1
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Tammara V, Das A. Governing dynamics and preferential binding of the AXH domain influence the aggregation pathway of Ataxin-1. Proteins 2023; 91:380-394. [PMID: 36208132 DOI: 10.1002/prot.26436] [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: 03/15/2022] [Revised: 08/30/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
The present state of understanding the mechanism of Spinocerebellar Ataxia-1, a fatal neurodegenerative disease linked to the protein Ataxin-1 (ATXN1), is baffled by a set of self-contradictory, and hence, inconclusive observations. This fallacy poses a bottleneck to the effective designing of curable drugs as the field is currently missing the specific druggable site. To understand the fundamentals of pathogenesis, we tried to decipher the intricacies of the extremely complicated landscape by targeting the relevant species that supposedly dictate the structure-function paradigm. The atomic-level description and characterization of the dynamism of the systems reveal the existence of structural polymorphism in all the leading stakeholders of the overall system. The very existence of conformational heterogeneity in every species creates numerous possible combinations of favorable interactions because of the variability in segmental cross-talks and hence claims its role in the choice of routes between functional activity and dysfunctional disease-causing aggregation. Despite this emergent configurational diversity, there is a common mode of operative intermolecular forces that dictates the extent of stability of all the multimeric complexes due to the localized population of a specific type of residue. The present research proposes a dynamic switch mechanism between aggregability and functional activity, based on the logical interpretation of the estimated variables, which is practically dictated by the effective concentration of the interacting species involved in the cell.
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Affiliation(s)
- Vaishnavi Tammara
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Miceli M, Deriu MA, Grasso G. Toward the design and development of peptidomimetic inhibitors of the Ataxin-1 aggregation pathway. Biophys J 2022; 121:4679-4688. [PMID: 36262042 PMCID: PMC9748251 DOI: 10.1016/j.bpj.2022.10.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/09/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022] Open
Abstract
Spinocerebellar ataxia type 1 is a degenerative disorder caused by polyglutamine expansions and aggregation of Ataxin-1. The interaction between Capicua (CIC) and the AXH domain of Ataxin-1 protein has been suggested as a possible driver of aggregation for the expanded Ataxin-1 protein and the subsequent onset of spinocerebellar ataxia 1. Experimental studies have demonstrated that short constructs of CIC may prevent such aggregation and suggested this as a possible candidate to inspire the rational design of peptidomimetics. In this work, molecular modeling techniques, namely the alchemical mutation and force field-based molecular dynamics, have been employed to propose a pipeline for the rational design of a CIC-inspired inhibitor of the ataxin-1 aggregation pathway. In particular, this study has shown that the alchemical mutation can estimate the affinity between AXH and CIC with good correlation with experimental data, while molecular dynamics shed light on molecular mechanisms that occur for stabilization of the interaction between the CIC-inspired construct and the AXH domain of Ataxin-1. This work lays the foundation for a rational methodology for the in silico screening and design of peptidomimetics, which can expedite and streamline experimental studies to identify strategies for inhibiting the ataxin-1 aggregation pathway.
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Affiliation(s)
- Marcello Miceli
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence Research, Scuola Universitaria Professionale della Svizzera Italiana, Lugano-Viganello, Switzerland.
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3
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Cannariato M, Miceli M, Deriu MA. In silico investigation of Alsin RLD conformational dynamics and phosphoinositides binding mechanism. PLoS One 2022; 17:e0270955. [PMID: 35849605 PMCID: PMC9292110 DOI: 10.1371/journal.pone.0270955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Alsin is a protein known for its major role in neuronal homeostasis and whose mutation is associated with early-onset neurodegenerative diseases. It has been shown that its relocalization from the cytoplasm to the cell membrane is crucial to induce early endosomes maturation. In particular, evidences suggest that the N-terminal regulator of chromosome condensation 1 like domain (RLD) is necessary for membrane association thanks to its affinity to phosphoinositides, membrane lipids involved in the regulation of several signaling processes. Interestingly, this domain showed affinity towards phosphatidylinositol 3-phosphate [PI(3)P], which is highly expressed in endosomes membrane. However, Alsin structure has not been experimentally resolved yet and molecular mechanisms associated with its biological functions are mostly unknown. In this work, Alsin RLD has been investigated through computational molecular modeling techniques to analyze its conformational dynamics and obtain a representative 3D model of this domain. Moreover, a putative phosphoinositide binding site has been proposed and PI(3)P interaction mechanism studied. Results highlight the substantial conformational stability of Alsin RLD secondary structure and suggest the role of one highly flexible region in the phosphoinositides selectivity of this domain.
