1
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Lentzsch AM, Yudin D, Gamerdinger M, Chandrasekar S, Rabl L, Scaiola A, Deuerling E, Ban N, Shan SO. NAC guides a ribosomal multienzyme complex for nascent protein processing. Nature 2024:10.1038/s41586-024-07846-7. [PMID: 39169182 DOI: 10.1038/s41586-024-07846-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Approximately 40% of the mammalian proteome undergoes N-terminal methionine excision and acetylation, mediated sequentially by methionine aminopeptidase (MetAP) and N-acetyltransferase A (NatA), respectively1. Both modifications are strictly cotranslational and essential in higher eukaryotic organisms1. The interaction, activity and regulation of these enzymes on translating ribosomes are poorly understood. Here we perform biochemical, structural and in vivo studies to demonstrate that the nascent polypeptide-associated complex2,3 (NAC) orchestrates the action of these enzymes. NAC assembles a multienzyme complex with MetAP1 and NatA early during translation and pre-positions the active sites of both enzymes for timely sequential processing of the nascent protein. NAC further releases the inhibitory interactions from the NatA regulatory protein huntingtin yeast two-hybrid protein K4,5 (HYPK) to activate NatA on the ribosome, enforcing cotranslational N-terminal acetylation. Our results provide a mechanistic model for the cotranslational processing of proteins in eukaryotic cells.
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Affiliation(s)
- Alfred M Lentzsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Denis Yudin
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Gamerdinger
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Sowmya Chandrasekar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Laurenz Rabl
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Elke Deuerling
- Department of Biology, Molecular Microbiology, University of Konstanz, Konstanz, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Trubitsina NP, Matiiv AB, Rogoza TM, Zudilova AA, Bezgina MD, Zhouravleva GA, Bondarev SA. Role of the Gut Microbiome and Bacterial Amyloids in the Development of Synucleinopathies. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:523-542. [PMID: 38648770 DOI: 10.1134/s0006297924030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 04/25/2024]
Abstract
Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson's disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson's disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson's disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.
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Affiliation(s)
- Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Tatyana M Rogoza
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- St. Petersburg Branch of the Vavilov Institute of General Genetics, Saint Petersburg, 198504, Russia
| | - Anna A Zudilova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Mariya D Bezgina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
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3
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Buhmann C, Magnus T, Choe CU. Blood neurofilament light chain in Parkinson's disease. J Neural Transm (Vienna) 2023; 130:755-762. [PMID: 37067597 PMCID: PMC10199845 DOI: 10.1007/s00702-023-02632-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/01/2023] [Indexed: 04/18/2023]
Abstract
Blood neurofilament light chain (NfL) is an easily accessible, highly sensitive and reliable biomarker for neuroaxonal damage. Currently, its role in Parkinson's disease (PD) remains unclear. Here, we demonstrate that blood NfL can distinguish idiopathic PD from atypical parkinsonian syndromes (APS) with high sensitivity and specificity. In cross-sectional studies, some found significant correlations between blood NfL with motor and cognitive function, whereas others did not. In contrast, prospective studies reported very consistent associations between baseline blood NfL with motor progression and cognitive worsening. Amongst PD subtypes, especially postural instability and gait disorder (PIGD) subtype, symptoms and scores are reliably linked with blood NfL. Different non-motor PD comorbidities have also been associated with high blood NfL levels suggesting that the neuroaxonal damage of the autonomic nervous system as well as serotonergic, cholinergic and noradrenergic neurons is quantifiable. Numerous absolute NfL cutoff levels have been suggested in different cohort studies; however, validation across cohorts remains weak. However, age-adjusted percentiles and intra-individual blood NfL changes might represent more valid and consistent parameters compared with absolute NfL concentrations. In summary, blood NfL has the potential as biomarker in PD patients to be used in clinical practice for prediction of disease severity and especially progression.
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Affiliation(s)
- Carsten Buhmann
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Magnus
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Experimental Research in Stroke and Inflammation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Chi-Un Choe
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Experimental Research in Stroke and Inflammation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Neurology, Klinikum Itzehoe, Robert-Koch-Straße 2, 25524, Itzehoe, Germany.
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4
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Zhu JJ, Zhang NJ, Wei T, Chen HF. Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder. Int J Mol Sci 2023; 24:ijms24086896. [PMID: 37108059 PMCID: PMC10138423 DOI: 10.3390/ijms24086896] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) account for more than 50% of the human proteome and are closely associated with tumors, cardiovascular diseases, and neurodegeneration, which have no fixed three-dimensional structure under physiological conditions. Due to the characteristic of conformational diversity, conventional experimental methods of structural biology, such as NMR, X-ray diffraction, and CryoEM, are unable to capture conformational ensembles. Molecular dynamics (MD) simulation can sample the dynamic conformations at the atomic level, which has become an effective method for studying the structure and function of IDPs. However, the high computational cost prevents MD simulations from being widely used for IDPs conformational sampling. In recent years, significant progress has been made in artificial intelligence, which makes it possible to solve the conformational reconstruction problem of IDP with fewer computational resources. Here, based on short MD simulations of different IDPs systems, we use variational autoencoders (VAEs) to achieve the generative reconstruction of IDPs structures and include a wider range of sampled conformations from longer simulations. Compared with the generative autoencoder (AEs), VAEs add an inference layer between the encoder and decoder in the latent space, which can cover the conformational landscape of IDPs more comprehensively and achieve the effect of enhanced sampling. Through experimental verification, the Cα RMSD between VAE-generated and MD simulation sampling conformations in the 5 IDPs test systems was significantly lower than that of AE. The Spearman correlation coefficient on the structure was higher than that of AE. VAE can also achieve excellent performance regarding structured proteins. In summary, VAEs can be used to effectively sample protein structures.
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Affiliation(s)
- Jun-Jie Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ning-Jie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ting Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200240, China
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5
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Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure 2023; 31:411-423.e6. [PMID: 36809765 PMCID: PMC10081966 DOI: 10.1016/j.str.2023.01.011] [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: 11/20/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.
