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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Leysen S, Burnley RJ, Rodriguez E, Milroy LG, Soini L, Adamski CJ, Nitschke L, Davis R, Obsil T, Brunsveld L, Crabbe T, Zoghbi HY, Ottmann C, Davis JM. A Structural Study of the Cytoplasmic Chaperone Effect of 14-3-3 Proteins on Ataxin-1. J Mol Biol 2021; 433:167174. [PMID: 34302818 PMCID: PMC8505757 DOI: 10.1016/j.jmb.2021.167174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
Expansion of the polyglutamine tract in the N terminus of Ataxin-1 is the main cause of the neurodegenerative disease, spinocerebellar ataxia type 1 (SCA1). However, the C-terminal part of the protein - including its AXH domain and a phosphorylation on residue serine 776 - also plays a crucial role in disease development. This phosphorylation event is known to be crucial for the interaction of Ataxin-1 with the 14-3-3 adaptor proteins and has been shown to indirectly contribute to Ataxin-1 stability. Here we show that 14-3-3 also has a direct anti-aggregation or "chaperone" effect on Ataxin-1. Furthermore, we provide structural and biophysical information revealing how phosphorylated S776 in the intrinsically disordered C terminus of Ataxin-1 mediates the cytoplasmic interaction with 14-3-3 proteins. Based on these findings, we propose that 14-3-3 exerts the observed chaperone effect by interfering with Ataxin-1 dimerization through its AXH domain, reducing further self-association. The chaperone effect is particularly important in the context of SCA1, as it was previously shown that a soluble form of mutant Ataxin-1 is the major driver of pathology.
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Affiliation(s)
- Seppe Leysen
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | | | | | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Lorenzo Soini
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK; Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Carolyn J Adamski
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larissa Nitschke
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Davis
- Global Chemistry, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic
| | - Lucas Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
| | - Tom Crabbe
- Immuno-Bone Discovery, UCB Biopharma UK, Slough SL1 3WE, UK
| | - Huda Yahya Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven 5600 MB, the Netherlands
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4
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Rocha S, Vieira J, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Sousa AD, Vieira CP. ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms. BMC Med Genomics 2019; 12:145. [PMID: 31655597 PMCID: PMC6814966 DOI: 10.1186/s12920-019-0594-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/24/2019] [Indexed: 12/21/2022] Open
Abstract
Background Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded (82Q) than the wt (29Q) protein. Methods To understand how the expanded polyQ affects PPI, protein structures were predicted for wt and expanded ATXN1, as well as, for 71 ATXN1 interactors. Then, the binding surfaces of wt and expanded ATXN1 with the reported interactors were inferred. Results Our data supports that the polyQ expansion alters the ATXN1 conformation and that it enhances the strength of interaction with ATXN1 partners. For both ATXN1 variants, the number of residues at the predicted binding interface are greater after the polyQ, mainly due to the AXH domain. Moreover, the difference in the interaction strength of the ATXN1 variants was due to an increase in the number of interactions at the N-terminal region, before the polyQ, for the expanded form. Conclusions There are three regions at the AXH domain that are essential for ATXN1 PPI. The N-terminal region is responsible for the strength of the PPI with the ATXN1 variants. How the predicted motifs in this region affect PPI is discussed, in the context of ATXN1 post-transcriptional modifications.
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Affiliation(s)
- Sara Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Noé Vázquez
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Hugo López-Fernández
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain.,SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur). SERGAS-UVIGO, Vigo, Spain
| | - André D Sousa
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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5
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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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6
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Konarev PV, Svergun DI. Direct shape determination of intermediates in evolving macromolecular solutions from small-angle scattering data. IUCRJ 2018; 5:402-409. [PMID: 30002841 PMCID: PMC6038953 DOI: 10.1107/s2052252518005900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Many important biological processes like amyloid formation, viral assembly etc. can be monitored in vitro. Small-angle X-ray scattering (SAXS) is one of the most effective techniques to structurally characterize these processes in solution. For monodisperse systems and some oligomeric mixtures, low-resolution shapes can be determined ab initio from the SAXS data, but for evolving systems, such analysis is hampered by the presence of multiple species and no direct reconstruction procedures are available. The authors consider a frequently occurring case where the scattering from the initial and final states of the process are known but there exists a major (unknown) intermediate component. A method is presented to directly reconstruct the low-resolution shape of this transient component together with its volume fractions from multiple scattering patterns recorded from an evolving system. The method is implemented in the computer program DAMMIX freely available to academic users and its effectiveness is illustrated in several synthetic and experimental examples.