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Affiliation(s)
- Marco Cannariato
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marcello Miceli
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
- * E-mail:
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4
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Sperti M, Malavolta M, Ciniero G, Borrelli S, Cavaglià M, Muscat S, Tuszynski JA, Afeltra A, Margiotta DPE, Navarini L. JAK inhibitors in immune-mediated rheumatic diseases: From a molecular perspective to clinical studies. J Mol Graph Model 2021; 104:107789. [DOI: 10.1016/j.jmgm.2020.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022]
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5
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Rapallo A, Gaspari R, Grasso G, Danani A. Extended diffusion theory: Recovering dynamics from biased/accelerated molecular simulations. J Comput Chem 2020; 42:586-599. [PMID: 33351966 DOI: 10.1002/jcc.26474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
Abstract
Dynamical properties are of great importance in determining the behavior of synthetic and natural molecules, but capturing them by computational methods is a nontrivial task. Very often the time scales of the relevant phenomena are far beyond the typical time windows accessible by classical Molecular Dynamics (MD) simulations, currently limited to the order of microseconds on standard laboratory workstations. On the other hand, biased and accelerated simulations allow for fast and thorough exploration of the molecular conformational space, but they lose the dynamic information. The problem of recovering dynamics from biased/accelerated simulations is a very active field of research, but no totally robust/reliable solutions have been given yet. In this paper it is shown how the Smoluchowski equation, in the framework of Diffusion Theory (DT), can be used to bridge this gap, and dynamical properties, in the form of time correlation functions (TCFs), can be extracted also from such kind of simulations. DT is first extended (EDT) to express the mobility tensors entering the Smoluchowski operator in terms of a recently introduced unified and regularized Rotne-Prager-Yamakawa approximation, [P. J. Zuk, E. Wajnryb, K. A. Mizerski, P. Szymczak, J. Fluid. Mech. 2014, 741, R5, 1-13] also involving mixed rotation-translation contributions, and rotation-rotation terms beside the classical translation-translation ones, so far used in DT. Then, the method is applied to recover the dynamics of a nontrivial example of a peptide in explicit water from the first 200 ns of a Replica Exchange Molecular Dynamics simulation, which is a popular computational method that destroys the long time dynamics. EDT dynamics were found to favorably compare against those coming from a standard MD simulation of the same system, requiring a time window of 30 μs to converge. This result shows that EDT is a tool of practical value to recover the long time dynamics of systems in diffusive regimes from biased/accelerated simulations, to be exploited in those cases when direct evaluation by standard MD is unfeasible.
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Affiliation(s)
- Arnaldo Rapallo
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Milano, Italy
| | - Roberto Gaspari
- CNR - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Milano, Italy
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), Università della Svizzera italiana (USI), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Lugano-Viganello, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), Università della Svizzera italiana (USI), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Lugano-Viganello, Switzerland
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6
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Miceli M, Muscat S, Morbiducci U, Cavaglià M, Deriu MA. Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics. J Mol Graph Model 2020; 96:107518. [DOI: 10.1016/j.jmgm.2019.107518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
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7
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Li C, Wang J, Li Y, Chen B, Tao J, Wang X, Yang H, Liu Y, Tong Y, Han W. Molecular mechanisms of metal ions in regulating the catalytic efficiency of D-psicose 3-epimerase revealed by multiple short molecular dynamic simulations and free energy predictions. J Biomol Struct Dyn 2020; 39:1887-1897. [PMID: 32193997 DOI: 10.1080/07391102.2020.1737232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Congcong Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jing Wang
- Nutrition & Health Research Institute, COFCO Corporation, Beijing, China
| | - Yi Li
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemistry Co. Ltd, Changchun, Jilin, China
| | - Bo Chen
- Nutrition & Health Research Institute, COFCO Corporation, Beijing, China
| | - Jin Tao
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemistry Co. Ltd, Changchun, Jilin, China
| | - Xiaoyan Wang
- Nutrition & Health Research Institute, COFCO Corporation, Beijing, China