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Affiliation(s)
- Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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6
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R K, Aouti S, Jos S, Prasad TK, K N K, Unni S, Padmanabhan B, Kamariah N, Padavattan S, Mythri RB. High-affinity binding of celastrol to monomeric α-synuclein mitigates in vitro aggregation. J Biomol Struct Dyn 2023; 41:12703-12713. [PMID: 36744543 DOI: 10.1080/07391102.2023.2175379] [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: 10/15/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023]
Abstract
α-Synuclein (αSyn) aggregation is associated with Parkinson's disease (PD). The region αSyn36-42 acts as the nucleation 'master controller' and αSyn1-12 as a 'secondary nucleation site'. They drive monomeric αSyn to aggregation. Small molecules targeting these motifs are promising for disease-modifying therapy. Using computational techniques, we screened thirty phytochemicals for αSyn binding. The top three compounds were experimentally validated for their binding affinity. Amongst them, celastrol showed high binding affinity. NMR analysis confirmed stable αSyn-celastrol interactions involving several residues in the N-terminus and NAC regions but not in the C-terminal tail. Importantly, celastrol interacted extensively with the key motifs that drive αSyn aggregation. Thioflavin-T assay indicated that celastrol reduced αSyn aggregation. Thus, celastrol holds promise as a potent drug candidate for PD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kavya R
- Department of Biotechnology, Mount Carmel College, Autonomous, Bengaluru, Karnataka, India
| | - Snehal Aouti
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Sneha Jos
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Kumuda K N
- Department of Biotechnology, Mount Carmel College, Autonomous, Bengaluru, Karnataka, India
| | - Sruthi Unni
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bengaluru, Karnataka, India
| | - Sivaraman Padavattan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Rajeswara Babu Mythri
- Department of Biotechnology, Mount Carmel College, Autonomous, Bengaluru, Karnataka, India
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7
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Jiang Y, Chen HF. Performance evaluation of the balanced force field ff03CMAP for intrinsically disordered and ordered proteins. Phys Chem Chem Phys 2022; 24:29870-29881. [PMID: 36468450 DOI: 10.1039/d2cp04501j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) have been found to be closely associated with various human diseases. Because IDPs have no fixed tertiary structure under physiological conditions, current experimental methods, such as X-ray spectroscopy, NMR, and CryoEM, cannot capture all the dynamic conformations. Molecular dynamics simulation is an useful tool that is widely used to study the conformer distributions of IDPs and has become an important complementary tool for experimental methods. However, the accuracy of MD simulations directly depends on utilizing a precise force field. Recently a CMAP optimized force field based on the Amber ff03 force field (termed ff03CMAP herein) was developed for a balanced sampling of IDPs and folded proteins. In order to further evaluate the performance, more types of disordered and ordered proteins were used to test the ability for conformer sampling. The results showed that simulated chemical shifts, J-coupling, and Rg distribution with the ff03CMAP force field were in better agreement with NMR measurements and were more accurate than those with the ff03 force field. The sampling conformations by ff03CMAP were more diverse than those of ff03. At the same time, ff03CMAP could stabilize the conformers of the ordered proteins. These findings indicate that ff03CMAP can be widely used to sample diverse conformers for proteins, including the intrinsically disordered regions.
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Affiliation(s)
- Yuxin Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Shanghai Center for Bioinformation Technology, 200240, Shanghai, China
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8
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Iyer A, Sidhu A, Subramaniam V. How important is the N-terminal acetylation of alpha-synuclein for its function and aggregation into amyloids? Front Neurosci 2022; 16:1003997. [PMID: 36466161 PMCID: PMC9709446 DOI: 10.3389/fnins.2022.1003997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
N-α-acetylation is a frequently occurring post-translational modification in eukaryotic proteins. It has manifold physiological consequences on the regulation and function of several proteins, with emerging studies suggesting that it is a global regulator of stress responses. For decades, in vitro biochemical investigations into the precise role of the intrinsically disordered protein alpha-synuclein (αS) in the etiology of Parkinson's disease (PD) were performed using non-acetylated αS. The N-terminus of α-synuclein is now unequivocally known to be acetylated in vivo, however, there are many aspects of this post-translational modifications that are not understood well. Is N-α-acetylation of αS a constitutive modification akin to most cellular proteins, or is it spatio-temporally regulated? Is N-α-acetylation of αS relevant to the as yet elusive function of αS? How does the N-α-acetylation of αS influence the aggregation of αS into amyloids? Here, we provide an overview of the current knowledge and discuss prevailing hypotheses on the impact of N-α-acetylation of αS on its conformational, oligomeric, and fibrillar states. The extent to which N-α-acetylation of αS is vital for its function, membrane binding, and aggregation into amyloids is also explored here. We further discuss the overall significance of N-α-acetylation of αS for its functional and pathogenic implications in Lewy body formation and synucleinopathies.
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Affiliation(s)
- Aditya Iyer
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arshdeep Sidhu
- Nitte University Centre for Science Education and Research, Nitte University (DU), Mangalore, India
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9
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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10
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Privat C, Madurga S, Mas F, Rubio-Martinez J. Molecular dynamics simulations of an α-synuclein NAC domain fragment with a ff14IDPSFF IDP-specific force field suggest β-sheet intermediate states of fibrillation. Phys Chem Chem Phys 2022; 24:18841-18853. [PMID: 35912724 DOI: 10.1039/d2cp02042d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
For the discovery of treatments against synucleinopathies, it is necessary to unravel and fully understand the mechanism of fibrillation of proteins involved. Among them, α-synuclein (αS) plays a key role in the development of these diseases through its aggregation into oligomers found in Lewy bodies. However, its structural disorder as an intrinsically disordered protein (IDP) makes its characterization by experimental techniques arduously difficult. Atomistic simulations aim to provide insights into this blank canvas and, fortunately, some studies have already suggested promising mechanisms. Still, it is urgent to consider the IDP features in simulations, so recently a lot of force fields designed to deal with IDPs have been developed. In this study, we have carried out a total of 12 μs simulations of an αS core fragment using a popular ff14SB AMBER force field and the ff14IDPSFF variation that includes a grid-based energy correction map (CMAP) method. The predicted chemical shifts from the simulations and those measured from the αS protein in the NMR solution indicate that ff14IDPSFF reproduces the experimental data more accurately. Moreover, structural analysis exhibits opposite trends between secondary structure propensities. The ff14SB force field preserves the α-helices found in the micelle-bound αS structure, which is used as an initial conformation, while ff14IDPSFF stands out with increased structural disorder and the formation of β-sheets, which suggests that the IDP-specific force field can capture more suitable conformations representing the possible intermediate states of the fibrillation process.
