1
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Moldovean-Cioroianu NS. Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches. Int J Mol Sci 2024; 25:6789. [PMID: 38928495 PMCID: PMC11204371 DOI: 10.3390/ijms25126789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.
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Affiliation(s)
- Nastasia Sanda Moldovean-Cioroianu
- Institute of Materials Science, Bioinspired Materials and Biosensor Technologies, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany;
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
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2
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Mishra R, Gerlach GJ, Sahoo B, Camacho CJ, Wetzel R. A Targetable Self-association Surface of the Huntingtin exon1 Helical Tetramer Required for Assembly of Amyloid Pre-nucleation Oligomers. J Mol Biol 2024; 436:168607. [PMID: 38734203 DOI: 10.1016/j.jmb.2024.168607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Polyglutamine (polyQ) sequences undergo repeat-length dependent formation of disease-associated, amyloid-like cross-β core structures with kinetics and aggregate morphologies often influenced by the flanking sequences. In Huntington's disease (HD), the httNT segment on the polyQ's N-terminal flank enhances aggregation rates by changing amyloid nucleation from a classical homogeneous mechanism to a two-step process requiring an ɑ-helix-rich oligomeric intermediate. A folded, helix-rich httNT tetrameric structure suggested to be this critical intermediate was recently reported. Here we employ single alanine replacements along the httNT sequence to assess this proposed structure and refine the mechanistic model. We find that Ala replacement of hydrophobic residues within simple httNT peptides greatly suppresses helicity, supporting the tetramer model. These same helix-disruptive replacements in the httNT segment of an exon-1 analog greatly reduce aggregation kinetics, suggesting that an ɑ-helix rich multimer - either the tetramer or a larger multimer - plays an on-pathway role in nucleation. Surprisingly, several other Ala replacements actually enhance helicity and/or amyloid aggregation. The spatial localization of these residues on the tetramer surface suggests a self-association interface responsible for formation of the octomers and higher-order multimers most likely required for polyQ amyloid nucleation. Multimer docking of the tetramer, using the protein-protein docking algorithm ClusPro, predicts this symmetric surface to be a viable tetramer dimerization interface. Intriguingly, octomer formation brings the emerging polyQ chains into closer proximity at this tetramer-tetramer interface. Further supporting the potential importance of tetramer super-assembly, computational docking with a known exon-1 aggregation inhibitor predicts ligand contacts with residues at this interface.
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Affiliation(s)
- Rakesh Mishra
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Gabriella J Gerlach
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA
| | - Bankanidhi Sahoo
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
| | - Ronald Wetzel
- Department Structural Biology, University of Pittsburgh School of Medicine Pittsburgh, PA 15260, USA.
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3
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Bonsor M, Ammar O, Schnoegl S, Wanker EE, Silva Ramos E. Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects. Proteomics 2024; 24:e2300114. [PMID: 38615323 DOI: 10.1002/pmic.202300114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
Currently, nine polyglutamine (polyQ) expansion diseases are known. They include spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 17), spinal and bulbar muscular atrophy (SBMA), dentatorubral-pallidoluysian atrophy (DRPLA), and Huntington's disease (HD). At the root of these neurodegenerative diseases are trinucleotide repeat mutations in coding regions of different genes, which lead to the production of proteins with elongated polyQ tracts. While the causative proteins differ in structure and molecular mass, the expanded polyQ domains drive pathogenesis in all these diseases. PolyQ tracts mediate the association of proteins leading to the formation of protein complexes involved in gene expression regulation, RNA processing, membrane trafficking, and signal transduction. In this review, we discuss commonalities and differences among the nine polyQ proteins focusing on their structure and function as well as the pathological features of the respective diseases. We present insights from AlphaFold-predicted structural models and discuss the biological roles of polyQ-containing proteins. Lastly, we explore reported protein-protein interaction networks to highlight shared protein interactions and their potential relevance in disease development.
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Affiliation(s)
- Megan Bonsor
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orchid Ammar
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sigrid Schnoegl
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Erich E Wanker
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Eduardo Silva Ramos
- Department of Neuroproteomics, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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4
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Mohanty P, Phan TM, Mittal J. Transient interdomain interactions modulate the monomeric structural ensemble and oligomerization landscape of Huntingtin Exon 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592468. [PMID: 38766024 PMCID: PMC11100600 DOI: 10.1101/2024.05.03.592468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Polyglutamine expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington's disease, a neurogenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyglutamine tract in Httex1 is flanked by an N-terminal coiled-coil domain - N17 (17 amino acids), which undergoes self-association to promote the formation of soluble Httex1 oligomers and brings the aggregation-prone polyQ tracts in close spatial proximity. However, the mechanisms underlying the subsequent conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. Current knowledge suggests that expansion of the polyQ tract increases its helicity, and this favors its oligomerization and aggregation. In addition, studies utilizing conformation-specific antibodies and a stable coiled-coil heterotetrametric system fused to polyQ indicate that domain "cross-talk" (i.e., interdomain interactions) may be necessary to efficiently promote the emergence of toxic conformations (in monomers and oligomers) and fibrillar aggregation. Here, we performed extensive atomistic molecular dynamics (MD) simulations (aggregate time ∼ 0.7 ms) of N17-polyQ fragments to uncover the interplay between structural transformation and domain "cross-talk" on the monomeric structural ensemble and oligomerization landscape of Httex1. Our simulation ensembles of N17-polyQ monomers validated against 13 C NMR chemical shifts indicated that in addition to elevated α-helicity, polyQ expansion also favors transient, interdomain (N17-polyQ) interactions which result in the emergence of β-conformations. Further, interdomain interactions decreased the overall stability of N17-mediated dimers by counteracting the stabilizing effect of increased α-helicity and promoted a heterogenous oligomerization landscape on the sub-microsecond timescale. Overall, our study uncovers the significance of domain "cross-talk" in modulating the monomeric conformational ensemble and oligomerization landscape of Httex1 to favor the formation of amyloid aggregates.
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5
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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6
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Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol 2023; 215:108023. [PMID: 37652396 DOI: 10.1016/j.jsb.2023.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a "proper" TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins.