| | - Hengzheng Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Yingrui Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Yi Tong
- National Engineering Research Center for Corn Deep Processing, Jilin COFCO Biochemistry Co. Ltd, Changchun, Jilin, China.,Nutrition & Health Research Institute, COFCO Corporation, Beijing, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
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8
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Grasso G, Leanza L, Morbiducci U, Danani A, Deriu MA. Aminoacid substitutions in the glycine zipper affect the conformational stability of amyloid beta fibrils. J Biomol Struct Dyn 2019; 38:3908-3915. [PMID: 31543007 DOI: 10.1080/07391102.2019.1671224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The aggregation of amyloid-beta peptides is associated with the pathogenesis of Alzheimer's disease. The hydrophobic core of the amyloid beta sequence contains a GxxxG repeated motif, called glycine zipper, which involves crucial residues for assuring stability and promoting the process of fibril formation. Mutations in this motif lead to a completely different oligomerization pathway and rate of fibril formation. In this work, we have tested G33L and G37L residue substitutions by molecular dynamics simulations. We found that both protein mutations may lead to remarkable changes in the fibril conformational stability. Results suggest the disruption of the glycine zipper as a possible strategy to reduce the aggregation propensity of amyloid beta peptides. On the basis of our data, further investigations may consider this key region as a binding site to design/discover novel effective inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Luigi Leanza
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| | - Umberto Morbiducci
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Applied Sciences of Southern Switzerland (SUPSI), University of Italian Switzerland (USI), Manno, Switzerland
| | - Marco A Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
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9
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Jójárt B, Orgován Z, Márki Á, Pándy-Szekeres G, Ferenczy GG, Keserű GM. Allosteric activation of metabotropic glutamate receptor 5. J Biomol Struct Dyn 2019; 38:2624-2632. [DOI: 10.1080/07391102.2019.1638302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Szeged, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Márki
- Department of Pharmacodynamics and Biopharmacy, University of Szeged, Szeged, Hungary
| | - Gáspár Pándy-Szekeres
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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10
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Dal Magro R, Simonelli S, Cox A, Formicola B, Corti R, Cassina V, Nardo L, Mantegazza F, Salerno D, Grasso G, Deriu MA, Danani A, Calabresi L, Re F. The Extent of Human Apolipoprotein A-I Lipidation Strongly Affects the β-Amyloid Efflux Across the Blood-Brain Barrier in vitro. Front Neurosci 2019; 13:419. [PMID: 31156358 PMCID: PMC6532439 DOI: 10.3389/fnins.2019.00419] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/11/2019] [Indexed: 12/20/2022] Open
Abstract
Much evidence suggests a protective role of high-density lipoprotein (HDL) and its major apolipoprotein apoA-I, in Alzheimer's disease (AD). The biogenesis of nascent HDL derived from a first lipidation of apoA-I, which is synthesized by the liver and intestine but not in the brain, in a process mediated by ABCA1. The maturation of nascent HDL in mature spherical HDL is due to a subsequent lipidation step, LCAT-mediated cholesterol esterification, and the change of apoA-I conformation. Therefore, different subclasses of apoA-I-HDL simultaneously exist in the blood circulation. Here, we investigated if and how the lipidation state affects the ability of apoA-I-HDL to target and modulate the cerebral β-amyloid (Aβ) content from the periphery, that is thus far unclear. In particular, different subclasses of HDL, each with different apoA-I lipidation state, were purified from human plasma and their ability to cross the blood-brain barrier (BBB), to interact with Aβ aggregates, and to affect Aβ efflux across the BBB was assessed in vitro using a transwell system. The results showed that discoidal HDL displayed a superior capability to promote Aβ efflux in vitro (9 × 10-5 cm/min), when compared to apoA-I in other lipidation states. In particular, no effect on Aβ efflux was detected when apoA-I was in mature spherical HDL, suggesting that apoA-I conformation, and lipidation could play a role in Aβ clearance from the brain. Finally, when apoA-I folded its structure in discoidal HDL, rather than in spherical ones, it was able to cross the BBB in vitro and strongly destabilize the conformation of Aβ fibrils by decreasing the order of the fibril structure (-24%) and the β-sheet content (-14%). These data suggest that the extent of apoA-I lipidation, and consequently its conformation, may represent crucial features that could exert their protective role in AD pathogenesis.