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Affiliation(s)
- Petr V. Konarev
- Laboratory of Reflectometry and Small-angle Scattering, A. V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky pr. 59, Moscow 119333, Russian Federation
- National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow 123182, Russian Federation
| | - Dmitri I. Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Notkestrasse 85, Hamburg 22607, Germany
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7
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Polyglutamine expansion diseases: More than simple repeats. J Struct Biol 2017; 201:139-154. [PMID: 28928079 DOI: 10.1016/j.jsb.2017.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/24/2017] [Accepted: 09/15/2017] [Indexed: 12/27/2022]
Abstract
Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease. Intrinsic features such as the presence of aggregation-prone regions (APRs) outside the polyQ segments and polyQ-flanking sequences, which synergistically participate in the aggregation process, are emerging for several disease-related proteins. The inherent polymorphic structure of polyQ stretches places the polyQ proteins in a central position in protein-protein interaction networks, where interacting partners may additionally shield APRs or reshape the aggregation course. Expansion of the polyQ tract perturbs the cellular homeostasis and contributes to neuronal failure by modulating protein-protein interactions and enhancing toxic oligomerization. Post-translational modifications further regulate self-assembly either by directly altering the intrinsic aggregation propensity of polyQ proteins, by modulating their interaction with different macromolecules or by modifying their withdrawal by the cell quality control machinery. Here we review the recent data on the multifaceted aggregation pathways of disease-related polyQ proteins, focusing on ataxin-3, the protein mutated in Machado-Joseph disease. Further mechanistic understanding of this network of events is crucial for the development of effective therapies for polyQ diseases.
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8
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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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9
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Popovic M, Pastore A. Chemical shift assignment of the alternative scaffold protein IscA. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:227-231. [PMID: 26887894 PMCID: PMC4788688 DOI: 10.1007/s12104-016-9672-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
The IscA protein (11.5 kDa) is an essential component of the iron sulphur cluster biogenesis machine. In bacteria, the machine components are clustered in operons, amongst which the most important is the isc operon. Bacterial IscA has direct homologues also in eukaryotes. Like the protein IscU, IscA is thought to assist cluster formation as an alternative scaffold protein which receives the cluster before transferring it further to the final acceptors. Several crystal structures have been published. They all report an IscA dimeric form, although the packing of the protomers in the dimers differs amongst structures. No solution studies have currently been reported. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the cluster-free E. coli IscA as a starting point for further studies of the structure and functions of this still poorly characterized protein. We show that IscA exists in solution as an equilibrium between different species. Spectrum assignment was thus challenging given the heterogeneous nature of the sample but doable through judicious choice of selective labelling and concentration dependent studies.
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Affiliation(s)
- Matija Popovic
- Maurice Wohl Institute, King's College London, 5 Cutcombe Rd., London, SE5 9RT, UK
| | - Annalisa Pastore
- Maurice Wohl Institute, King's College London, 5 Cutcombe Rd., London, SE5 9RT, UK.
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10
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Deriu MA, Grasso G, Tuszynski JA, Massai D, Gallo D, Morbiducci U, Danani A. Characterization of the AXH domain of Ataxin-1 using enhanced sampling and functional mode analysis. Proteins 2016; 84:666-73. [DOI: 10.1002/prot.25017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 01/25/2016] [Accepted: 02/02/2016] [Indexed: 12/29/2022]
Affiliation(s)
- 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
| | - 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 Physics; University of Alberta; Edmonton Alberta Canada
| | - Diana Massai
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
- Department of Cardiothoracic; Transplantation, and Vascular Surgery (HTTG), Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Hannover Medical School; Carl-Neuberg-Strabe 1 Hannover 30625 Germany
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering; Politecnico Di Torino; Corso Duca Degli Abruzzi 24 Torino IT-10128 Italy
| | - 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
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11
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Grasso G, Deriu MA, Tuszynski JA, Gallo D, Morbiducci U, Danani A. Conformational fluctuations of the AXH monomer of Ataxin-1. Proteins 2015; 84:52-9. [PMID: 26522012 DOI: 10.1002/prot.24954] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/07/2015] [Accepted: 10/19/2015] [Indexed: 12/17/2022]
Abstract
In this paper, we report the results of molecular dynamics simulations of AXH monomer of Ataxin-1. The AXH domain plays a crucial role in Ataxin-1 aggregation, which accompanies the initiation and progression of Spinocerebellar ataxia type 1. Our simulations involving both classical and replica exchange molecular dynamics, followed by principal component analysis of the trajectories obtained, reveal substantial conformational fluctuations of the protein structure, especially in the N-terminal region. We show that these fluctuations can be generated by thermal noise since the free energy barriers between conformations are small enough for thermally stimulated transitions. In agreement with the previous experimental findings, our results can be considered as a basis for a future design of ataxin aggregation inhibitors that will require several key conformations identified in the present study as molecular targets for ligand binding.