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Affiliation(s)
- Alexander Miguel Monzon
- Dept. of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Paula Nazarena Arrías
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Arne Elofsson
- Dept. of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 171 21 Solna, Sweden
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Martina Bevilacqua
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Clementel
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Layla Hirsh
- Dept. of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru, Av. Universitaria 1801 San Miguel, Lima 32, Lima, Peru
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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7
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Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 2023; 83:102726. [PMID: 37924569 DOI: 10.1016/j.sbi.2023.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
Abstract
Homorepeats (or polyX), protein segments containing repetitions of the same amino acid, are abundant in proteomes from all kingdoms of life and are involved in crucial biological functions as well as several neurodegenerative and developmental diseases. Mainly inserted in disordered segments of proteins, the structure/function relationships of homorepeats remain largely unexplored. In this review, we summarize present knowledge for the most abundant homorepeats, highlighting the role of the inherent structure and the conformational influence exerted by their flanking regions. Recent experimental and computational methods enable residue-specific investigations of these regions and promise novel structural and dynamic information for this elusive group of proteins. This information should increase our knowledge about the structural bases of phenomena such as liquid-liquid phase separation and trinucleotide repeat disorders.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France. https://twitter.com/carloselenareal
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz. Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS. 29 rue de Navacelles, 34090 Montpellier, France.
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8
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Elena-Real CA, Urbanek A, Imbert L, Morató A, Fournet A, Allemand F, Sibille N, Boisbouvier J, Bernadó P. Site-Specific Introduction of Alanines for the Nuclear Magnetic Resonance Investigation of Low-Complexity Regions and Large Biomolecular Assemblies. ACS Chem Biol 2023; 18:2039-2049. [PMID: 37582223 DOI: 10.1021/acschembio.3c00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Nuclear magnetic resonance (NMR) studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning frequencies to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. The general applicability of this approach for NMR assignment has been demonstrated by introducing isotopically labeled alanines into four distinct proteins: huntingtin exon-1, HMA8 ATPase, the 300 kDa molecular chaperone ClpP, and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enabled unambiguous assignments while avoiding potential artifacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observed that the helical stability is strongly dependent on the homorepeat length. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of challenging biomolecular systems.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Lionel Imbert
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jérôme Boisbouvier
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29 rue de Navacelles, 34090 Montpellier, France
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9
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Gonçalves-Kulik M, Schmid F, Andrade-Navarro MA. One Step Closer to the Understanding of the Relationship IDR-LCR-Structure. Genes (Basel) 2023; 14:1711. [PMID: 37761851 PMCID: PMC10531472 DOI: 10.3390/genes14091711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Intrinsically disordered regions (IDRs) in protein sequences are emerging as functionally important elements for interaction and regulation. While being generally flexible, we previously showed, by observation of experimentally obtained structures, that they contain regions of reduced sequence complexity that have an increased propensity to form structure. Here we expand the universe of cases taking advantage of structural predictions by AlphaFold. Our studies focus on low complexity regions (LCRs) found within IDRs, where these LCRs have only one or two residue types (polyX and polyXY, respectively). In addition to confirming previous observations that polyE and polyEK have a tendency towards helical structure, we find a similar tendency for other LCRs such as polyQ and polyER, most of them including charged residues. We analyzed the position of polyXY containing IDRs within proteins, which allowed us to show that polyAG and polyAK accumulate at the N-terminal, with the latter showing increased helical propensity at that location. Functional enrichment analysis of polyXY with helical propensity indicated functions requiring interaction with RNA and DNA. Our work adds evidence of the function of LCRs in interaction-dependent structuring of disordered regions, encouraging the development of tools for the prediction of their dynamic structural properties.
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Affiliation(s)
- Mariane Gonçalves-Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Friederike Schmid
- Faculty of Physics, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
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Tsai TY, Chen CY, Lin TW, Lin TC, Chiu FL, Shih O, Chang MY, Lin YC, Su AC, Chen CM, Jeng US, Kuo HC, Chang CF, Chen YR. Amyloid modifier SERF1a interacts with polyQ-expanded huntingtin-exon 1 via helical interactions and exacerbates polyQ-induced toxicity. Commun Biol 2023; 6:767. [PMID: 37479809 PMCID: PMC10361993 DOI: 10.1038/s42003-023-05142-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023] Open
Abstract
Abnormal polyglutamine (polyQ) expansion and fibrillization occur in Huntington's disease (HD). Amyloid modifier SERF enhances amyloid formation, but the underlying mechanism is not revealed. Here, the fibrillization and toxicity effect of SERF1a on Htt-exon1 are examined. SERF1a enhances the fibrillization of and interacts with mutant thioredoxin (Trx)-fused Httex1. NMR studies with Htt peptides show that TrxHttex1-39Q interacts with the helical regions in SERF1a and SERF1a preferentially interacts with the N-terminal 17 residues of Htt. Time-course analysis shows that SERF1a induces mutant TrxHttex1 to a single conformation enriched of β-sheet. Co-expression of SERF1a and Httex1-polyQ in neuroblastoma and lentiviral infection of SERF1a in HD-induced polypotent stem cell (iPSC)-derived neurons demonstrates the detrimental effect of SERF1a in HD. Higher level of SERF1a transcript or protein is detected in HD iPSC, transgenic mice, and HD plasma. Overall, this study provides molecular mechanism for SERF1a and mutant Httex1 to facilitate therapeutic development for HD.
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Affiliation(s)
- Tien-Ying Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, 128, Academia Road, Sec. 2. Nankang, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chun-Yu Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Wei Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Tien-Chang Lin
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Feng-Lan Chiu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
| | - Ming-Yun Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Lin
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - An-Chung Su
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Linkou Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 300, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, 128, Academia Rd., Sec. 2, Nankang District, Taipei, 115, Taiwan.
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11
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Barbosa Pereira PJ, Manso JA, Macedo-Ribeiro S. The structural plasticity of polyglutamine repeats. Curr Opin Struct Biol 2023; 80:102607. [PMID: 37178477 DOI: 10.1016/j.sbi.2023.102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
Abstract
From yeast to humans, polyglutamine (polyQ) repeat tracts are found frequently in the proteome and are particularly prominent in the activation domains of transcription factors. PolyQ is a polymorphic motif that modulates functional protein-protein interactions and aberrant self-assembly. Expansion of the polyQ repeated sequences beyond critical physiological repeat length thresholds triggers self-assembly and is linked to severe pathological implications. This review provides an overview of the current knowledge on the structures of polyQ tracts in the soluble and aggregated states and discusses the influence of neighboring regions on polyQ secondary structure, aggregation, and fibril morphologies. The influence of the genetic context of the polyQ-encoding trinucleotides is briefly discussed as a challenge for future endeavors in this field.