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Affiliation(s)
- Roberta Dal Magro
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Sara Simonelli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Centro Grossi Paoletti, Università degli Studi di Milano, Milan, Italy
| | - Alysia Cox
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Beatrice Formicola
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Roberta Corti
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Valeria Cassina
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Luca Nardo
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Domenico Salerno
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di Studi sull’Intelligenza Artificiale, Scuola Universitaria Professionale della Svizzera Italiana, Università della Svizzera Italiana, Manno, Switzerland
| | - Laura Calabresi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Centro Grossi Paoletti, Università degli Studi di Milano, Milan, Italy
| | - Francesca Re
- School of Medicine and Surgery, Nanomedicine Center NANOMIB, University of Milano-Bicocca, Monza, Italy
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Grasso G, Morbiducci U, Massai D, Tuszynski JA, Danani A, Deriu MA. Destabilizing the AXH Tetramer by Mutations: Mechanisms and Potential Antiaggregation Strategies. Biophys J 2019; 114:323-330. [PMID: 29401430 DOI: 10.1016/j.bpj.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 01/12/2023] Open
Abstract
The AXH domain of protein Ataxin 1 is thought to play a key role in the misfolding and aggregation pathway responsible for Spinocerebellar ataxia 1. For this reason, a molecular level understanding of AXH oligomerization pathway is crucial to elucidate the aggregation mechanism, which is thought to trigger the disease. This study employs classical and enhanced molecular dynamics to identify the structural and energetic basis of AXH tetramer stability. Results of this work elucidate molecular mechanisms behind the destabilizing effect of protein mutations, which consequently affect the AXH tetramer assembly. Moreover, results of the study draw attention for the first time, to our knowledge, to the R638 protein residue, which is shown to play a key role in AXH tetramer stability. Therefore, R638 might be also implicated in the AXH oligomerization pathway and stands out as a target for future experimental studies focused on self-association mechanisms and fibril formation of full-length ATX1.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland
| | - Marco A Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Manno, Switzerland.
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Martínez-Archundia M, Correa-Basurto J, Montaño S, Rosas-Trigueros JL. Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis. J Biomol Struct Dyn 2019; 37:4685-4700. [DOI: 10.1080/07391102.2018.1564700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan, Sinaloa, Mexico
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Cómputo, Instituto Politécnico Nacional, Mexico City, Mexico
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13
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Visentin C, Navarro S, Grasso G, Regonesi ME, Deriu MA, Tortora P, Ventura S. Protein Environment: A Crucial Triggering Factor in Josephin Domain Aggregation: The Role of 2,2,2-Trifluoroethanol. Int J Mol Sci 2018; 19:ijms19082151. [PMID: 30042316 PMCID: PMC6121581 DOI: 10.3390/ijms19082151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 11/28/2022] Open
Abstract
The protein ataxin-3 contains a polyglutamine stretch that triggers amyloid aggregation when it is expanded beyond a critical threshold. This results in the onset of the spinocerebellar ataxia type 3. The protein consists of the globular N-terminal Josephin domain and a disordered C-terminal tail where the polyglutamine stretch is located. Expanded ataxin-3 aggregates via a two-stage mechanism: first, Josephin domain self-association, then polyQ fibrillation. This highlights the intrinsic amyloidogenic potential of Josephin domain. Therefore, much effort has been put into investigating its aggregation mechanism(s). A key issue regards the conformational requirements for triggering amyloid aggregation, as it is believed that, generally, misfolding should precede aggregation. Here, we have assayed the effect of 2,2,2-trifluoroethanol, a co-solvent capable of stabilizing secondary structures, especially α-helices. By combining biophysical methods and molecular dynamics, we demonstrated that both secondary and tertiary JD structures are virtually unchanged in the presence of up to 5% 2,2,2-trifluoroethanol. Despite the preservation of JD structure, 1% of 2,2,2-trifluoroethanol suffices to exacerbate the intrinsic aggregation propensity of this domain, by slightly decreasing its conformational stability. These results indicate that in the case of JD, conformational fluctuations might suffice to promote a transition towards an aggregated state without the need for extensive unfolding, and highlights the important role played by the environment on the aggregation of this globular domain.
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Affiliation(s)
- Cristina Visentin
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
| | - Gianvito Grasso
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Maria Elena Regonesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), CH-6928 Manno, Switzerland.
| | - Paolo Tortora
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy.
- Centro di Neuroscienze di Milano (Neuro-MI), 20126 Milano, Italy.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain.