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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, 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, 6928, Switzerland
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Diego Gallo
- Department of Mechanical and Aerospace Engineering, Politecnico Di Torino, Corso Duca Degli Abruzzi 24, Torino, 10128, Italy
| | - Umberto Morbiducci
- Department of Mechanical and Aerospace Engineering, Politecnico Di Torino, Corso Duca Degli Abruzzi 24, Torino, 10128, Italy
| | - 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, 6928, Switzerland
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de Chiara C, Kelly G, Menon RP, McCormick J, Pastore A. Chemical shift assignment of the ataxin-1 AXH domain in complex with a CIC ligand peptide. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:325-7. [PMID: 23853075 PMCID: PMC4145211 DOI: 10.1007/s12104-013-9509-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/01/2013] [Indexed: 05/16/2023]
Abstract
Ataxin-1 is the protein responsible for the genetically-inherited neurodegenerative disease spinocerebellar ataxia type-1 linked to the expansion of a polyglutamine tract within the protein sequence. The AXH domain of ataxin-1 is essential for the protein to function as a transcriptional co-repressor and mediates the majority of the interactions of ataxin-1 with cellular partners, mainly transcriptional regulators. One of the best characterized ataxin-1 functional partners is Capicua (CIC), a transcriptional repressor involved in signalling pathways that regulate mammalian development, tumorigenesis and, through the interaction with ataxin-1, also neurodegeneration. Complex formation of ataxin-1 with CIC is important both for the function of the wild-type protein and for pathogenesis as transcriptional disregulation is observed since the early stages of the development of the disease. Here we report the (1)H, (13)C and (15)N backbone and side-chain chemical shift assignments of the human ataxin-1 AXH domain in complex with a CIC ligand-peptide.
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Affiliation(s)
- Cesira de Chiara
- MRC National Institute for Medical Research, The Ridgeway, London, NW7 1AA UK
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Ridgeway, London, NW7 1AA UK
| | - Rajesh P. Menon
- MRC National Institute for Medical Research, The Ridgeway, London, NW7 1AA UK
| | - John McCormick
- MRC National Institute for Medical Research, The Ridgeway, London, NW7 1AA UK
| | - Annalisa Pastore
- MRC National Institute for Medical Research, The Ridgeway, London, NW7 1AA UK
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13
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Tezenas du Montcel S, Durr A, Bauer P, Figueroa KP, Ichikawa Y, Brussino A, Forlani S, Rakowicz M, Schöls L, Mariotti C, van de Warrenburg BPC, Orsi L, Giunti P, Filla A, Szymanski S, Klockgether T, Berciano J, Pandolfo M, Boesch S, Melegh B, Timmann D, Mandich P, Camuzat A, Goto J, Ashizawa T, Cazeneuve C, Tsuji S, Pulst SM, Brusco A, Riess O, Brice A, Stevanin G. Modulation of the age at onset in spinocerebellar ataxia by CAG tracts in various genes. ACTA ACUST UNITED AC 2014; 137:2444-55. [PMID: 24972706 DOI: 10.1093/brain/awu174] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Polyglutamine-coding (CAG)n repeat expansions in seven different genes cause spinocerebellar ataxias. Although the size of the expansion is negatively correlated with age at onset, it accounts for only 50-70% of its variability. To find other factors involved in this variability, we performed a regression analysis in 1255 affected individuals with identified expansions (spinocerebellar ataxia types 1, 2, 3, 6 and 7), recruited through the European Consortium on Spinocerebellar Ataxias, to determine whether age at onset is influenced by the size of the normal allele in eight causal (CAG)n-containing genes (ATXN1-3, 6-7, 17, ATN1 and HTT). We confirmed the negative effect of the expanded allele and detected threshold effects reflected by a quadratic association between age at onset and CAG size in spinocerebellar ataxia types 1, 3 and 6. We also evidenced an interaction between the expanded and normal alleles in trans in individuals with spinocerebellar ataxia types 1, 6 and 7. Except for individuals with spinocerebellar ataxia type 1, age at onset was also influenced by other (CAG)n-containing genes: ATXN7 in spinocerebellar ataxia type 2; ATXN2, ATN1 and HTT in spinocerebellar ataxia type 3; ATXN1 and ATXN3 in spinocerebellar ataxia type 6; and ATXN3 and TBP in spinocerebellar ataxia type 7. This suggests that there are biological relationships among these genes. The results were partially replicated in four independent populations representing 460 Caucasians and 216 Asian samples; the differences are possibly explained by ethnic or geographical differences. As the variability in age at onset is not completely explained by the effects of the causative and modifier sister genes, other genetic or environmental factors must also play a role in these diseases.