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Affiliation(s)
- Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
| | - José A Manso
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
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Elena-Real CA, Urbanek A, Lund XL, Morató A, Sagar A, Fournet A, Estaña A, Bellande T, Allemand F, Cortés J, Sibille N, Melki R, Bernadó P. Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1. Structure 2023:S0969-2126(23)00126-0. [PMID: 37119819 DOI: 10.1016/j.str.2023.04.003] [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: 02/02/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Huntington's disease neurodegeneration occurs when the number of consecutive glutamines in the huntingtin exon-1 (HTTExon1) exceeds a pathological threshold of 35. The sequence homogeneity of HTTExon1 reduces the signal dispersion in NMR spectra, hampering its structural characterization. By simultaneously introducing three isotopically labeled glutamines in a site-specific manner in multiple concatenated samples, 18 glutamines of a pathogenic HTTExon1 with 36 glutamines were unambiguously assigned. Chemical shift analyses indicate the α-helical persistence in the homorepeat and the absence of an emerging toxic conformation around the pathological threshold. Using the same type of samples, the recognition mechanism of Hsc70 molecular chaperone has been investigated, indicating that it binds to the N17 region of HTTExon1, inducing the partial unfolding of the poly-Q. The proposed strategy facilitates high-resolution structural and functional studies in low-complexity regions.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Xamuel L Lund
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France; Institut Laue Langevin, 38000 Grenoble, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France; LAAS-CNRS, Université de Toulouse, CNRS, 31400, Toulouse, France
| | - Tracy Bellande
- Institut François Jacob, Molecular Imaging Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) and Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, CEA-Fontenay-aux-Roses Bâtiment 61, 18, route du Panorama, 92265 Fontenay-aux-Rses cedex, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31400, Toulouse, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Ronald Melki
- Institut François Jacob, Molecular Imaging Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) and Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, CEA-Fontenay-aux-Roses Bâtiment 61, 18, route du Panorama, 92265 Fontenay-aux-Rses cedex, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France.
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13
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Sun X, Dyson HJ, Wright PE. Role of conformational dynamics in pathogenic protein aggregation. Curr Opin Chem Biol 2023; 73:102280. [PMID: 36878172 PMCID: PMC10033434 DOI: 10.1016/j.cbpa.2023.102280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
The accumulation of pathogenic protein oligomers and aggregates is associated with several devastating amyloid diseases. As protein aggregation is a multi-step nucleation-dependent process beginning with unfolding or misfolding of the native state, it is important to understand how innate protein dynamics influence aggregation propensity. Kinetic intermediates composed of heterogeneous ensembles of oligomers are frequently formed on the aggregation pathway. Characterization of the structure and dynamics of these intermediates is critical to the understanding of amyloid diseases since oligomers appear to be the main cytotoxic agents. In this review, we highlight recent biophysical studies of the roles of protein dynamics in driving pathogenic protein aggregation, yielding new mechanistic insights that can be leveraged for design of aggregation inhibitors.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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14
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Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morató A, Estaña A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortés J, Sinnaeve D, Sibille N, Bernadó P. The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity. Nat Struct Mol Biol 2023; 30:309-320. [PMID: 36864173 DOI: 10.1038/s41594-023-00920-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/05/2023] [Indexed: 03/04/2023]
Abstract
Huntington's disease is a neurodegenerative disorder caused by a CAG expansion in the first exon of the HTT gene, resulting in an extended polyglutamine (poly-Q) tract in huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood due to its intrinsic flexibility and the strong compositional bias. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. Integrative data analysis reveals that the poly-Q tract adopts long α-helical conformations propagated and stabilized by glutamine side chain to backbone hydrogen bonds. We show that α-helical stability is a stronger signature in defining aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. Our observations provide a structural perspective of the pathogenicity of expanded httex1 and pave the way to a deeper understanding of poly-Q-related diseases.
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Affiliation(s)
- Carlos A Elena-Real
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Amin Sagar
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Annika Urbanek
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Matija Popovic
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Anna Morató
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Alejandro Estaña
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Aurélie Fournet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Christine Doucet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Xamuel L Lund
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- Institute of Laue Langevin, Grenoble, France
| | - Zhen-Dan Shi
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Luca Costa
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | | | - Frédéric Allemand
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Rolf E Swenson
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Barcelona, Spain
| | - Alessandro Barducci
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Davy Sinnaeve
- Univ. Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002, Integrative Structural Biology, Lille, France
| | - Nathalie Sibille
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Pau Bernadó
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France.
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15
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Shukla S, Lazarchuk P, Pavlova MN, Sidorova JM. Genome-wide survey of D/E repeats in human proteins uncovers their instability and aids in identifying their role in the chromatin regulator ATAD2. iScience 2022; 25:105464. [PMCID: PMC9672403 DOI: 10.1016/j.isci.2022.105464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/03/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022] Open
Abstract
D/E repeats are stretches of aspartic and/or glutamic acid residues found in over 150 human proteins. We examined genomic stability of D/E repeats and functional characteristics of D/E repeat-containing proteins vis-à-vis the proteins with poly-Q or poly-A repeats, which are known to undergo pathologic expansions. Mining of tumor sequencing data revealed that D/E repeat-coding regions are similar to those coding poly-Qs and poly-As in increased incidence of trinucleotide insertions/deletions but differ in types and incidence of substitutions. D/E repeat-containing proteins preferentially function in chromatin metabolism and are the more likely to be nuclear and interact with core histones, the longer their repeats are. One of the longest D/E repeats of unknown function is in ATAD2, a bromodomain family ATPase frequently overexpressed in tumors. We demonstrate that D/E repeat deletion in ATAD2 suppresses its binding to nascent and mature chromatin and to the constitutive pericentromeric heterochromatin, where ATAD2 represses satellite transcription. Many human proteins contain runs of aspartic/glutamic acid residues (D/E repeats) D/E repeats show increased incidence of in-frame insertions/deletions in tumors Nuclear and histone-interacting proteins often have long D/E repeats D/E repeat of the oncogene ATAD2 controls its binding to pericentric chromatin
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Affiliation(s)
- Shalabh Shukla
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Pavlo Lazarchuk
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Maria N. Pavlova
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
| | - Julia M. Sidorova
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St., Box 357705, Seattle, WA 98195, USA
- Corresponding author
