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Jiang K, Rocha S, Kumar R, Westerlund F, Wittung-Stafshede P. C-terminal truncation of α-synuclein alters DNA structure from extension to compaction. Biochem Biophys Res Commun 2021; 568:43-47. [PMID: 34175689 DOI: 10.1016/j.bbrc.2021.06.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022]
Abstract
Parkinson's disease (PD) is linked to aggregation of the protein α-synuclein (aS) into amyloid fibers. aS is proposed to regulate synaptic activity and may also play a role in gene regulation via interaction with DNA in the cell nucleus. Here, we address the role of the negatively-charged C-terminus in the interaction between aS and DNA using single-molecule techniques. Using nanofluidic channels, we demonstrate that truncation of the C-terminus of aS induces differential effects on DNA depending on the extent of the truncation. The DNA extension increases for full-length aS and the (1-119)aS variant, but decreases about 25% upon binding to the (1-97)aS variant. Atomic force microscopy imaging showed full protein coverage of the DNA at high aS concentration. The characterization of biophysical properties of DNA when in complex with aS variants may provide important insights into the role of such interactions in PD, especially since C-terminal aS truncations have been found in clinical samples from PD patients.
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Affiliation(s)
- Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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Du Z, Li M, Ren J, Qu X. Current Strategies for Modulating Aβ Aggregation with Multifunctional Agents. Acc Chem Res 2021; 54:2172-2184. [PMID: 33881820 DOI: 10.1021/acs.accounts.1c00055] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD), as the primary cause of dementia, has seriously affected millions of people worldwide and brought a very heavy financial and social burden. With the growth of population and aging, the situation will worsen unless efficacious drugs are found to reverse, stop, or even slow down disease progression. More and more evidence has demonstrated that amyloid-β (Aβ) aggregation is an upstream causative factor in AD pathogenesis and then triggers a slew of pathological events. Furthermore, the concentrated redox metal ions in the AD brain, especially Cu(II), can significantly exacerbate Aβ aggregation and contribute to the formation of neurotoxic reactive oxygen species (ROS). Therefore, the inhibition of Aβ aggregation and relief of amyloidosis-initiated neurotoxicity play a critical role in AD treatment. Until now, several methods have been proposed to modulate Aβ aggregation, such as developing aggregation inhibitors to interfere with Aβ assembly via noncovalent interactions, copper chelators to cut off metal-accelerated Aβ aggregation and concomitant cytotoxicity, photooxidation to reduce the hydrophobicity and aggregation tendency of Aβ, thermal dissociation to disrupt amyloid aggregates susceptible to temperature, degradation with artificial protease to fracture the Aβ peptide into small fragments, and the clearance of peripheral Aβ to bypass the obstruction of the BBB and reduce the Aβ burden.In this Account, we focus on our contributions to the development of Aβ-targeted multifunctional molecules and nanoparticles, emphasizing the diversified strategies and synergistic therapeutic effects. These therapeutic agents possess the following multifunctionalities: (1) compared with frequently used aggregation inhibitors restricted by intrinsically feeble and sensitive noncovalent interactions, multifunctional agents can efficiently block Aβ aggregation by exploiting two or more Aβ-specific inhibition strategies simultaneously; (2) apart from regulating Aβ aggregation, multipronged agents can also target and modulate other pathological factors in AD pathogenesis, such as increased oxidative stress, abnormal copper accumulation, and irreversible neuron loss; (3) multifunctional platforms with both diagnostic and therapeutic modalities through integrating in situ imaging, real-time diagnostics, a multitarget direction, stimuli-responsive drug release, and the blood-brain barrier (BBB) translocation features are instrumental in improving drug levels at trouble sites, diminishing off-target adverse reactions, evaluating therapeutic effects, and averting overtreatment.Given the fact that amyloid aggregation, local inflammation, and metal dyshomeostasis are universal biomarkers shared by various neurodegenerative disorders, this Account provides a perspective for the evolution of customized therapeutic agents with multiple reactivities for other neurodegenerative diseases. In addition, recent studies have indicated that Aβ aggregates can enter the nucleus and induce DNA damage and anomalous conformational transition. We also explore the influences of DNA on the biological effects of Aβ aggregates.