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Deriu MA, Cangiotti M, Grasso G, Licandro G, Lavasanifar A, Tuszynski JA, Ottaviani MF, Danani A. Self-Assembled Ligands Targeting TLR7: A Molecular Level Investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14460-14471. [PMID: 29200306 DOI: 10.1021/acs.langmuir.7b03168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Toll-like receptors (TLRs) are pattern recognition transmembrane proteins that play an important role in innate immunity. In particular, TLR7 plays a role in detecting nucleic acids derived from viruses and bacteria. The huge number of pathologies in which TLR7 is involved has led to an increasing interest in developing new compounds targeting this protein. Several conjugation strategies were proposed for TLR7 agonists to increase the potency while maintaining a low toxicity. In this work, we focus the attention on two promising classes of TLR7 compounds derived from the same pharmacophore conjugated with phospholipid and polyethylene glycol (PEG). A multidisciplinary investigation has been carried out by molecular dynamics (MD), dynamic light scattering (DLS), electron paramagnetic resonance (EPR), and cytotoxicity assessment. DLS and MD indicated how only the phospholipid conjugation provides the compound abilities to self-assemble in an orderly fashion with a maximal pharmacophore exposition to the solvent. Further EPR and cytotoxicity experiments highlighted that phospholipid compounds organize in stable aggregates and well interact with TLR7, whereas PEG conjugation was characterized by poorly stable aggregates at the cells surface. The methodological framework proposed in this study may be used to investigate, at a molecular level, the interactions generally occurring between aggregated ligands, to be used as drugs, and protein receptors.
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Affiliation(s)
- Marco A Deriu
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | - Michela Cangiotti
- Department of Pure and Applied Sciences, University of Urbino , Via Ca' Le Suore 2/4, Urbino,Marche 61029, Italy
| | - Gianvito Grasso
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | - Ginevra Licandro
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
| | | | | | - Maria Francesca Ottaviani
- Department of Pure and Applied Sciences, University of Urbino , Via Ca' Le Suore 2/4, Urbino,Marche 61029, Italy
| | - Andrea Danani
- Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Università della Svizzera Italiana (USI) , Manno CH-6928, Switzerland
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15
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Grasso G, Deriu MA, Patrulea V, Borchard G, Möller M, Danani A. Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization. PLoS One 2017; 12:e0186816. [PMID: 29088239 PMCID: PMC5663398 DOI: 10.1371/journal.pone.0186816] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022] Open
Abstract
The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety) of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine) to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
| | - Marco Agostino Deriu
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
| | - Viorica Patrulea
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Gerrit Borchard
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Michael Möller
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, Geneva, Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di Studi Sull'Intelligenza Artificiale (IDSIA), Scuola Universitaria Professionale della Svizzera Italiana (SUPSI), Università della Svizzera Italiana (USI), Centro Galleria 2, Manno, Switzerland
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16
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Lepre MG, Omar SI, Grasso G, Morbiducci U, Deriu MA, Tuszynski JA. Insights into the Effect of the G245S Single Point Mutation on the Structure of p53 and the Binding of the Protein to DNA. Molecules 2017; 22:E1358. [PMID: 28813011 PMCID: PMC6152093 DOI: 10.3390/molecules22081358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 08/13/2017] [Accepted: 08/13/2017] [Indexed: 12/20/2022] Open
Abstract
The transcription factor p53 is a potent tumor suppressor dubbed as the "guardian of the genome" because of its ability to orchestrate protective biological outputs in response to a variety of oncogenic stresses. Mutation and thus inactivation of p53 can be found in 50% of human tumors. The majority are missense mutations located in the DNA binding region. Among them, G245S is known to be a structural hotspot mutation. To understand the behaviors and differences between the wild-type and mutant, both a dimer of the wild type p53 (wt-p53) and its G245S mutant (G245S-mp53), complexed with DNA, were simulated using molecular dynamics for more than 1 μs. wt-p53 and G245S-mp53 apo monomers were simulated for 1 μs as well. Conformational analyses and binding energy evaluations performed underline important differences and therefore provide insights to understand the G245S-mp53 loss of function. Our results indicate that the G245S mutation destabilizes several structural regions in the protein that are crucial for DNA binding when found in its apo form and highlight differences in the mutant-DNA complex structure compared to the wt protein. These findings not only provide means that can be applied to other p53 mutants but also serve as structural basis for further studies aimed at the development of cancer therapies based on restoring the function of p53.