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Affiliation(s)
- Cristian Privat
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain.
| | - Sergio Madurga
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain.
| | - Francesc Mas
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain.
| | - Jaime Rubio-Martinez
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain.
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11
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Bell R, Thrush RJ, Castellana-Cruz M, Oeller M, Staats R, Nene A, Flagmeier P, Xu CK, Satapathy S, Galvagnion C, Wilson MR, Dobson CM, Kumita JR, Vendruscolo M. N-Terminal Acetylation of α-Synuclein Slows down Its Aggregation Process and Alters the Morphology of the Resulting Aggregates. Biochemistry 2022; 61:1743-1756. [PMID: 35944093 PMCID: PMC9454101 DOI: 10.1021/acs.biochem.2c00104] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Parkinson’s disease is associated with the aberrant
aggregation
of α-synuclein. Although the causes of this process are still
unclear, post-translational modifications of α-synuclein are
likely to play a modulatory role. Since α-synuclein is constitutively
N-terminally acetylated, we investigated how this post-translational
modification alters the aggregation behavior of this protein. By applying
a three-pronged aggregation kinetics approach, we observed that N-terminal
acetylation results in a reduced rate of lipid-induced aggregation
and slows down both elongation and fibril-catalyzed aggregate proliferation.
An analysis of the amyloid fibrils produced by the aggregation process
revealed different morphologies for the acetylated and non-acetylated
forms in both lipid-induced aggregation and seed-induced aggregation
assays. In addition, we found that fibrils formed by acetylated α-synuclein
exhibit a lower β-sheet content. These findings indicate that
N-terminal acetylation of α-synuclein alters its lipid-dependent
aggregation behavior, reduces its rate of in vitro aggregation, and
affects the structural properties of its fibrillar aggregates.
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Affiliation(s)
- Rosie Bell
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Rebecca J Thrush
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Marta Castellana-Cruz
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Marc Oeller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Roxine Staats
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Aishwarya Nene
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Patrick Flagmeier
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Sandeep Satapathy
- Department of Cell Biology, Blavantik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Celine Galvagnion
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Mark R Wilson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Janet R Kumita
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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12
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Serum neurofilament light chain and postural instability/gait difficulty (PIGD) subtypes of Parkinson’s disease in the MARK-PD study. J Neural Transm (Vienna) 2022; 129:295-300. [PMID: 35072765 PMCID: PMC8930951 DOI: 10.1007/s00702-022-02464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/12/2022] [Indexed: 11/04/2022]
Abstract
The PIGD (postural instability / gait difficulty) subtype of Parkinson´s disease (PD) is associated with faster cognitive and motor decline. So far, there are no quantifiable biomarkers to aid clinical subtyping. Neurofilament light chain (NfL) is a highly specific marker of neuro-axonal damage and can be assessed in blood. Here, we investigated if serum NfL concentrations are associated with PIGD subtype and PIGD scores in PD patients at advanced disease stages. Furthermore, we evaluated if serum NfL is associated with motor and cognitive function assessed with MDS-UPDRS part III and Montreal cognitive assessment (MoCA). Serum NfL levels were analyzed with Single Molecule Assays (Simoa) in blood of 223 PD patients from the bioMARKers in Parkinson’s Disease (MARK-PD) study. Serum NfL concentrations were higher in PIGD patients independent of age, sex and disease duration. In linear regression analysis, serum NfL levels were associated with MoCA, MDS-UPDRS III and PIGD scores in unadjusted models, but remained significant after adjustment only with PIGD scores. In conclusion, increased serum NfL levels were associated with PIGD subtype and PIGD scores in patients with advanced PD.
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13
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Atieh TB, Roth J, Yang X, Hoop CL, Baum J. DJ-1 Acts as a Scavenger of α-Synuclein Oligomers and Restores Monomeric Glycated α-Synuclein. Biomolecules 2021; 11:biom11101466. [PMID: 34680099 PMCID: PMC8533443 DOI: 10.3390/biom11101466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 12/03/2022] Open
Abstract
Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson’s disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that plays a critical role in PD pathology, has been proposed to repair glycation in proteins, yet a mechanism has not been elucidated. In this study, we integrate solution nuclear magnetic resonance (NMR) spectroscopy and liquid atomic force microscopy (AFM) techniques to characterize glycated N-terminally acetylated-αSyn (glyc-ac-αSyn) and its interaction with DJ-1. Glycation of ac-αSyn by methylglyoxal increases oligomer formation, as visualized by AFM in solution, resulting in decreased dynamics of the monomer amide backbone around the Lys residues, as measured using NMR. Upon addition of DJ-1, this NMR signature of glyc-ac-αSyn monomers reverts to a native ac-αSyn-like character. This phenomenon is reversible upon removal of DJ-1 from the solution. Using relaxation-based NMR, we have identified the binding site on DJ-1 for glycated and native ac-αSyn as the catalytic pocket and established that the oxidation state of the catalytic cysteine is imperative for binding. Based on our results, we propose a novel mechanism by which DJ-1 scavenges glyc-ac-αSyn oligomers without chemical deglycation, suppresses glyc-ac-αSyn monomer–oligomer interactions, and releases free glyc-ac-αSyn monomers in solution. The interference of DJ-1 with ac-αSyn oligomers may promote free ac-αSyn monomer in solution and suppress the propagation of toxic oligomer and fibril species. These results expand the understanding of the role of DJ-1 in PD pathology by acting as a scavenger for aggregated αSyn.