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Affiliation(s)
- Zhi Du
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Meng Li
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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Wien F, Martinez D, Le Brun E, Jones NC, Vrønning Hoffmann S, Waeytens J, Berbon M, Habenstein B, Arluison V. The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment. Microorganisms 2019; 7:microorganisms7120639. [PMID: 31816864 PMCID: PMC6956100 DOI: 10.3390/microorganisms7120639] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, B1050 Bruxelles, Belgique;
- Laboratoire de Chimie Physique d’Orsay, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay 91400 Orsay, France
| | - Melanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
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Jiang K, Rocha S, Westling A, Kesarimangalam S, Dorfman KD, Wittung-Stafshede P, Westerlund F. Alpha-Synuclein Modulates the Physical Properties of DNA. Chemistry 2018; 24:15685-15690. [PMID: 30102440 PMCID: PMC6217799 DOI: 10.1002/chem.201803933] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 11/06/2022]
Abstract
Fundamental research on Parkinson's disease (PD) most often focuses on the ability of α-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here, the interaction between monomeric aS and DNA in vitro has been investigated with single-molecule techniques. Using a nanofluidic channel system, it was discovered that aS binds to DNA and by studying the DNA-protein complexes at different confinements we determined that aS binding increases the persistence length of DNA from 70 to 90 nm at high coverage. By atomic force microscopy it was revealed that at low protein-to-DNA ratio, the aS binding occurs as small protein clusters scattered along the DNA; at high protein-to-DNA ratio, the DNA is fully covered by protein. As DNA-aS interactions may play roles in PD, it is of importance to characterize biophysical properties of such complexes in detail.
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Affiliation(s)
- Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alvina Westling
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kesarimangalam
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | | | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Affiliation(s)
- Jancy Nixon Abraham
- Polymer Science and Engineering Division; CSIR National Chemical Laboratory; Pune India
| | - Corinne Nardin
- Université de Pau et des Pays de l'Adour (UPPA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les matériaux (IPREM); Equipe Physique et Chimie des Polymères (EPCP); Pau France
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Qi H, Cantrelle FX, Benhelli-Mokrani H, Smet-Nocca C, Buée L, Lippens G, Bonnefoy E, Galas MC, Landrieu I. Nuclear magnetic resonance spectroscopy characterization of interaction of Tau with DNA and its regulation by phosphorylation. Biochemistry 2015; 54:1525-33. [PMID: 25623359 DOI: 10.1021/bi5014613] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The capacity of endogenous Tau to bind DNA has been recently identified in neurons under physiological or oxidative stress conditions. Characterization of the protein domains involved in Tau-DNA complex formation is an essential first step in clarifying the contribution of Tau-DNA interactions to neurological biological processes. To identify the amino acid residues involved in the interaction of Tau with oligonucleotides, we have characterized a Tau-DNA complex using nuclear magnetic resonance spectroscopy. Interaction of an AT-rich or GC-rich 22 bp oligonucleotide with Tau showed multiple points of anchoring along the intrinsically disordered Tau protein. The main sites of contact characterized here correspond to the second half of the proline-rich domain (PRD) of Tau and the R2 repeat in the microtubule binding domain. This latter interaction site includes the PHF6* sequence known to govern Tau aggregation. The characterization was pursued by studying the binding of phosphorylated forms of Tau, displaying multiple phosphorylation sites mainly in the PRD, to the same oligonucleotide. No interaction of phospho-Tau with the oligonucleotide was detected, suggesting that pathological Tau phosphorylation could affect the physiological function of Tau mediated by DNA binding.
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Affiliation(s)
- Haoling Qi
- UMR8576 CNRS-Lille University , 59655 Villeneuve d'Ascq, France
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Pathological implications of nucleic acid interactions with proteins associated with neurodegenerative diseases. Biophys Rev 2014; 6:97-110. [PMID: 28509960 DOI: 10.1007/s12551-013-0132-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022] Open
Abstract
Protein misfolding disorders (PMDs) refer to a group of diseases related to the misfolding of particular proteins that aggregate and deposit in the cells and tissues of humans and other mammals. The mechanisms that trigger protein misfolding and aggregation are still not fully understood. Increasing experimental evidence indicates that abnormal interactions between PMD-related proteins and nucleic acids (NAs) can induce conformational changes. Here, we discuss these protein-NA interactions and address the role of deoxyribonucleic (DNA) and ribonucleic (RNA) acid molecules in the conformational conversion of different proteins that aggregate in PMDs, such as Alzheimer's, Parkinson's, and prion diseases. Studies on the affinity, stability, and specificity of proteins involved in neurodegenerative diseases and NAs are specifically addressed. A landscape of reciprocal effects resulting from the binding of prion proteins, amyloid-β peptides, tau proteins, huntingtin, and α-synuclein are presented here to clarify the possible role of NAs, not only as encoders of genetic information but also in triggering PMDs.
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