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Wang J, Xu Y, Wang X, Li J, Hua Z. Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study. Molecules 2024; 29:1071. [PMID: 38474583 DOI: 10.3390/molecules29051071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp's ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design.
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Affiliation(s)
- Jingyao Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yicong Xu
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xujian Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
| | - Zichun Hua
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing 210023, China
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2
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Ripoli C, Dagliyan O, Renna P, Pastore F, Paciello F, Sollazzo R, Rinaudo M, Battistoni M, Martini S, Tramutola A, Sattin A, Barone E, Saneyoshi T, Fellin T, Hayashi Y, Grassi C. Engineering memory with an extrinsically disordered kinase. SCIENCE ADVANCES 2023; 9:eadh1110. [PMID: 37967196 PMCID: PMC10651130 DOI: 10.1126/sciadv.adh1110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
Synaptic plasticity plays a crucial role in memory formation by regulating the communication between neurons. Although actin polymerization has been linked to synaptic plasticity and dendritic spine stability, the causal link between actin polymerization and memory encoding has not been identified yet. It is not clear whether actin polymerization and structural changes in dendritic spines are a driver or a consequence of learning and memory. Using an extrinsically disordered form of the protein kinase LIMK1, which rapidly and precisely acts on ADF/cofilin, a direct modifier of actin, we induced long-term enlargement of dendritic spines and enhancement of synaptic transmission in the hippocampus on command. The activation of extrinsically disordered LIMK1 in vivo improved memory encoding and slowed cognitive decline in aged mice exhibiting reduced cofilin phosphorylation. The engineered memory by an extrinsically disordered LIMK1 supports a direct causal link between actin-mediated synaptic transmission and memory.
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Affiliation(s)
- Cristian Ripoli
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Onur Dagliyan
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17165 Stockholm, Sweden
| | - Pietro Renna
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Francesco Pastore
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Fabiola Paciello
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Raimondo Sollazzo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Marco Rinaudo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Martina Battistoni
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sara Martini
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Antonella Tramutola
- Department of Biochemical Sciences “A. Rossi-Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
| | - Andrea Sattin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Eugenio Barone
- Department of Biochemical Sciences “A. Rossi-Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
| | - Takeo Saneyoshi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Tommaso Fellin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Yasunori Hayashi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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3
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Li Puma DD, Colussi C, Bandiera B, Puliatti G, Rinaudo M, Cocco S, Paciello F, Re A, Ripoli C, De Chiara G, Bertozzi A, Palamara AT, Piacentini R, Grassi C. Interleukin 1β triggers synaptic and memory deficits in Herpes simplex virus type-1-infected mice by downregulating the expression of synaptic plasticity-related genes via the epigenetic MeCP2/HDAC4 complex. Cell Mol Life Sci 2023; 80:172. [PMID: 37261502 DOI: 10.1007/s00018-023-04817-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/02/2023]
Abstract
Extensive research provides evidence that neuroinflammation underlies numerous brain disorders. However, the molecular mechanisms by which inflammatory mediators determine synaptic and cognitive dysfunction occurring in neurodegenerative diseases (e.g., Alzheimer's disease) are far from being fully understood. Here we investigated the role of interleukin 1β (IL-1β), and the molecular cascade downstream the activation of its receptor, to the synaptic dysfunction occurring in the mouse model of multiple Herpes simplex virus type-1 (HSV-1) reactivations within the brain. These mice are characterized by neuroinflammation and memory deficits associated with a progressive accumulation of neurodegenerative hallmarks (e.g., amyloid-β protein and tau hyperphosphorylation). Here we show that mice undergone two HSV-1 reactivations in the brain exhibited increased levels of IL-1β along with significant alterations of: (1) cognitive performances; (2) hippocampal long-term potentiation; (3) expression synaptic-related genes and pre- and post-synaptic proteins; (4) dendritic spine density and morphology. These effects correlated with activation of the epigenetic repressor MeCP2 that, in association with HDAC4, affected the expression of synaptic plasticity-related genes. Specifically, in response to HSV-1 infection, HDAC4 accumulated in the nucleus and promoted MeCP2 SUMOylation that is a post-translational modification critically affecting the repressive activity of MeCP2. The blockade of IL-1 receptors by the specific antagonist Anakinra prevented the MeCP2 increase and the consequent downregulation of gene expression along with rescuing structural and functional indices of neurodegeneration. Collectively, our findings provide novel mechanistic evidence on the role played by HSV-1-activated IL-1β signaling pathways in synaptic deficits leading to cognitive impairment.