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16
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Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, Crehuet R, Salvatella X. A glutamine-based single α-helix scaffold to target globular proteins. Nat Commun 2022; 13:7073. [PMID: 36400768 PMCID: PMC9674830 DOI: 10.1038/s41467-022-34793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
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Affiliation(s)
- Albert Escobedo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.473715.30000 0004 6475 7299Present Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan Piccirillo
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.428469.50000 0004 1794 1018Present Address: Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Aranda
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Tammo Diercks
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Borja Mateos
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Macarena Sánchez-Navarro
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Armilla, Granada Spain
| | - Busra Topal
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Mateusz Biesaga
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lasse Staby
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- grid.5254.60000 0001 0674 042XREPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jesús García
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Millet
- grid.420161.0CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Modesto Orozco
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.5841.80000 0004 1937 0247Department of Biochemistry and Biomedicine, University of Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
| | - Murray Coles
- grid.419580.10000 0001 0942 1125Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tubingen, Germany
| | - Ramon Crehuet
- grid.4711.30000 0001 2183 4846Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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17
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Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA. Functional Tuning of Intrinsically Disordered Regions in Human Proteins by Composition Bias. Biomolecules 2022; 12:biom12101486. [PMID: 36291695 PMCID: PMC9599065 DOI: 10.3390/biom12101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered regions (IDRs) in protein sequences are flexible, have low structural constraints and as a result have faster rates of evolution. This lack of evolutionary conservation greatly limits the use of sequence homology for the classification and functional assessment of IDRs, as opposed to globular domains. The study of IDRs requires other properties for their classification and functional prediction. While composition bias is not a necessary property of IDRs, compositionally biased regions (CBRs) have been noted as frequent part of IDRs. We hypothesized that to characterize IDRs, it could be helpful to study their overlap with particular types of CBRs. Here, we evaluate this overlap in the human proteome. A total of 2/3 of residues in IDRs overlap CBRs. Considering CBRs enriched in one type of amino acid, we can distinguish CBRs that tend to be fully included within long IDRs (R, H, N, D, P, G), from those that partially overlap shorter IDRs (S, E, K, T), and others that tend to overlap IDR terminals (Q, A). CBRs overlap more often IDRs in nuclear proteins and in proteins involved in liquid-liquid phase separation (LLPS). Study of protein interaction networks reveals the enrichment of CBRs in IDRs by tandem repetition of short linear motifs (rich in S or P), and the existence of E-rich polar regions that could support specific protein interactions with non-specific interactions. Our results open ways to pin down the function of IDRs from their partial compositional biases.
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Affiliation(s)
- Kristina Kastano
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter stny 1/c, H-1117 Budapest, Hungary
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
- Correspondence:
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18
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Rizuan A, Jovic N, Phan TM, Kim YC, Mittal J. Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins. J Chem Inf Model 2022; 62:4474-4485. [PMID: 36066390 PMCID: PMC10165611 DOI: 10.1021/acs.jcim.2c00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at Cα atoms to faithfully capture the transient helical structures of IDPs. In order to parameterize and validate our new model, we propose Cα-based helix assignment rules based on dihedral angles that succeed in reproducing the atomistic helicity results of a polyalanine peptide and folded proteins. We then introduce sequence-dependent dihedral angle potential parameters (εd) and use experimentally available helical propensities of naturally occurring 20 amino acids to find their optimal values. The single-chain helical propensities from the CG simulations for commonly studied prion-like IDPs are in excellent agreement with the NMR-based α-helix fraction, demonstrating that the new HPS-SS model can accurately produce structural features of IDPs. Furthermore, this model can be easily implemented for large-scale assembly simulations due to its simplicity.
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Affiliation(s)
- Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Nina Jovic
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Tien M Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, District of Columbia 20375, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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19
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Mier P, Elena-Real CA, Cortés J, Bernadó P, Andrade-Navarro MA. The sequence context in poly-alanine regions: structure, function and conservation. Bioinformatics 2022; 38:4851-4858. [PMID: 36106994 PMCID: PMC9620824 DOI: 10.1093/bioinformatics/btac610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/07/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
Motivation Poly-alanine (polyA) regions are protein stretches mostly composed of alanines. Despite their abundance in eukaryotic proteomes and their association to nine inherited human diseases, the structural and functional roles exerted by polyA stretches remain poorly understood. In this work we study how the amino acid context in which polyA regions are settled in proteins influences their structure and function. Results We identified glycine and proline as the most abundant amino acids within polyA and in the flanking regions of polyA tracts, in human proteins as well as in 17 additional eukaryotic species. Our analyses indicate that the non-structuring nature of these two amino acids influences the α-helical conformations predicted for polyA, suggesting a relevant role in reducing the inherent aggregation propensity of long polyA. Then, we show how polyA position in protein N-termini relates with their function as transit peptides. PolyA placed just after the initial methionine is often predicted as part of mitochondrial transit peptides, whereas when placed in downstream positions, polyA are part of signal peptides. A few examples from known structures suggest that short polyA can emerge by alanine substitutions in α-helices; but evolution by insertion is observed for longer polyA. Our results showcase the importance of studying the sequence context of homorepeats as a mechanism to shape their structure–function relationships. Availability and implementation The datasets used and/or analyzed during the current study are available from the corresponding author onreasonable request. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pablo Mier
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz , 55128 Mainz, Germany
| | - Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS , 34090 Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS , Toulouse, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS , 34090 Montpellier, France
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz , 55128 Mainz, Germany
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20
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Mier P, Andrade-Navarro MA. Regions with two amino acids in protein sequences: a step forward from homorepeats into the low complexity landscape. Comput Struct Biotechnol J 2022; 20:5516-5523. [PMID: 36249567 PMCID: PMC9550522 DOI: 10.1016/j.csbj.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types ‘X’ and ‘Y’: direpeats (e.g. ‘XYXYXY’), joined (e.g. ‘XXXYYY’) and shuffled (e.g. ‘XYYXXY’). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.
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Affiliation(s)
- Pablo Mier
- Corresponding author at: Hanns-Dieter-Hüsch-Weg 15 55118 Mainz (Germany).