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Affiliation(s)
- Sophie Tezenas du Montcel
- 1 Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013, Paris, France2 INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013, Paris, France3 AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Biostatistics Unit, Paris, F-75013, France
| | - Alexandra Durr
- 4 AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Genetics and Cytogenetics, F-75013, Paris, France5 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Peter Bauer
- 6 Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Karla P Figueroa
- 7 Department of Neurology, University of Utah, Salt Lake City, USA
| | - Yaeko Ichikawa
- 8 Department of Neurology, University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Alessandro Brussino
- 9 University of Torino, Department of Medical Sciences, and Medical Genetics Unit, Az. Osp. 'Città della Salute e della Scienza', Torino, Italy
| | - Sylvie Forlani
- 5 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Maria Rakowicz
- 10 Institute of Psychiatry and Neurology Warsaw, Sobieskiego 9, 02-957 Warsaw, Poland
| | - Ludger Schöls
- 11 Department of Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany12 German Centre of Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Caterina Mariotti
- 13 SOSD Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS, Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Bart P C van de Warrenburg
- 14 Department of Neurology, Donders Institute for Brain, Cognition, and Behaviour, Radbound University Medical Centre, Nijmegen, The Netherlands
| | - Laura Orsi
- 15 Neurologic Division I, Department of Neuroscience and Mental Health, AOU Città della Salute e della Scienza, Torino, Italy
| | - Paola Giunti
- 16 Institute of Neurology, Department of Molecular Neuroscience, UCL, Queen Square, London, UK
| | - Alessandro Filla
- 17 Department of Neurological Sciences, Federico II University, Naples, Italy
| | - Sandra Szymanski
- 18 Department of Neurology, St. Josef Hospital, University Hospital of Bochum, Bochum, Germany
| | | | - José Berciano
- 20 Department of Neurology, University Hospital 'Marqués de Valdecilla', UC, IDIVAL and CIBERNED, 39008 Santander, Spain
| | - Massimo Pandolfo
- 21 Department of Neurology, ULB-Hôpital Erasme, Université Libre de Bruxelles, CP 231, Campus Plaine, ULB, Brusssels, Belgium
| | - Sylvia Boesch
- 22 Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Bela Melegh
- 23 Department of Medical Genetics, and Szentagothai Research Centre, University Pécs, Hungary
| | - Dagmar Timmann
- 24 Department of Neurology, University Clinic Essen, University of Duisburg-Essen, Essen, Germany
| | - Paola Mandich
- 25 Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal Child Health, University of Genova, and U.O. Medical Genetics of IRCCS AOU S. Martino Institute, Genova, Italy
| | - Agnès Camuzat
- 5 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | | | | | - Jun Goto
- 8 Department of Neurology, University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Tetsuo Ashizawa
- 26 Department of Neurology and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Cécile Cazeneuve
- 4 AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Genetics and Cytogenetics, F-75013, Paris, France
| | - Shoji Tsuji
- 8 Department of Neurology, University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Stefan-M Pulst
- 7 Department of Neurology, University of Utah, Salt Lake City, USA
| | - Alfredo Brusco
- 9 University of Torino, Department of Medical Sciences, and Medical Genetics Unit, Az. Osp. 'Città della Salute e della Scienza', Torino, Italy
| | - Olaf Riess
- 6 Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Alexis Brice
- 4 AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Genetics and Cytogenetics, F-75013, Paris, France5 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Giovanni Stevanin
- 4 AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Department of Genetics and Cytogenetics, F-75013, Paris, France5 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France27 Ecole Pratique des Hautes Etudes, heSam Université, laboratoire de neurogénétique, ICM, Groupe Hospitalier Pitié-Salpêtrière, F-75013 Paris, France
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Menon RP, Soong D, de Chiara C, Holt M, McCormick JE, Anilkumar N, Pastore A. Mapping the self-association domains of ataxin-1: identification of novel non overlapping motifs. PeerJ 2014; 2:e323. [PMID: 24711972 PMCID: PMC3970802 DOI: 10.7717/peerj.323] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/07/2014] [Indexed: 12/13/2022] Open
Abstract
The neurodegenerative disease spinocerebellar ataxia type 1 (SCA1) is caused by aggregation and misfolding of the ataxin-1 protein. While the pathology correlates with mutations that lead to expansion of a polyglutamine tract in the protein, other regions contribute to the aggregation process as also non-expanded ataxin-1 is intrinsically aggregation-prone and forms nuclear foci in cell. Here, we have used a combined approach based on FRET analysis, confocal microscopy and in vitro techniques to map aggregation-prone regions other than polyglutamine and to establish the importance of dimerization in self-association/foci formation. Identification of aggregation-prone regions other than polyglutamine could greatly help the development of SCA1 treatment more specific than that based on targeting the low complexity polyglutamine region.