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14
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Jos S, Gogoi H, Prasad TK, Hurakadli MA, Kamariah N, Padmanabhan B, Padavattan S. Molecular insights into α-synuclein interaction with individual human core histones, linker histone, and dsDNA. Protein Sci 2021; 30:2121-2131. [PMID: 34382268 DOI: 10.1002/pro.4167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/26/2021] [Accepted: 08/04/2021] [Indexed: 12/28/2022]
Abstract
α-Synuclein (αS) plays a key role in Parkinson's disease (PD). The αS nuclear role, its binding affinity and specificity to histones and dsDNA remains unknown. Here, we have measured the binding affinity ( K d ) between αS wild-type (wt) and PD-specific αS S129-phosphorylation mimicking (S129E) mutant with full-length and flexible tail truncated individual core histones (H2a, H2b, H3, and H4), linker histone (H1), and carried out αS-dsDNA interaction studies. This study revealed that αS(wt) interacts specifically with N-terminal flexible tails of histone H3, H4, and flexible tails of H1. The αS(S129E) mutant recognizes histones similar to αS(wt) but binds with higher affinity. Intriguingly, αS(S129E) showed a binding affinity for control proteins (bovine serum albumin and lysozyme), while no interaction was seen for αS(wt). Based on our above observation, we contemplate that the physio-chemical properties of αS with S129-phosphorylation has changed compared to αS(wt), resulting in interaction for other proteins, which is the basis for Lewy body formation. Besides, this study showed αS binding to dsDNA is weak and nonspecific. Overall, αS specificity for histone binding suggests that its nuclear role is possibly driven through histone interaction.
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Affiliation(s)
- Sneha Jos
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Hemanga Gogoi
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Thazhe Kootteri Prasad
- Center for Chemical Biology & Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Manjunath A Hurakadli
- Center for Chemical Biology & Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Neelagandan Kamariah
- Center for Chemical Biology & Therapeutics, Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
| | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Sivaraman Padavattan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore, India
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15
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Jan A, Gonçalves NP, Vaegter CB, Jensen PH, Ferreira N. The Prion-Like Spreading of Alpha-Synuclein in Parkinson's Disease: Update on Models and Hypotheses. Int J Mol Sci 2021; 22:8338. [PMID: 34361100 PMCID: PMC8347623 DOI: 10.3390/ijms22158338] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
The pathological aggregation of the presynaptic protein α-synuclein (α-syn) and propagation through synaptically coupled neuroanatomical tracts is increasingly thought to underlie the pathophysiological progression of Parkinson's disease (PD) and related synucleinopathies. Although the precise molecular mechanisms responsible for the spreading of pathological α-syn accumulation in the CNS are not fully understood, growing evidence suggests that de novo α-syn misfolding and/or neuronal internalization of aggregated α-syn facilitates conformational templating of endogenous α-syn monomers in a mechanism reminiscent of prions. A refined understanding of the biochemical and cellular factors mediating the pathological neuron-to-neuron propagation of misfolded α-syn will potentially elucidate the etiology of PD and unravel novel targets for therapeutic intervention. Here, we discuss recent developments on the hypothesis regarding trans-synaptic propagation of α-syn pathology in the context of neuronal vulnerability and highlight the potential utility of novel experimental models of synucleinopathies.
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Affiliation(s)
- Asad Jan
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
| | - Nádia Pereira Gonçalves
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
- International Diabetic Neuropathy Consortium (IDNC), Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Christian Bjerggaard Vaegter
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
- International Diabetic Neuropathy Consortium (IDNC), Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Poul Henning Jensen
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
| | - Nelson Ferreira
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
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16
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The N-terminal Acetylation of α-Synuclein Changes the Affinity for Lipid Membranes but not the Structural Properties of the Bound State. Sci Rep 2020; 10:204. [PMID: 31937832 PMCID: PMC6959233 DOI: 10.1038/s41598-019-57023-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
The aggregation of α-synuclein (αS), a protein abundant at presynaptic terminals, is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Emerging evidence indicates that the interaction of αS with lipid membranes defines both its physiological function and pathological effects. The characterisation of the modes of membrane binding by αS is therefore crucial to clarify the balance between normal and aberrant behaviour of this protein. Here we used solid-state nuclear magnetic resonance (ssNMR) spectroscopy to probe the nature of the N-terminally acetylated form of αS (NTAc-αS) bound to synaptic-like lipid vesicles. This post-translational modification is prevalent for the physiological form of αS and modulates the binding to lipid bilayers. By probing the structure, dynamics and membrane topology of NTAc-αS, we found that N-terminal acetylation does not alter significantly the conformational and topological properties of the membrane-bound state of αS, despite increasing its propensity for binding. Taken together, our data and previous characterisations of the cytosolic state of NTAc-αS clarify that the role of the N-terminal acetylation is to regulate the binding affinity of αS for synaptic vesicles without altering the structural properties of the bound state.
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17
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Abstract
Parkinson's disease etiology involves amyloid formation by α-synuclein (αSyn). In vivo, αSyn is constitutively acetylated at the α-amino N-terminus. Here, we find N-terminally acetylated αSyn (Ac-αSyn) aggregates more slowly than non-acetylated αSyn (NH3-αSyn) with significantly reduced sensitivity to thioflavin T (ThT). Fibril differences were characterized by transmission electron microscopy, circular dichroism spectroscopy, and limited proteolysis. Interestingly, the low-ThT Ac-αSyn fibrils seed both acetylated and non-acetylated αSyn and faithfully propagate the low-ThT character through several generations, indicating a stable fibril polymorph. In contrast, the high-ThT NH3-αSyn seeds lose fidelity over subsequent generations. Despite it being outside of the amyloid core, the chemical nature of the N-terminus modulates αSyn aggregation and fibril polymorphism.