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21
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Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered. Biomolecules 2022; 12:biom12081098. [PMID: 36008992 PMCID: PMC9405754 DOI: 10.3390/biom12081098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/02/2022] [Accepted: 08/06/2022] [Indexed: 01/02/2023] Open
Abstract
There is increasing evidence that many intrinsically disordered regions (IDRs) in proteins play key functional roles through interactions with other proteins or nucleic acids. These interactions often exhibit a context-dependent structural behavior. We hypothesize that low complexity regions (LCRs), often found within IDRs, could have a role in inducing local structure in IDRs. To test this, we predicted IDRs in the human proteome and analyzed their structures or those of homologous sequences in the Protein Data Bank (PDB). We then identified two types of simple LCRs within IDRs: regions with only one (polyX or homorepeats) or with only two types of amino acids (polyXY). We were able to assign structural information from the PDB more often to these LCRs than to the surrounding IDRs (polyX 61.8% > polyXY 50.5% > IDRs 39.7%). The most frequently observed polyX and polyXY within IDRs contained E (Glu) or G (Gly). Structural analyses of these sequences and of homologs indicate that polyEK regions induce helical conformations, while the other most frequent LCRs induce coil structures. Our work proposes bioinformatics methods to help in the study of the structural behavior of IDRs and provides a solid basis suggesting a structuring role of LCRs within them.
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22
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Zhang L, Kang H, Perez-Aguilar JM, Zhou R. Possible Co-Evolution of Polyglutamine and Polyproline in Huntingtin Protein: Proline-Rich Domain as Transient Folding Chaperone. J Phys Chem Lett 2022; 13:6331-6341. [PMID: 35796410 DOI: 10.1021/acs.jpclett.2c01184] [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] [Indexed: 06/15/2023]
Abstract
Huntington's disease is an inherited neurodegenerative disorder caused by the overduplication of CAG repeats in the Huntingtin gene. Recent findings revealed that among the orthologs, the expansion of CAG repeats (polyQ) in the Huntingtin gene occurs in tandem with the duplication of CCG repeats (polyP). However, the molecular mechanism of this possible co-evolution remains unknown. We examined the structures of Huntingtin exon 1 (HttEx1) from six species along with five designed mutants. We found that the polyP segments "chaperone" the rest of the HttEx1 by forming ad hoc polyP binding grooves. Such a process elongates the otherwise poorly solvated polyQ domain, while modulating its secondary structure propensity from β-strands to α-helices. This chaperoning effect is achieved mostly through transient hydrogen bond interactions between polyP and the rest of HttEx1, resulting in a striking golden ratio of ∼2:1 between the chain lengths of polyQ and polyP.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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23
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Seim I, Posey AE, Snead WT, Stormo BM, Klotsa D, Pappu RV, Gladfelter AS. Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate. Proc Natl Acad Sci U S A 2022; 119:e2120799119. [PMID: 35333653 PMCID: PMC9060498 DOI: 10.1073/pnas.2120799119] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/16/2022] [Indexed: 01/02/2023] Open
Abstract
SignificanceA large subclass of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.
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Affiliation(s)
- Ian Seim
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ammon E. Posey
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Wilton T. Snead
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Benjamin M. Stormo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daphne Klotsa
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Amy S. Gladfelter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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24
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Abstract
![]()
Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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25
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Sahariah B, Sarma BK. Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts. J Phys Chem B 2021; 125:13394-13405. [PMID: 34851647 DOI: 10.1021/acs.jpcb.1c07875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol-1) nO → σ*Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their Cα-Cβ bonds. As the nO → σ*Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) → σ*C-N interaction (∼0.3 kcal·mol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (σ*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.
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Affiliation(s)
- Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore 560064, India
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26
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Jarosińska OD, Rüdiger SGD. Molecular Strategies to Target Protein Aggregation in Huntington's Disease. Front Mol Biosci 2021; 8:769184. [PMID: 34869596 PMCID: PMC8636123 DOI: 10.3389/fmolb.2021.769184] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by the aggregation of the mutant huntingtin (mHTT) protein in nerve cells. mHTT self-aggregates to form soluble oligomers and insoluble fibrils, which interfere in a number of key cellular functions. This leads to cell quiescence and ultimately cell death. There are currently still no treatments available for HD, but approaches targeting the HTT levels offer systematic, mechanism-driven routes towards curing HD and other neurodegenerative diseases. This review summarizes the current state of knowledge of the mRNA targeting approaches such as antisense oligonucleotides and RNAi system; and the novel methods targeting mHTT and aggregates for degradation via the ubiquitin proteasome or the autophagy-lysosomal systems. These methods include the proteolysis-targeting chimera, Trim-Away, autophagosome-tethering compound, autophagy-targeting chimera, lysosome-targeting chimera and approach targeting mHTT for chaperone-mediated autophagy. These molecular strategies provide a knowledge-based approach to target HD and other neurodegenerative diseases at the origin.
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Affiliation(s)
- Olga D. Jarosińska
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Science for Life, Utrecht University, Utrecht, Netherlands
| | - Stefan G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Science for Life, Utrecht University, Utrecht, Netherlands
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27
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Sinnaeve D, Ben Bouzayene A, Ottoy E, Hofman GJ, Erdmann E, Linclau B, Kuprov I, Martins J, Torbeev V, Kieffer B. Fluorine NMR study of proline-rich sequences using fluoroprolines. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:795-813. [PMID: 37905223 PMCID: PMC10539733 DOI: 10.5194/mr-2-795-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/28/2021] [Indexed: 11/01/2023]
Abstract
Proline homopolymer motifs are found in many proteins; their peculiar conformational and dynamic properties are often directly involved in those proteins' functions. However, the dynamics of proline homopolymers is hard to study by NMR due to a lack of amide protons and small chemical shift dispersion. Exploiting the spectroscopic properties of fluorinated prolines opens interesting perspectives to address these issues. Fluorinated prolines are already widely used in protein structure engineering - they introduce conformational and dynamical biases - but their use as 19 F NMR reporters of proline conformation has not yet been explored. In this work, we look at model peptides where Cγ -fluorinated prolines with opposite configurations of the chiral Cγ centre have been introduced at two positions in distinct polyproline segments. By looking at the effects of swapping these (4R )-fluoroproline and (4S )-fluoroproline within the polyproline segments, we were able to separate the intrinsic conformational properties of the polyproline sequence from the conformational alterations instilled by fluorination. We assess the fluoroproline 19 F relaxation properties, and we exploit the latter in elucidating binding kinetics to the SH3 (Src homology 3) domain.