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Affiliation(s)
- Rajesh P Menon
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Daniel Soong
- Randall Division for Cell and Molecular Biophysics, New Hunt's House, King's College London , Guy's Campus, London , UK ; British Heart Foundation Centre of Research Excellence, King's College London , Denmark Hill Campus, London , UK
| | - Cesira de Chiara
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Mark Holt
- Randall Division for Cell and Molecular Biophysics, New Hunt's House, King's College London , Guy's Campus, London , UK
| | - John E McCormick
- MRC National Institute for Medical Research, The Ridgeway , London , UK
| | - Narayana Anilkumar
- British Heart Foundation Centre of Research Excellence, King's College London , Denmark Hill Campus, London , UK
| | - Annalisa Pastore
- MRC National Institute for Medical Research, The Ridgeway , London , UK ; Department of Molecular Neuroscience, Institute of Psychiatry, King's College London , Denmark Hill Campus, London , UK
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15
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de Chiara C, Pastore A. Kaleidoscopic protein-protein interactions in the life and death of ataxin-1: new strategies against protein aggregation. Trends Neurosci 2014; 37:211-8. [PMID: 24636457 PMCID: PMC3988977 DOI: 10.1016/j.tins.2014.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 01/26/2014] [Accepted: 02/06/2014] [Indexed: 12/11/2022]
Abstract
Understanding how proteins protect themselves from aberrant aggregation is of primary interest for understanding basic biology, protein biochemistry, and human disease. We discuss the paradigmatic example of ataxin-1 (Atx1), the protein responsible for neurodegenerative spinocerebellar ataxia type 1 (SCA1). This disease is part of the increasing family of pathologies caused by protein aggregation and misfolding. We discuss the importance of protein-protein interactions not only in the nonpathological function of Atx1 but also in protecting the protein from aggregation and misfolding. The lessons learned from Atx1 may lead to a more general understanding of the cell's protective strategies against aggregation. The obtained knowledge may suggest a new perspective for designing specific therapeutic strategies for the cure of misfolding diseases.
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Affiliation(s)
- Cesira de Chiara
- National Institute for Medical Research (NIMR), Medical Research Council (MRC), The Ridgeway, London NW7 1AA, UK
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King's College London, Denmark Hill Campus, London, UK.
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16
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Protein-protein interactions as a strategy towards protein-specific drug design: the example of ataxin-1. PLoS One 2013; 8:e76456. [PMID: 24155902 PMCID: PMC3796545 DOI: 10.1371/journal.pone.0076456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/26/2013] [Indexed: 11/20/2022] Open
Abstract
A main challenge for structural biologists is to understand the mechanisms that discriminate between molecular interactions and determine function. Here, we show how partner recognition of the AXH domain of the transcriptional co-regulator ataxin-1 is fine-tuned by a subtle balance between self- and hetero-associations. Ataxin-1 is the protein responsible for the hereditary spinocerebellar ataxia type 1, a disease linked to protein aggregation and transcriptional dysregulation. Expansion of a polyglutamine tract is essential for ataxin-1 aggregation, but the sequence-wise distant AXH domain plays an important aggravating role in the process. The AXH domain is also a key element for non-aberrant function as it intervenes in interactions with multiple protein partners. Previous data have shown that AXH is dimeric in solution and forms a dimer of dimers when crystallized. By solving the structure of a complex of AXH with a peptide from the interacting transcriptional repressor CIC, we show that the dimer interface of AXH is displaced by the new interaction and that, when blocked by the CIC peptide AXH aggregation and misfolding are impaired. This is a unique example in which palindromic self- and hetero-interactions within a sequence with chameleon properties discriminate the partner. We propose a drug design strategy for the treatment of SCA1 that is based on the information gained from the AXH/CIC complex.
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