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K P, Madhana PN, Eswaramoorthy R, Ramasamy M. A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis. Metab Brain Dis 2024; 39:545-558. [PMID: 38185715 DOI: 10.1007/s11011-024-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.
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Affiliation(s)
- Priyanka K
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Priya N Madhana
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, TamilNadu, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India.
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Rapid assembly of 1,3-indanedione-based spirocyclic tetrahydroquinolines for inducing human lung cancer cell apoptosis. GREEN SYNTHESIS AND CATALYSIS 2022. [DOI: 10.1016/j.gresc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Kim WD, Wilson-Smillie MLDM, Thanabalasingam A, Lefrancois S, Cotman SL, Huber RJ. Autophagy in the Neuronal Ceroid Lipofuscinoses (Batten Disease). Front Cell Dev Biol 2022; 10:812728. [PMID: 35252181 PMCID: PMC8888908 DOI: 10.3389/fcell.2022.812728] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs), also referred to as Batten disease, are a family of neurodegenerative diseases that affect all age groups and ethnicities around the globe. At least a dozen NCL subtypes have been identified that are each linked to a mutation in a distinct ceroid lipofuscinosis neuronal (CLN) gene. Mutations in CLN genes cause the accumulation of autofluorescent lipoprotein aggregates, called ceroid lipofuscin, in neurons and other cell types outside the central nervous system. The mechanisms regulating the accumulation of this material are not entirely known. The CLN genes encode cytosolic, lysosomal, and integral membrane proteins that are associated with a variety of cellular processes, and accumulated evidence suggests they participate in shared or convergent biological pathways. Research across a variety of non-mammalian and mammalian model systems clearly supports an effect of CLN gene mutations on autophagy, suggesting that autophagy plays an essential role in the development and progression of the NCLs. In this review, we summarize research linking the autophagy pathway to the NCLs to guide future work that further elucidates the contribution of altered autophagy to NCL pathology.
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Affiliation(s)
- William D. Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | | | - Aruban Thanabalasingam
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Stephane Lefrancois
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique, Laval, QC, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre D'Excellence en Recherche sur Les Maladies Orphelines–Fondation Courtois (CERMO-FC), Université Du Québec à Montréal (UQAM), Montréal, QC, Canada
| | - Susan L. Cotman
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA, United States
| | - Robert J. Huber
- Department of Biology, Trent University, Peterborough, ON, Canada
- *Correspondence: Robert J. Huber,
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McGinn RJ, Von Stein EL, Summers Stromberg JE, Li Y. Precision medicine in epilepsy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 190:147-188. [DOI: 10.1016/bs.pmbts.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gardner E, Bailey M, Schulz A, Aristorena M, Miller N, Mole SE. Mutation update: Review of TPP1 gene variants associated with neuronal ceroid lipofuscinosis CLN2 disease. Hum Mutat 2019; 40:1924-1938. [PMID: 31283065 PMCID: PMC6851559 DOI: 10.1002/humu.23860] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 01/03/2023]
Abstract
Neuronal ceroid lipofuscinosis type 2 (CLN2 disease) is an autosomal recessive condition caused by variants in the TPP1 gene, leading to deficient activity of the lysosomal enzyme tripeptidyl peptidase I (TPP1). We update on the spectrum of TPP1 variants associated with CLN2 disease, comprising 131 unique variants from 389 individuals (717 alleles) collected from the literature review, public databases, and laboratory communications. Previously unrecorded individuals were added to the UCL TPP1‐specific database. Two known pathogenic variants, c.509–1 G>C and c.622 C>T (p.(Arg208*)), collectively occur in 60% of affected individuals in the sample, and account for 50% of disease‐associated alleles. At least 86 variants (66%) are private to single families. Homozygosity occurs in 45% of individuals where both alleles are known (87% of reported individuals). Atypical CLN2 disease, TPP1 enzyme deficiency with disease onset and/or progression distinct from classic late‐infantile CLN2, represents 13% of individuals recorded with associated phenotype. NCBI ClinVar currently holds records for 37% of variants collected here. Effective CLN2 disease management requires early diagnosis; however, irreversible neurodegeneration occurs before a diagnosis is typically reached at age 5. Timely classification and public reporting of TPP1 variants is essential as molecular testing increases in use as a first‐line diagnostic test for pediatric‐onset neurological disease.