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Affiliation(s)
- Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 – Risk Factors and Molecular Determinants of
Aging-Related Diseases (RID-AGE), 59000 Lille, France
- CNRS, ERL9002 – Integrative Structural Biology, 59000 Lille, France
| | - Abir Ben Bouzayene
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Gert-Jan Hofman
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Eva Erdmann
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - José C. Martins
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS),
International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg,
CNRS UMR 7006, 67000 Strasbourg, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
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28
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N-alpha-acetylation of Huntingtin protein increases its propensity to aggregate. J Biol Chem 2021; 297:101363. [PMID: 34732320 PMCID: PMC8640455 DOI: 10.1016/j.jbc.2021.101363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
Huntington’s disease (HD) is a neurodegenerative disorder caused by a poly-CAG expansion in the first exon of the HTT gene, resulting in an extended poly-glutamine tract in the N-terminal domain of the Huntingtin (Htt) protein product. Proteolytic fragments of the poly-glutamine–containing N-terminal domain form intranuclear aggregates that are correlated with HD. Post-translational modification of Htt has been shown to alter its function and aggregation properties. However, the effect of N-terminal Htt acetylation has not yet been considered. Here, we developed a bacterial system to produce unmodified or N-terminally acetylated and aggregation-inducible Htt protein. We used this system together with biochemical, biophysical, and imaging studies to confirm that the Htt N-terminus is an in vitro substrate for the NatA N-terminal acetyltransferase and show that N-terminal acetylation promotes aggregation. These studies represent the first link between N-terminal acetylation and the promotion of a neurodegenerative disease and implicates NatA-mediated Htt acetylation as a new potential therapeutic target in HD.
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29
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Pigazzini ML, Lawrenz M, Margineanu A, Kaminski Schierle GS, Kirstein J. An Expanded Polyproline Domain Maintains Mutant Huntingtin Soluble in vivo and During Aging. Front Mol Neurosci 2021; 14:721749. [PMID: 34720872 PMCID: PMC8554126 DOI: 10.3389/fnmol.2021.721749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/30/2021] [Indexed: 02/02/2023] Open
Abstract
Huntington's disease is a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat, encoding for the amino acid glutamine (Q), present in the first exon of the protein huntingtin. Over the threshold of Q39 HTT exon 1 (HTTEx1) tends to misfold and aggregate into large intracellular structures, but whether these end-stage aggregates or their on-pathway intermediates are responsible for cytotoxicity is still debated. HTTEx1 can be separated into three domains: an N-terminal 17 amino acid region, the polyglutamine (polyQ) expansion and a C-terminal proline rich domain (PRD). Alongside the expanded polyQ, these flanking domains influence the aggregation propensity of HTTEx1: with the N17 initiating and promoting aggregation, and the PRD modulating it. In this study we focus on the first 11 amino acids of the PRD, a stretch of pure prolines, which are an evolutionary recent addition to the expanding polyQ region. We hypothesize that this proline region is expanding alongside the polyQ to counteract its ability to misfold and cause toxicity, and that expanding this proline region would be overall beneficial. We generated HTTEx1 mutants lacking both flanking domains singularly, missing the first 11 prolines of the PRD, or with this stretch of prolines expanded. We then followed their aggregation landscape in vitro with a battery of biochemical assays, and in vivo in novel models of C. elegans expressing the HTTEx1 mutants pan-neuronally. Employing fluorescence lifetime imaging we could observe the aggregation propensity of all HTTEx1 mutants during aging and correlate this with toxicity via various phenotypic assays. We found that the presence of an expanded proline stretch is beneficial in maintaining HTTEx1 soluble over time, regardless of polyQ length. However, the expanded prolines were only advantageous in promoting the survival and fitness of an organism carrying a pathogenic stretch of Q48 but were extremely deleterious to the nematode expressing a physiological stretch of Q23. Our results reveal the unique importance of the prolines which have and still are evolving alongside expanding glutamines to promote the function of HTTEx1 and avoid pathology.
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Affiliation(s)
- Maria Lucia Pigazzini
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mandy Lawrenz
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
| | - Anca Margineanu
- Advanced Light Microscopy, Max-Delbrück Centrum for Molecular Medicine (MDC), Berlin, Germany
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- Department of Cell Biology, University of Bremen, Bremen, Germany
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30
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Ruff KM, Pappu RV. AlphaFold and Implications for Intrinsically Disordered Proteins. J Mol Biol 2021; 433:167208. [PMID: 34418423 DOI: 10.1016/j.jmb.2021.167208] [Citation(s) in RCA: 222] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Accurate predictions of the three-dimensional structures of proteins from their amino acid sequences have come of age. AlphaFold, a deep learning-based approach to protein structure prediction, shows remarkable success in independent assessments of prediction accuracy. A significant epoch in structural bioinformatics was the structural annotation of over 98% of protein sequences in the human proteome. Interestingly, many predictions feature regions of very low confidence, and these regions largely overlap with intrinsically disordered regions (IDRs). That over 30% of regions within the proteome are disordered is congruent with estimates that have been made over the past two decades, as intense efforts have been undertaken to generalize the structure-function paradigm to include the importance of conformational heterogeneity and dynamics. With structural annotations from AlphaFold in hand, there is the temptation to draw inferences regarding the "structures" of IDRs and their interactomes. Here, we offer a cautionary note regarding the misinterpretations that might ensue and highlight efforts that provide concrete understanding of sequence-ensemble-function relationships of IDRs. This perspective is intended to emphasize the importance of IDRs in sequence-function relationships (SERs) and to highlight how one might go about extracting quantitative SERs to make sense of how IDRs function.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA.
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31
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Ceccon A, Tugarinov V, Clore GM. Quantitative Exchange NMR-Based Analysis of Huntingtin-SH3 Interactions Suggests an Allosteric Mechanism of Inhibition of Huntingtin Aggregation. J Am Chem Soc 2021; 143:9672-9681. [PMID: 34137596 DOI: 10.1021/jacs.1c04786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Huntingtin polypeptides (httex1), encoded by exon 1 of the htt gene and containing an expanded polyglutamine tract, form fibrils that accumulate within neuronal inclusion bodies, resulting in the fatal neurodegenerative condition known as Huntington's disease. Httex1 comprises three regions: a 16-residue N-terminal amphiphilic domain (NT), a polyglutamine tract of variable length (Qn), and a polyproline-rich domain containing two polyproline tracts. The NT region of httex1 undergoes prenucleation transient oligomerization on the sub-millisecond time scale, resulting in a productive tetramer that promotes self-association and nucleation of the polyglutamine tracts. Here we show that binding of Fyn SH3, a small intracellular proline-binding domain, to the first polyproline tract of httex1Q35 inhibits fibril formation by both NMR and a thioflavin T fluorescence assay. The interaction of Fyn SH3 with httex1Q7 was investigated using NMR experiments designed to probe kinetics and equilibria at atomic resolution, including relaxation dispersion, and concentration-dependent exchange-induced chemical shifts and transverse relaxation in the rotating frame. Sub-millisecond exchange between four species is demonstrated: two major states comprising free (P) and SH3-bound (PL) monomeric httex1Q7, and two sparsely populated dimers in which either both subunits (P2L2) or only a single subunit (P2L) is bound to SH3. Binding of SH3 increases the helical propensity of the NT domain, resulting in a 25-fold stabilization of the P2L2 dimer relative to the unliganded P2 dimer. The P2L2 dimer, in contrast to P2, does not undergo any detectable oligomerization to a tetramer, thereby explaining the allosteric inhibition of httex1 fibril formation by Fyn SH3.