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Affiliation(s)
- Domenica Donatella Li Puma
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Claudia Colussi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, 00185, Rome, Italy
| | - Bruno Bandiera
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Giulia Puliatti
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Rinaudo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Sara Cocco
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Fabiola Paciello
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Agnese Re
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Cristian Ripoli
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Giovanna De Chiara
- Institute of Translational Pharmacology, National Research Council (CNR), 00133, Rome, Italy
| | - Alessia Bertozzi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti", National Research Council, 00185, Rome, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore Di Sanità, 00161, Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Cenci Bolognetti Foundation, 00185, Rome, Italy
| | - Roberto Piacentini
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
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Colussi C, Aceto G, Ripoli C, Bertozzi A, Li Puma DD, Paccosi E, D'Ascenzo M, Grassi C. Cytoplasmic HDAC4 recovers synaptic function in the 3×Tg mouse model of Alzheimer's disease. Neuropathol Appl Neurobiol 2023; 49:e12861. [PMID: 36331820 PMCID: PMC10099707 DOI: 10.1111/nan.12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/26/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
Abstract
AIMS Early dysfunction in Alzheimer's disease (AD) is characterised by alterations of synapse structure and function leading to dysmorphic neurites, decreased spine density, impaired synaptic plasticity and cognitive deficits. The class II member HDAC4, which recently emerged as a crucial factor in shaping synaptic plasticity and memory, was found to be altered in AD. We investigated how the modulation of HDAC4 may contribute to counteracting AD pathogenesis. METHODS Using a cytoplasmic HDAC4 mutant (HDAC4SD ), we studied the recovery of synaptic function in hippocampal tissue and primary neurons from the triple-transgenic mouse model of AD (3×Tg-AD). RESULTS Here, we report that in wild-type mice, HDAC4 is localised at synapses and interacts with postsynaptic proteins, whereas in the 3×Tg-AD, it undergoes nuclear import, reducing its interaction with synaptic proteins. Of note, HDAC4 delocalisation was induced by both amyloid-β and tau accumulation. Overexpression of the HDAC4SD mutant in CA1 pyramidal neurons of organotypic hippocampal slices obtained from 3×Tg-AD mice increased dendritic length and promoted the enrichment of N-cadherin, GluA1, PSD95 and CaMKII proteins at the synaptic level compared with AD neurons transfected with the empty vector. Moreover, HDAC4 overexpression recovered the level of SUMO2/3ylation of PSD95 in AD hippocampal tissue, and in AD organotypic hippocampal slices, the HDAC4SD rescued spine density and synaptic transmission. CONCLUSIONS These results highlight a new role of cytoplasmic HDAC4 in providing a structural and enzymatic regulation of postsynaptic proteins. Our findings suggest that controlling HDAC4 localisation may represent a promising strategy to rescue synaptic function in AD, potentially leading to memory improvement.
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Affiliation(s)
- Claudia Colussi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Giuseppe Aceto
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Cristian Ripoli
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alessia Bertozzi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy
| | - Domenica Donatella Li Puma
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Elena Paccosi
- Department of Engineering, Istituto di Analisi dei Sistemi ed Informatica 'Antonio Ruberti', National Research Council, Rome, Italy
| | - Marcello D'Ascenzo
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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A Bioengineering Strategy to Control ADAM10 Activity in Living Cells. Int J Mol Sci 2023; 24:ijms24020917. [PMID: 36674432 PMCID: PMC9863580 DOI: 10.3390/ijms24020917] [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: 12/08/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
A Disintegrin and Metalloprotease 10, also known as ADAM10, is a cell surface protease ubiquitously expressed in mammalian cells where it cuts several membrane proteins implicated in multiple physiological processes. The dysregulation of ADAM10 expression and function has been implicated in pathological conditions, including Alzheimer's disease (AD). Although it has been suggested that ADAM10 is expressed as a zymogen and the removal of the prodomain results in its activation, other potential mechanisms for the ADAM10 proteolytic function and activation remain unclear. Another suggested mechanism is post-translational modification of the cytoplasmic domain, which regulates ADAM10-dependent protein ectodomain shedding. Therefore, the precise and temporal activation of ADAM10 is highly desirable to reveal the fine details of ADAM10-mediated cleavage mechanisms and protease-dependent therapeutic applications. Here, we present a strategy to control prodomain and cytosolic tail cleavage to regulate ADAM10 shedding activity without the intervention of small endogenous molecule signaling pathways. We generated a series of engineered ADAM10 analogs containing Tobacco Etch Virus protease (TEV) cleavage site (TEVcs), rendering ADAM10 cleavable by TEV. This strategy revealed that, in the absence of other stimuli, the TEV-mediated removal of the prodomain could not activate ADAM10. However, the TEV-mediated cleavage of the cytosolic domain significantly increased ADAM10 activity. Then, we generated ADAM10 with a minimal constitutively catalytic activity that increased significantly in the presence of TEV or after activating a chemically activatable TEV. Our results revealed a bioengineering strategy for controlling the ADAM10 activity in living cells, paving the way to obtain spatiotemporal control of ADAM10. Finally, we proved that our approach of controlling ADAM10 promoted α-secretase activity and the non-amyloidogenic cleavage of amyloid-β precursor protein (APP), thereby increasing the production of the neuroprotective soluble ectodomain (sAPPα). Our bioengineering strategy has the potential to be exploited as a next-generation gene therapy for AD.
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Barbati SA, Podda MV, Grassi C. Tuning brain networks: The emerging role of transcranial direct current stimulation on structural plasticity. Front Cell Neurosci 2022; 16:945777. [PMID: 35936497 PMCID: PMC9351051 DOI: 10.3389/fncel.2022.945777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique (NIBS) that has been proven to promote beneficial effects in a range of neurological and psychiatric disorders. Unfortunately, although has been widely investigated, the mechanism comprehension around tDCS effects presents still some gaps. Therefore, scientists are still trying to uncover the cellular and molecular mechanisms behind its positive effects to permit a more suitable application. Experimental models have provided converging evidence that tDCS elicits improvements in learning and memory by modulating both excitability and synaptic plasticity in neurons. Recently, among tDCS neurobiological effects, neural synchronization and dendritic structural changes have been reported in physiological and pathological conditions, suggesting possible effects at the neuronal circuit level. In this review, we bring in to focus the emerging effects of tDCS on the structural plasticity changes and neuronal rewiring, with the intent to match these two aspects with the underpinning molecular mechanisms identified so far, providing a new perspective to work on to unveil novel tDCS therapeutic use to treat brain dysfunctions.
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Affiliation(s)
| | - Maria Vittoria Podda
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- *Correspondence: Maria Vittoria Podda,
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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