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Affiliation(s)
- Emily Gardner
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Mitch Bailey
- Global Scientific Affairs, BioMarin Pharmaceutical Inc, Novato, California
| | - Angela Schulz
- Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mikel Aristorena
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nicole Miller
- Global Scientific Affairs, BioMarin Pharmaceutical Inc, Novato, California
| | - Sara E Mole
- UCL MRC Laboratory for Molecular Cell Biology and UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Zorov DB, Vorobjev IA, Popkov VA, Babenko VA, Zorova LD, Pevzner IB, Silachev DN, Zorov SD, Andrianova NV, Plotnikov EY. Lessons from the Discovery of Mitochondrial Fragmentation (Fission): A Review and Update. Cells 2019; 8:E175. [PMID: 30791381 PMCID: PMC6406845 DOI: 10.3390/cells8020175] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/12/2023] Open
Abstract
Thirty-five years ago, we described fragmentation of the mitochondrial population in a living cell into small vesicles (mitochondrial fission). Subsequently, this phenomenon has become an object of general interest due to its involvement in the process of oxidative stress-related cell death and having high relevance to the incidence of a pathological phenotype. Tentatively, the key component of mitochondrial fission process is segregation and further asymmetric separation of a mitochondrial body yielding healthy (normally functioning) and impaired (incapable to function in a normal way) organelles with subsequent decomposition and removal of impaired elements through autophagy (mitophagy). We speculate that mitochondria contain cytoskeletal elements, which maintain the mitochondrial shape, and also are involved in the process of intramitochondrial segregation of waste products. We suggest that perturbation of the mitochondrial fission/fusion machinery and slowdown of the removal process of nonfunctional mitochondrial structures led to the increase of the proportion of impaired mitochondrial elements. When the concentration of malfunctioning mitochondria reaches a certain threshold, this can lead to various pathologies, including aging. Overall, we suggest a process of mitochondrial fission to be an essential component of a complex system controlling a healthy cell phenotype. The role of reactive oxygen species in mitochondrial fission is discussed.
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Affiliation(s)
- Dmitry B Zorov
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Ivan A Vorobjev
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana 010000, Kazakhstan.
| | - Vasily A Popkov
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Valentina A Babenko
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Ljubava D Zorova
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Irina B Pevzner
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Denis N Silachev
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
| | - Savva D Zorov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Nadezda V Andrianova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Egor Y Plotnikov
- A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia.
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow 117997, Russia.
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119146, Russia.
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Dimitrova MB, Atanasova DY, Lazarov NE. Histochemical Demonstration of Tripeptidyl Aminopeptidase I. Methods Mol Biol 2017; 1560:55-68. [PMID: 28155145 DOI: 10.1007/978-1-4939-6788-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Enzyme histochemical methods are valuable for the studies on the enzyme involvement in different pathological processes. Here we describe two protocols for chromogenic and fluorogenic histochemical demonstration of tripeptidyl aminopeptidase I (TPPI), a protease that is crucial for neuronal functions. The procedures are based on newly synthesized substrates for TPPI-glycyl-L-prolyl-L-metionyl-5-chloro-1-anthraquinonylhydrazide (GPM-CAH) and glycyl-L-prolyl-L-metionyl-4-hydrazido-N-hexyl-1,8-naphthalimide (GPM-HHNI). Using such protocols, precise enzyme localization can be obtained in tissue sections of mammalian organs.
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Affiliation(s)
- Mashenka B Dimitrova
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Dimitrinka Y Atanasova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Department of Anatomy, Faculty of Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nikolai E Lazarov
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
- Department of Anatomy and Histology, Medical University of Sofia, 2, Zdrave Street, 1431, Sofia, Bulgaria.