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Affiliation(s)
- Matthew D Watson
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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19
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Dong C, Garen CR, Mercier P, Petersen NO, Woodside MT. Characterizing the inhibition of α-synuclein oligomerization by a pharmacological chaperone that prevents prion formation by the protein PrP. Protein Sci 2019; 28:1690-1702. [PMID: 31306510 DOI: 10.1002/pro.3684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/17/2022]
Abstract
Aggregation of the disordered protein α-synuclein into amyloid fibrils is a central feature of synucleinopathies, neurodegenerative disorders that include Parkinson's disease. Small, pre-fibrillar oligomers of misfolded α-synuclein are thought to be the key toxic entities, and α-synuclein misfolding can propagate in a prion-like way. We explored whether a compound with anti-prion activity that can bind to unfolded parts of the protein PrP, the cyclic tetrapyrrole Fe-TMPyP, was also active against α-synuclein aggregation. Observing the initial stages of aggregation via fluorescence cross-correlation spectroscopy, we found that Fe-TMPyP inhibited small oligomer formation in a dose-dependent manner. Fe-TMPyP also inhibited the formation of mature amyloid fibrils in vitro, as detected by thioflavin T fluorescence. Isothermal titration calorimetry indicated Fe-TMPyP bound to monomeric α-synuclein with a stoichiometry of 2, and two-dimensional heteronuclear single quantum coherence NMR spectra revealed significant interactions between Fe-TMPyP and the C-terminus of the protein. These results suggest commonalities among aggregation mechanisms for α-synuclein and the prion protein may exist that can be exploited as therapeutic targets.
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Affiliation(s)
- Chunhua Dong
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Craig R Garen
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Pascal Mercier
- National High Field Nuclear Magnetic Resonance Centre (NANUC), Edmonton, Alberta, Canada
| | - Nils O Petersen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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20
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Wang Z, Gao G, Duan C, Yang H. Progress of immunotherapy of anti-α-synuclein in Parkinson's disease. Biomed Pharmacother 2019; 115:108843. [PMID: 31055236 DOI: 10.1016/j.biopha.2019.108843] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 12/12/2022] Open
Abstract
Many neurodegenerative diseases are characterized by progressive loss of neurons and abnormal protein accumulation, including amyloid (A)β and tau in Alzheimer's disease and Lewy bodies and α-synuclein (α-syn) in Parkinson's disease (PD). Recent evidence suggests that adaptive immunity plays an important role in PD, and that anti-α-syn antibodies can be used as therapy in neurodegenerative diseases; monoclonal antibodies were shown to inhibit α-syn propagation and aggregation in PD models and patients. In this review, we summarize the different pathological states of α-syn, including gene mutations, truncation, phosphorylation, and the high molecular weight form, and describe the specific antibodies that recognize the α-syn monomer or oligomer, some of which have been tested in clinic trials. We also discuss future research directions and potential targets in PD therapy.
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Affiliation(s)
- Zhipeng Wang
- Department of Neurobiology School of Basic Medical Sciences, Center of Parkinson Disease Beijing Institute for Brain Disorders, Beijing Key Laboratory for Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Capital Medical University, Beijing, 100069, China
| | - Ge Gao
- Department of Neurobiology School of Basic Medical Sciences, Center of Parkinson Disease Beijing Institute for Brain Disorders, Beijing Key Laboratory for Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Capital Medical University, Beijing, 100069, China
| | - Chunli Duan
- Department of Neurobiology School of Basic Medical Sciences, Center of Parkinson Disease Beijing Institute for Brain Disorders, Beijing Key Laboratory for Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Capital Medical University, Beijing, 100069, China
| | - Hui Yang
- Department of Neurobiology School of Basic Medical Sciences, Center of Parkinson Disease Beijing Institute for Brain Disorders, Beijing Key Laboratory for Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Capital Medical University, Beijing, 100069, China.
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21
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Hajiraissi R, Hanke M, Gonzalez Orive A, Duderija B, Hofmann U, Zhang Y, Grundmeier G, Keller A. Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29). ACS OMEGA 2019; 4:2649-2660. [PMID: 31459500 PMCID: PMC6649277 DOI: 10.1021/acsomega.8b03028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/22/2019] [Indexed: 06/10/2023]
Abstract
The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.
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Affiliation(s)
- Roozbeh Hajiraissi
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Marcel Hanke
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Alejandro Gonzalez Orive
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Belma Duderija
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Ulrike Hofmann
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Yixin Zhang
- B
CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Guido Grundmeier
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Adrian Keller
- Technical
and Macromolecular Chemistry, Paderborn
University, Warburger Str. 100, 33098 Paderborn, Germany
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22
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Liu Y, Jovcevski B, Pukala TL. C-Phycocyanin from Spirulina Inhibits α-Synuclein and Amyloid-β Fibril Formation but Not Amorphous Aggregation. JOURNAL OF NATURAL PRODUCTS 2019; 82:66-73. [PMID: 30620188 DOI: 10.1021/acs.jnatprod.8b00610] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteinopathies including cataracts and neurodegenerative diseases, such as Alzheimer's and Parkinson's disease, are characterized by a series of aberrant protein folding events, resulting in amorphous aggregate or amyloid fibril formation. In the latter case, research has heavily focused on the development of small-molecule inhibitors with limited success during clinical trials. However, very few studies have focused on utilizing exogenous proteins as potential aggregation inhibitors. C-Phycocyanin, derived from Spirulina sp., has been known to exert anti-inflammatory properties; however, the ability of C-phycocyanin to inhibit protein aggregation has yet to be investigated. We have demonstrated that C-phycocyanin is an effective inhibitor of A53Tα-synuclein at extremely low substoichiometric ratios (200-fold excess of α-synuclein) and Aβ40/42 fibril formation. However, C-phycocyanin is relatively ineffective in inhibiting the reduction-induced amorphous aggregation of ADH and heat-induced aggregation of catalase. In addition, 2D NMR, ion mobility-mass spectrometry, and analytical-SEC demonstrate that the interaction between C-phycocyanin and α-synuclein is through nonstable interactions, indicating that transient interactions are likely to be responsible for preventing fibril formation. Overall, this work highlights how biomolecules from natural sources could be used to aid in the development of therapeutics to combat protein misfolding diseases.
