria Nazarova
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02129, USA
- Center for Cognition and Decision Making, Institute for Cognitive Neuroscience, National Research University Higher School of Economics, Moscow, 101000, Russian Federation
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Petrushanko IY, Mitkevich VA, Makarov AA. Effect of β-amyloid on blood-brain barrier properties and function. Biophys Rev 2023; 15:183-197. [PMID: 37124923 PMCID: PMC10133432 DOI: 10.1007/s12551-023-01052-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
The deposition of beta-amyloid (Aβ) aggregates in the brain, accompanied by impaired cognitive function, is a characteristic feature of Alzheimer's disease (AD). An important role in this process is played by vascular disorders, in particular, a disturbance of the blood-brain barrier (BBB). The BBB controls the entry of Aβ from plasma to the brain via the receptor for advanced glycation end products (RAGE) and the removal of brain-derived Aβ via the low-density lipoprotein receptor-related protein (LRP1). The balance between the input of Aβ to the brain from the periphery and its output is disturbed during AD. Aβ changes the redox-status of BBB cells, which in turn changes the functioning of mitochondria and disrupts the barrier function of endothelial cells by affecting tight junction proteins. Aβ oligomers have the greatest toxic effect on BBB cells, and oligomers are most rapidly transferred by transcytosis from the brain side of the BBB to the blood side. Both the cytotoxic effect of Aβ and the impairment of barrier function are partly due to the interaction of Aβ monomers and oligomers with membrane-bound RAGE. AD therapies based on the disruption of this interaction or the creation of decoys for Aβ are being developed. The question of the transfer of various Aβ isoforms through the BBB is important, since it can influence the development of AD. It is shown that the rate of input of Aβ40 and Aβ42 from the blood into the brain is different. The actual question of the transfer of pathogenic Aβ isoforms with post-translational modifications or mutations through the BBB still remains open.
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Affiliation(s)
- Irina Yu. Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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