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Effect of acute hypoxic shock on the rat brain morphology and tripeptidyl peptidase I activity. Acta Histochem 2016; 118:496-504. [PMID: 27263093 DOI: 10.1016/j.acthis.2016.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/17/2016] [Indexed: 11/21/2022]
Abstract
Hypoxic events are known to cause substantial damage to the hippocampus, cerebellum and striatum. The impact of hypoxic shock on other brain parts is not sufficiently studied. Recent studies show that tripeptidyl peptidase I (TPPI) activity in fish is altered after a hypoxic stress pointing out at a possible enzyme involvement in response to hypoxia. Similar studies are not performed in mammals. In this work, the effect of sodium nitrite-induced acute hypoxic shock on the rat brain was studied at different post-treatment periods. Morphological changes in cerebral cortex, cerebellum, medulla oblongata, thalamus, mesencephalon and pons were assessed using silver-copper impregnation for neurodegeneration. TPPI activity was biochemically assayed and localized by enzyme histochemistry. Although less vulnerable to oxidative stress, the studied brain areas showed different histopathological changes, such as neuronal loss and tissue vacuolization, dilatation of the smallest capillaries and impairment of neuronal processes. TPPI activity was strictly regulated following the hypoxic stress. It was found to increase 12-24h post-treatment, then decreased followed by a slow process of recovery. The enzyme histochemistry revealed a temporary enzyme deficiency in all types of neurons. These findings indicate a possible involvement of the enzyme in rat brain response to hypoxic stress.
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Kiselyov K, Muallem S. ROS and intracellular ion channels. Cell Calcium 2016; 60:108-14. [PMID: 26995054 DOI: 10.1016/j.ceca.2016.03.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 12/15/2022]
Abstract
Oxidative stress is a well-known driver of numerous pathological processes involving protein and lipid peroxidation and DNA damage. The resulting increase of pro-apoptotic pressure drives tissue damage in a host of conditions, including ischemic stroke and reperfusion injury, diabetes, death in acute pancreatitis and neurodegenerative diseases. Somewhat less frequently discussed, but arguably as important, is the signaling function of oxidative stress stemming from the ability of oxidative stress to modulate ion channel activity. The evidence for the modulation of the intracellular ion channels and transporters by oxidative stress is constantly emerging and such evidence suggests new regulatory and pathological circuits that can be explored towards new treatments for diseases in which oxidative stress is an issue. In this review we summarize the current knowledge on the effects of oxidative stress on the intracellular ion channels and transporters and their role in cell function.
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Affiliation(s)
- Kirill Kiselyov
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States; Epithelial Signaling and Transport Section, Molecular Physiology and Therapeutics Branch NIH, NIDCR, Bethesda, MD 20892, United States.
| | - Shmuel Muallem
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States; Epithelial Signaling and Transport Section, Molecular Physiology and Therapeutics Branch NIH, NIDCR, Bethesda, MD 20892, United States.
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Heiss EH, Kramer MP, Atanasov AG, Beres H, Schachner D, Dirsch VM. Glycolytic switch in response to betulinic acid in non-cancer cells. PLoS One 2014; 9:e115683. [PMID: 25531780 PMCID: PMC4274109 DOI: 10.1371/journal.pone.0115683] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022] Open
Abstract
The naturally occurring triterpenoid betulinic acid (BA) shows pronounced polypharmacology ranging from anti-inflammatory to anti-lipogenic activities. Recent evidence suggests that rather diverse cellular signaling events may be attributed to the same common upstream switch in cellular metabolism. In this study we therefore examined the metabolic changes induced by BA (10 µM) administration, with focus on cellular glucose metabolism. We demonstrate that BA elevates the rates of cellular glucose uptake and aerobic glycolysis in mouse embryonic fibroblasts with concomitant reduction of glucose oxidation. Without eliciting signs of obvious cell death BA leads to compromised mitochondrial function, increased expression of mitochondrial uncoupling proteins (UCP) 1 and 2, and liver kinase B1 (LKB1)-dependent activation AMP-activated protein kinase. AMPK activation accounts for the increased glucose uptake and glycolysis which in turn are indispensable for cell viability upon BA treatment. Overall, we show for the first time a significant impact of BA on cellular bioenergetics which may be a central mediator of the pleiotropic actions of BA.
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Affiliation(s)
- Elke H. Heiss
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Matthias P. Kramer
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Atanas G. Atanasov
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Hortenzia Beres
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Daniel Schachner
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Verena M. Dirsch
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
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