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Affiliation(s)
- Yanqin Liu
- The School of Technology , Hebei Agricultural University , Cangzhou , Hebei 061100 , People's Republic of China
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Blagojce Jovcevski
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
| | - Tara L Pukala
- The School of Physical Sciences , The University of Adelaide , Adelaide , South Australia 5005 , Australia
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23
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Computational insights into the role of α-strand/sheet in aggregation of α-synuclein. Sci Rep 2019; 9:59. [PMID: 30635607 PMCID: PMC6329781 DOI: 10.1038/s41598-018-37276-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023] Open
Abstract
The α-synuclein is a major component of amyloid fibrils found in Lewy bodies, the characteristic intracellular proteinaceous deposits which are pathological hallmarks of neurodegenerative diseases such as Parkinson’s disease (PD) and dementia. It is an intrinsically disordered protein that may undergo dramatic structural changes to form amyloid fibrils. Aggregation process from α-synuclein monomers to amyloid fibrils through oligomeric intermediates is considered as the disease-causative toxic mechanism. However, mechanism underlying aggregation is not well-known despite several attempts. To characterize the mechanism, we have explored the effects of pH and temperature on the structural properties of wild-type and mutant α-synuclein using molecular dynamics (MD) simulation technique. MD studies suggested that amyloid fibrils can grow by monomer. Conformational transformation of the natively unfolded protein into partially folded intermediate could be accountable for aggregation and fibrillation. An intermediate α-strand was observed in the hydrophobic non-amyloid-β component (NAC) region of α-synuclein that could proceed to α-sheet and initiate early assembly events. Water network around the intermediate was analyzed to determine its influence on the α-strand structure. Findings of this study provide novel insights into possible mechanism of α-synuclein aggregation and promising neuroprotective strategy that could aid alleviate PD and its symptoms.
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24
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Williams JK, Yang X, Baum J. Interactions between the Intrinsically Disordered Proteins β-Synuclein and α-Synuclein. Proteomics 2018; 18:e1800109. [PMID: 30142698 PMCID: PMC6447293 DOI: 10.1002/pmic.201800109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/18/2018] [Indexed: 12/31/2022]
Abstract
Several intrinsically disordered proteins have been implicated in the process of amyloid fibril formation in neurodegenerative disease, and developing approaches to inhibit the aggregation of these intrinsically disordered proteins is critical for establishing effective therapies against disease progression. The aggregation pathway of the intrinsically disordered protein alpha-synuclein, which is implicated in several neurodegenerative diseases known as synucleinopathies, has been extensively characterized. Less attention has been leveraged on beta-synuclein, a homologous intrinsically disordered protein that co-localizes with alpha-synuclein and is known to delay alpha-synuclein fibril formation. In this review, we focus on beta-synuclein and the molecular-level interactions between alpha-synuclein and beta-synuclein that underlie the delay of fibril formation. We highlight studies that begin to define alpha-synuclein and beta-synuclein interactions at the monomer, oligomer, and surface levels, and suggest that beta-synuclein plays a role in regulation of inhibition at many different stages of alpha-synuclein aggregation.
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Affiliation(s)
- Jonathan K Williams
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Xue Yang
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
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25
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Liu H, Song D, Lu H, Luo R, Chen HF. Intrinsically disordered protein-specific force field CHARMM36IDPSFF. Chem Biol Drug Des 2018; 92:1722-1735. [DOI: 10.1111/cbdd.13342] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Dong Song
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering; University of California; Irvine California
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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26
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Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein. J Mol Biol 2018; 430:2360-2371. [PMID: 29782835 DOI: 10.1016/j.jmb.2018.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/19/2018] [Accepted: 05/14/2018] [Indexed: 02/07/2023]
Abstract
The intrinsically disordered protein β-synuclein is known to inhibit the aggregation of its intrinsically disordered homolog, α-synuclein, which is implicated in Parkinson's disease. While β-synuclein itself does not form fibrils at the cytoplasmic pH 7.4, alteration of pH and other environmental perturbations are known to induce its fibrilization. However, the sequence and structural determinants of β-synuclein inhibition and self-aggregation are not well understood. We have utilized a series of domain-swapped chimeras of α-synuclein and β-synuclein to probe the relative contributions of the N-terminal, C-terminal, and the central non-amyloid-β component domains to the inhibition of α-synuclein aggregation. Changes in the rates of α-synuclein fibril formation in the presence of the chimeras indicate that the non-amyloid-β component domain is the primary determinant of self-association leading to fibril formation, while the N- and C-terminal domains play critical roles in the fibril inhibition process. Our data provide evidence that all three domains of β-synuclein together contribute to providing effective inhibition, and support a model of transient, multi-pronged interactions between IDP chains in both processes. Inclusion of such multi-site inhibitory interactions spread over the length of synuclein chains may be critical for the development of therapeutics that are designed to mimic the inhibitory effects of β-synuclein.
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27
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Viennet T, Wördehoff MM, Uluca B, Poojari C, Shaykhalishahi H, Willbold D, Strodel B, Heise H, Buell AK, Hoyer W, Etzkorn M. Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation. Commun Biol 2018; 1:44. [PMID: 30271927 PMCID: PMC6123806 DOI: 10.1038/s42003-018-0049-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/23/2018] [Indexed: 01/24/2023] Open
Abstract
The protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve cytosolic and membrane-bound forms of αS. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR-spectroscopic, biophysical, and computational methods, we structurally and kinetically characterize αS interaction with different membrane discs in a quantitative and site-resolved way. We obtain global and residue-specific αS membrane affinities, and determine modulations of αS membrane binding due to αS acetylation, membrane plasticity, lipid charge density, and accessible membrane surface area, as well as the consequences of the different binding modes for αS amyloid fibril formation. Our results establish a structural and kinetic link between the observed dissimilar binding modes and either aggregation-inhibiting properties, largely unperturbed aggregation, or accelerated aggregation due to membrane-assisted fibril nucleation. Thibault Viennet and colleagues gain structural insight into amyloid fibril formation from their innovative use of lipid bilayer nanodiscs. This study connects α-Synuclein membrane binding modes to its aggregation properties, furthering our understanding of the cause of neurodegerative diseases.