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Affiliation(s)
- Alberto Ceccon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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32
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Dyson HJ, Wright PE. NMR illuminates intrinsic disorder. Curr Opin Struct Biol 2021; 70:44-52. [PMID: 33951592 DOI: 10.1016/j.sbi.2021.03.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Nuclear magnetic resonance (NMR) has long been instrumental in the characterization of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). This method continues to offer rich insights into the nature of IDPs in solution, especially in combination with other biophysical methods such as small-angle scattering, single-molecule fluorescence, electron paramagnetic resonance (EPR), and mass spectrometry. Substantial advances have been made in recent years in studies of proteins containing both ordered and disordered domains and in the characterization of problematic sequences containing repeated tracts of a single or a few amino acids. These sequences are relevant to disease states such as Alzheimer's, Parkinson's, and Huntington's diseases, where disordered proteins misfold into harmful amyloid. Innovative applications of NMR are providing novel insights into mechanisms of protein aggregation and the complexity of IDP interactions with their targets. As a basis for understanding the solution structural ensembles, dynamic behavior, and functional mechanisms of IDPs and IDRs, NMR continues to prove invaluable.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA.
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33
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Wälti MA, Kotler SA, Clore GM. Probing the Interaction of Huntingtin Exon-1 Polypeptides with the Chaperonin Nanomachine GroEL. Chembiochem 2021; 22:1985-1991. [PMID: 33644966 DOI: 10.1002/cbic.202100055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/28/2021] [Indexed: 12/14/2022]
Abstract
Huntington's disease arises from polyQ expansion within the exon-1 region of huntingtin (httex1 ), resulting in an aggregation-prone protein that accumulates in neuronal inclusion bodies. We investigate the interaction of various httex1 constructs with the bacterial analog (GroEL) of the human chaperonin Hsp60. Using fluorescence spectroscopy and electron and atomic force microscopy, we show that GroEL inhibits fibril formation. The binding kinetics of httex1 constructs with intact GroEL and a mini-chaperone comprising the apical domain is characterized by relaxation-based NMR measurements. The lifetimes of the complexes range from 100 to 400 μs with equilibrium dissociation constants (KD ) of ∼1-2 mM. The binding interface is formed by the N-terminal amphiphilic region of httex1 (which adopts a partially helical conformation) and the H and I helices of the GroEL apical domain. Sequestration of monomeric httex1 by GroEL likely increases the critical concentration required for fibrillization.
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Affiliation(s)
- Marielle A Wälti
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
| | - Samuel A Kotler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
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Kastano K, Mier P, Andrade-Navarro MA. The Role of Low Complexity Regions in Protein Interaction Modes: An Illustration in Huntingtin. Int J Mol Sci 2021; 22:1727. [PMID: 33572172 PMCID: PMC7915032 DOI: 10.3390/ijms22041727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Low complexity regions (LCRs) are very frequent in protein sequences, generally having a lower propensity to form structured domains and tending to be much less evolutionarily conserved than globular domains. Their higher abundance in eukaryotes and in species with more cellular types agrees with a growing number of reports on their function in protein interactions regulated by post-translational modifications. LCRs facilitate the increase of regulatory and network complexity required with the emergence of organisms with more complex tissue distribution and development. Although the low conservation and structural flexibility of LCRs complicate their study, evolutionary studies of proteins across species have been used to evaluate their significance and function. To investigate how to apply this evolutionary approach to the study of LCR function in protein-protein interactions, we performed a detailed analysis for Huntingtin (HTT), a large protein that is a hub for interaction with hundreds of proteins, has a variety of LCRs, and for which partial structural information (in complex with HAP40) is available. We hypothesize that proteins RASA1, SYN2, and KAT2B may compete with HAP40 for their attachment to the core of HTT using similar LCRs. Our results illustrate how evolution might favor the interplay of LCRs with domains, and the possibility of detecting multiple modes of LCR-mediated protein-protein interactions with a large hub such as HTT when enough protein interaction data is available.
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Affiliation(s)
| | | | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany; (K.K.); (P.M.)
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Chiki A, Ricci J, Hegde R, Abriata LA, Reif A, Boudeffa D, Lashuel HA. Site-Specific Phosphorylation of Huntingtin Exon 1 Recombinant Proteins Enabled by the Discovery of Novel Kinases. Chembiochem 2021; 22:217-231. [PMID: 32805086 PMCID: PMC8698011 DOI: 10.1002/cbic.202000508] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Post-translational modifications (PTMs) within the first 17 amino acids (Nt17) of exon 1 of the Huntingtin protein (Httex1) play important roles in modulating its cellular properties and functions in health and disease. In particular, phosphorylation of threonine and serine residues (T3, S13, and/or S16) has been shown to inhibit Htt aggregation in vitro and inclusion formation in cellular and animal models of Huntington's disease (HD). In this paper, we describe a new and simple methodology for producing milligram quantities of highly pure wild-type or mutant Httex1 proteins that are site-specifically phosphorylated at T3 or at both S13 and S16. This advance was enabled by 1) the discovery and validation of novel kinases that efficiently phosphorylate Httex1 at S13 and S16 (TBK1), at T3 (GCK) or T3 and S13 (TNIK and HGK), and 2) the development of an efficient methodology for producing recombinant native Httex1 proteins by using a SUMO-fusion expression and purification strategy.[26] As a proof of concept, we demonstrate how this method can be applied to produce Httex1 proteins that are both site-specifically phosphorylated and fluorescently or isotopically labeled. Together, these advances should increase access to these valuable tools and expand the range of methods and experimental approaches that can be used to elucidate the mechanisms by which phosphorylation influences Httex1 or HTT structure, aggregation, interactome, and function(s) in health and disease.