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Affiliation(s)
- Marco Gaetano Lepre
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Sara Ibrahim Omar
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | - Gianvito Grasso
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
| | - Marco Agostino Deriu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy.
- Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, CH-6928 Manno, Switzerland.
| | - Jack A Tuszynski
- Department of Oncology, Department of Physics, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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Kuiper EFE, de Mattos EP, Jardim LB, Kampinga HH, Bergink S. Chaperones in Polyglutamine Aggregation: Beyond the Q-Stretch. Front Neurosci 2017; 11:145. [PMID: 28386214 PMCID: PMC5362620 DOI: 10.3389/fnins.2017.00145] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/08/2017] [Indexed: 01/12/2023] Open
Abstract
Expanded polyglutamine (polyQ) stretches in at least nine unrelated proteins lead to inherited neuronal dysfunction and degeneration. The expansion size in all diseases correlates with age at onset (AO) of disease and with polyQ protein aggregation, indicating that the expanded polyQ stretch is the main driving force for the disease onset. Interestingly, there is marked interpatient variability in expansion thresholds for a given disease. Between different polyQ diseases the repeat length vs. AO also indicates the existence of modulatory effects on aggregation of the upstream and downstream amino acid sequences flanking the Q expansion. This can be either due to intrinsic modulation of aggregation by the flanking regions, or due to differential interaction with other proteins, such as the components of the cellular protein quality control network. Indeed, several lines of evidence suggest that molecular chaperones have impact on the handling of different polyQ proteins. Here, we review factors differentially influencing polyQ aggregation: the Q-stretch itself, modulatory flanking sequences, interaction partners, cleavage of polyQ-containing proteins, and post-translational modifications, with a special focus on the role of molecular chaperones. By discussing typical examples of how these factors influence aggregation, we provide more insight on the variability of AO between different diseases as well as within the same polyQ disorder, on the molecular level.
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Affiliation(s)
- E F E Kuiper
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Eduardo P de Mattos
- Department of Cell Biology, University Medical Center Groningen, University of GroningenGroningen, Netherlands; Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil
| | - Laura B Jardim
- Programa de Pós-Graduação em Genética e Biologia Molecular, Department of Genetics, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Medical Genetics Service, Hospital de Clínicas de Porto AlegrePorto Alegre, Brazil; Departamento de Medicina Interna, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Harm H Kampinga
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
| | - Steven Bergink
- Department of Cell Biology, University Medical Center Groningen, University of Groningen Groningen, Netherlands
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Grasso G, Tuszynski JA, Morbiducci U, Licandro G, Danani A, Deriu MA. Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics. Biol Direct 2017; 12:2. [PMID: 28103906 PMCID: PMC5244572 DOI: 10.1186/s13062-016-0173-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/21/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. In this connection, computational modeling has demonstrated to be helpful in exploring the protein molecular dynamics and mechanism of action. RESULTS Conformational dynamics of the JD is here finely investigated by replica exchange molecular dynamics simulations able to sample the microsecond time scale and to provide both a thermodynamic and kinetic description of the protein conformational changes. Accessible structural conformations of the JD have been identified in: open, intermediate and closed like arrangement. Data indicated the closed JD arrangement as the most likely protein arrangement. The protein transition from closed toward intermediate/open states was characterized by a rate constant higher than 700 ns. This result also explains the inability of classical molecular dynamics to explore transitions from closed to open JD configuration on a time scale of hundreds of nanoseconds. CONCLUSION This work provides the first kinetic estimation of the JD transition pathway from open-like to closed-like arrangement and vice-versa, indicating the closed-like arrangement as the most likely configuration for a JD in water environment. More widely, the importance of our results is also underscored considering that the ability to provide a kinetic description of the protein conformational changes is a scientific challenge for both experimental and theoretical approaches to date. REVIEWERS This article was reviewed by Oliviero Carugo, Bojan Zagrovic.
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Affiliation(s)
- Gianvito Grasso
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Jack A. Tuszynski
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, IT-10128 Torino, Italy
| | | | - Ginevra Licandro
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Andrea Danani
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
| | - Marco A. Deriu
- Istituto Dalle Molle di studi sull’Intelligenza Artificiale (IDSIA), Scuola universitaria professionale della Svizzera italiana (SUPSI), Università della Svizzera italiana (USI), Centro Galleria 2, Manno, CH-6928 Switzerland
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