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Affiliation(s)
- Thibault Viennet
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Michael M Wördehoff
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Chetan Poojari
- Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany.,Department of Physics, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland.,Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2a, 00560, Helsinki, Finland
| | - Hamed Shaykhalishahi
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Birgit Strodel
- Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Henrike Heise
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Alexander K Buell
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany.,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany
| | - Manuel Etzkorn
- Institute of Physical Biology, Heinrich-Heine-University, Universitätsstrasse 1, 40225, Düsseldorf, Germany. .,Instititue of Complex Systems (ICS-6), Forschungszentrum Jülich, Wilhelm-Johnen-Strasse, 52428, Jülich, Germany.
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28
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Moriarty GM, Olson MP, Atieh TB, Janowska MK, Khare SD, Baum J. A pH-dependent switch promotes β-synuclein fibril formation via glutamate residues. J Biol Chem 2017; 292:16368-16379. [PMID: 28710275 DOI: 10.1074/jbc.m117.780528] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 07/11/2017] [Indexed: 01/10/2023] Open
Abstract
α-Synuclein (αS) is the primary protein associated with Parkinson's disease, and it undergoes aggregation from its intrinsically disordered monomeric form to a cross-β fibrillar form. The closely related homolog β-synuclein (βS) is essentially fibril-resistant under cytoplasmic physiological conditions. Toxic gain-of-function by βS has been linked to dysfunction, but the aggregation behavior of βS under altered pH is not well-understood. In this work, we compare fibril formation of αS and βS at pH 7.3 and mildly acidic pH 5.8, and we demonstrate that pH serves as an on/off switch for βS fibrillation. Using αS/βS domain-swapped chimera constructs and single residue substitutions in βS, we localized the switch to acidic residues in the N-terminal and non-amyloid component domains of βS. Computational models of βS fibril structures indicate that key glutamate residues (Glu-31 and Glu-61) in these domains may be sites of pH-sensitive interactions, and variants E31A and E61A show dramatically altered pH sensitivity for fibril formation supporting the importance of these charged side chains in fibril formation of βS. Our results demonstrate that relatively small changes in pH, which occur frequently in the cytoplasm and in secretory pathways, may induce the formation of βS fibrils and suggest a complex role for βS in synuclein cellular homeostasis and Parkinson's disease.
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Affiliation(s)
- Gina M Moriarty
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Michael P Olson
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Tamr B Atieh
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Maria K Janowska
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Sagar D Khare
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
| | - Jean Baum
- From the Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854
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29
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Ruzafa D, Hernandez-Gomez YS, Bisello G, Broersen K, Morel B, Conejero-Lara F. The influence of N-terminal acetylation on micelle-induced conformational changes and aggregation of α-Synuclein. PLoS One 2017; 12:e0178576. [PMID: 28562630 PMCID: PMC5451137 DOI: 10.1371/journal.pone.0178576] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/15/2017] [Indexed: 12/15/2022] Open
Abstract
The biological function of α-Synuclein has been related to binding to lipids and membranes but these interactions can also mediate α-Synuclein aggregation, which is associated to Parkinson’s disease and other neuropathologies. In brain tissue α-Synuclein is constitutively N-acetylated, a modification that plays an important role in its conformational propensity, lipid and membrane binding, and aggregation propensity. We studied the interactions of the lipid-mimetic SDS with N-acetylated and non-acetylated α-Synuclein, as well as their early-onset Parkinson’s disease variants A30P, E46K and A53T. At low SDS/protein ratios α-Synuclein forms oligomeric complexes with SDS micelles with relatively low α-helical structure. These micellar oligomers can efficiently nucleate aggregation of monomeric α-Synuclein, with successive formation of oligomers, protofibrils, curly fibrils and mature amyloid fibrils. N-acetylation reduces considerably the rate of aggregation of WT α-Synuclein. However, in presence of any of the early-onset Parkinson’s disease mutations the protective effect of N-acetylation against micelle-induced aggregation becomes impaired. At higher SDS/protein ratios, N-acetylation favors another conformational transition, in which a second type of α-helix-rich, non-aggregating oligomers become stabilized. Once again, the Parkinson’s disease mutations disconnect the influence of N-acetylation in promoting this transition. These results suggest a cooperative link between the N-terminus and the region of the mutations that may be important for α-Synuclein function.
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Affiliation(s)
- David Ruzafa
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Yuriko S. Hernandez-Gomez
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Giovanni Bisello
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Kerensa Broersen
- Nanobiophysics Group, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology, Universiteit Twente, Enschede, The Netherlands
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- * E-mail:
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30
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Dörfel MJ, Fang H, Crain J, Klingener M, Weiser J, Lyon GJ. Proteomic and genomic characterization of a yeast model for Ogden syndrome. Yeast 2017; 34:19-37. [PMID: 27668839 PMCID: PMC5248646 DOI: 10.1002/yea.3211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/12/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022] Open
Abstract
Naa10 is an Nα -terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harbouring a c.109 T > C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function and reduces cellular fitness during heat shock, possibly owing to dysregulation of chaperone expression and accumulation. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, probably responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome. Data are available via GEO under identifier GSE86482 or with ProteomeXchange under identifier PXD004923. © 2016 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Max J. Dörfel
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Han Fang
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jonathan Crain
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Michael Klingener
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Jake Weiser
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
| | - Gholson J. Lyon
- Stanley Institute for Cognitive Genomics, One Bungtown RoadCold Spring Harbor LaboratoryCold Spring HarborNYUSA
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31
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Sivanesam K, Andersen NH. Modulating the Amyloidogenesis of α-Synuclein. Curr Neuropharmacol 2016; 14:226-37. [PMID: 26517049 PMCID: PMC4857621 DOI: 10.2174/1570159x13666151030103153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/16/2022] Open
Abstract
Alpha-Synuclein is found in the neuronal cells but its native function is not well known. While α -synuclein is an intrinsically disordered protein that adopts a helical conformation upon membrane binding, numerous studies have shown that oligomeric β-forms of this protein are cytotoxic. This response to misfolded species contributes to Parkinson's Disease etiology and symptoms. The resulting amyloid fibrils are an established diagnostic in Parkinson's Disease. In this review, we focus on strategies that have been used to inhibit the amyloidogenesis of α -synuclein either by stabilizing the native state, or by redirecting the pathway to less toxic aggregates. Small molecules such as polyphenols, peptides as well as large proteins have proven effective at protecting cells against the cytotoxicity of α-synuclein. These strategies may lead to the development of therapeutic agents that could prove useful in combating this disease.