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Affiliation(s)
- Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Jonathan Ricci
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Ramanath Hegde
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Luciano A. Abriata
- Protein Production and Structure Core Facility and Laboratory for Biomolecular ModelingEcole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB)1015LausanneSwitzerland
| | - Andreas Reif
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind InstituteEcole Polytechnique Fédérale de Lausanne (EPFL)Station 191015LausanneSwitzerland
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Mier P, Andrade-Navarro MA. Assessing the low complexity of protein sequences via the low complexity triangle. PLoS One 2020; 15:e0239154. [PMID: 33378336 PMCID: PMC7773278 DOI: 10.1371/journal.pone.0239154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/31/2020] [Indexed: 11/24/2022] Open
Abstract
Background Proteins with low complexity regions (LCRs) have atypical sequence and structural features. Their amino acid composition varies from the expected, determined proteome-wise, and they do not follow the rules of structural folding that prevail in globular regions. One way to characterize these regions is by assessing the repeatability of a sequence, that is, calculating the local propensity of a region to be part of a repeat. Results We combine two local measures of low complexity, repeatability (using the RES algorithm) and fraction of the most frequent amino acid, to evaluate different proteomes, datasets of protein regions with specific features, and individual cases of proteins with extreme compositions. We apply a representation called ‘low complexity triangle’ as a proof-of-concept to represent the low complexity measured values. Results show that proteomes have distinct signatures in the low complexity triangle, and that these signatures are associated to complexity features of the sequences. We developed a web tool called LCT (http://cbdm-01.zdv.uni-mainz.de/~munoz/lct/) to allow users to calculate the low complexity triangle of a given protein or region of interest. Conclusions The low complexity triangle proves to be a suitable procedure to represent the general low complexity of a sequence or protein dataset. Homorepeats, direpeats, compositionally biased regions and globular regions occupy characteristic positions in the triangle. The described pipeline can be used to characterize LCRs and may help in quantifying the content of degenerated tandem repeats in proteins and proteomes.
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Affiliation(s)
- Pablo Mier
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| | - Miguel A. Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
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Delhommel F, Sattler M. When Less Is More: Combining Site-Specific Isotope Labeling and NMR Unravels Structural Details of Huntingtin Repeats. Structure 2020; 28:730-732. [PMID: 32640252 DOI: 10.1016/j.str.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this issue of Structure, Urbanek et al. (2020a) combine site-specific isotope labeling and NMR spectroscopy to investigate opposing effects of flanking regions onto the conformation of the poly-Q region in Huntingtin. Poly-Q interactions with preceding residues promote an α-helical conformation while a following proline-rich region favors extended conformations.
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Affiliation(s)
- Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Bavarian NMR Center and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany.
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Wetzel R. Exploding the Repeat Length Paradigm while Exploring Amyloid Toxicity in Huntington's Disease. Acc Chem Res 2020; 53:2347-2357. [PMID: 32975927 DOI: 10.1021/acs.accounts.0c00450] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Huntington's disease (HD) is a progressive, familial neurodegenerative disease triggered by the expansion of a polyglutamine (polyQ) track in the protein huntingtin (htt). PolyQ sequences up to Q36 in htt are not known to be toxic, while polyQ lengths above Q36 almost invariably lead to increased disease risk and decreased ages of onset. The large number of physical states (monomers, dimers, tetramers, non-β oligomers, nanofibrils, and clustered amyloid fibrils) on the self-association landscape, with their overlapping kinetics of formation, have greatly complicated identification of the molecular species responsible for HD toxicity, drawing attention to the need for innovative approaches.After reports of HD-associated intraneuronal htt inclusions in 1997, we elucidated aggregation mechanisms of both simple polyQ sequences and the more complex polyQ-containing "exon1" fragment of htt (htt-ex1). Grounded in this work, the more recent results described here were made possible by breakthroughs in the molecular design of diagnostic polyQ derivatives and in fluorescence applications for characterizing amyloid assembly intermediates. Thus, insertion of β-turn-promoting mutations into relatively short, disordered polyQ sequences created "pro-β-hairpin" polyQs (βHPs) that exhibit amyloid formation rates comparable to the enhanced rates seen with expanded polyQ peptides. Introduction of "β-breaker" mutations into these βHP polyQ sequences created molecules that are blocked from aggregating into amyloid and also can inhibit amyloid formation by other polyQ proteins. These mutational effects were then successfully transferred into more complex htt-ex1 sequence backgrounds. Insights into the aggregation properties of htt-ex1 derivatives-as well as into the nucleation process itself-were obtained using fluorescence correlation spectroscopy (FCS) and a novel thioflavin-T (ThT) protocol that allows quantitation of htt-ex1 assembly intermediates.Using these tools, we quantified physical states of htt-ex1 at different growth times in mammalian PC12 cells engineered for inducible expression of both normal and expanded polyQ repeat length versions of htt-ex1. For expanded polyQ versions, we found tetramers, oligomers, and fibrils (but no monomers) all populated in these cells at a time when the first indication of toxicity (nuclear DNA damage) was observed. These experiments provided a strong hint that monomeric forms of htt-ex1 are not involved in toxicity, but we were otherwise unable to implicate a specific toxic self-assembled state because of the overlapping kinetics of formation. To gain a more intimate focus and control over the timelines of htt-ex1 self-assembly and the resulting toxic response, we engineered various htt-ex1-βHP molecules-with and without added β-breaker mutations-that could be expressed in rat neuronal and Drosophila models of HD. In both models, novel htt-ex1-βHP analogues exhibiting strong aggregation in spite of their very short polyQ repeat lengths proved to be toxic, dramatically breaking the "repeat length paradigm" and strongly suggesting that the toxic species must be some kind of aggregate. In both models, β-breaker analogues of htt-ex1-βHP that are slow to make amyloid-instead favoring accumulation of non-β oligomers-were nontoxic. In contrast, htt-ex1-βHP analogues that rapidly progress to amyloid states were toxic, suggesting that an aggregate possessing the fundamental amyloid folding motif is very likely the major toxic species in HD.
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Affiliation(s)
- Ronald Wetzel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Sciences Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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Morató A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernadó P. Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins. Biomolecules 2020; 10:E1458. [PMID: 33086646 PMCID: PMC7603387 DOI: 10.3390/biom10101458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022] Open
Abstract
The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.
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Affiliation(s)
| | | | | | | | | | | | | | - Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
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