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Affiliation(s)
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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32
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Mason RJ, Paskins AR, Dalton CF, Smith DP. Copper Binding and Subsequent Aggregation of α-Synuclein Are Modulated by N-Terminal Acetylation and Ablated by the H50Q Missense Mutation. Biochemistry 2016; 55:4737-41. [PMID: 27517125 DOI: 10.1021/acs.biochem.6b00708] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Parkinson's disease-associated protein α-synuclein exhibits significant conformational heterogeneity. Bacterially expressed α-synuclein is known to bind to copper, resulting in the formation of aggregation-prone compact conformations. However, in vivo, α-synuclein undergoes acetylation at its N-terminus. Here the effect of this modification and the pathological H50Q mutation on copper binding and subsequent conformational transitions were investigated by electrospray ionization-ion mobility spectrometry-mass spectrometry. We demonstrate that acetylation perturbs the ability of α-synuclein to bind copper and that the H50Q missense mutation in the presence of N-terminal acetylation prevents copper binding. These modifications and mutations prevent the formation of the most compact conformations and inhibit copper-induced aggregation.
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Affiliation(s)
- Rebecca J Mason
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - Aimee R Paskins
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - Caroline F Dalton
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
| | - David P Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University , Sheffield S1 1WB, U.K
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33
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Janowska MK, Baum J. The loss of inhibitory C-terminal conformations in disease associated P123H β-synuclein. Protein Sci 2015; 25:286-94. [PMID: 26332674 DOI: 10.1002/pro.2798] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/27/2015] [Indexed: 11/06/2022]
Abstract
β-synuclein (βS) is a homologue of α-synuclein (αS), the major protein component of Lewy bodies in patients with Parkinson's disease. In contrast to αS, βS does not form fibrils, mitigates αS toxicity in vivo and inhibits αS fibril formation in vitro. Previously a missense mutation of βS, P123H, was identified in patients with Dementia with Lewy Body disease. The single P123H mutation at the C-terminus of βS is able to convert βS from a nontoxic to a toxic protein that is also able to accelerate formation of inclusions when it is in the presence of αS in vivo. To elucidate the molecular mechanisms of these processes, we compare the conformational properties of the monomer forms of αS, βS and P123H-βS, and the effects on fibril formation of coincubation of αS with βS, and with P123H-βS. NMR residual dipolar couplings and secondary structure propensities show that the P123H mutation of βS renders it more flexible C-terminal to the mutation site and more αS-like. In vitro Thioflavin T fluorescence experiments show that P123H-βS accelerates αS fibril formation upon coincubation, as opposed to wild type βS that acts as an inhibitor of αS aggregation. When P123H-βS becomes more αS-like it is unable to perform the protective function of βS, which suggests that the extended polyproline II motif of βS in the C-terminus is critical to its nontoxic nature and to inhibition of αS upon coincubation. These studies may provide a basis for understanding which regions to target for therapeutic intervention in Parkinson's disease.
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Affiliation(s)
- Maria K Janowska
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854
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34
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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35
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Sivanesam K, Byrne A, Bisaglia M, Bubacco L, Andersen N. Binding Interactions of Agents That Alter α-Synuclein Aggregation. RSC Adv 2015; 5:11577-11590. [PMID: 25705374 DOI: 10.1039/c5ra00325c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Further examination of peptides with well-folded antiparallel β strands as inhibitors of amyloid formation from α-synuclein has resulted in more potent inhibitors. Several of these had multiple Tyr residues and represent a new lead for inhibitor design by small peptides that do not divert α-synuclein to non-amyloid aggregate formation. The most potent inhibitor obtained in this study is a backbone cyclized version of a previously studied β hairpin, designated as WW2, with a cross-strand Trp/Trp cluster. The cyclization was accomplished by adding a d-Pro-l-Pro turn locus across strand termini. At a 2:1 peptide to α-synuclein ratio, cyclo-WW2 displays complete inhibition of β-structure formation. Trp-bearing antiparallel β-sheets held together by a disulphide bond are also potent inhibitors. 15N HSQC spectra of α-synuclein provided new mechanistic details. The time course of 15N HSQC spectral changes observed during β-oligomer formation has revealed which segments of the structure become part of the rigid core of an oligomer at early stages of amyloidogenesis and that the C-terminus remains fully flexible throughout the process. All of the effective peptide inhibitors display binding-associated titration shifts in 15N HSQC spectra of α-synuclein in the C-terminal Q109-E137 segment. Cyclo-WW2, the most potent inhibitor, also displays titration shifts in the G41-T54 span of α-synuclein, an additional binding site. The earliest aggregation event appears to be centered about H50 which is also a binding site for our most potent inhibitor.
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Affiliation(s)
- K Sivanesam
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - A Byrne
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - M Bisaglia
- Department of Biology, University of Padua, 35121 Padova, Italy
| | - L Bubacco
- Department of Biology, University of Padua, 35121 Padova, Italy
| | - N Andersen
- Department of Chemistry, University of Washington, Seattle, WA 98195
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36
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Holmes WM, Mannakee BK, Gutenkunst RN, Serio TR. Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding. Nat Commun 2014; 5:4383. [PMID: 25023910 PMCID: PMC4140192 DOI: 10.1038/ncomms5383] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/13/2014] [Indexed: 01/08/2023] Open
Abstract
N-terminal acetylation is among the most ubiquitous of protein modifications in eukaryotes. While loss of N-terminal acetylation is associated with many abnormalities, the molecular basis of these effects is known for only a few cases, where acetylation of single factors has been linked to binding avidity or metabolic stability. In contrast, the impact of N-terminal acetylation for the majority of the proteome, and its combinatorial contributions to phenotypes, are unknown. Here, by studying the yeast prion [PSI+], an amyloid of the Sup35 protein, we show that loss of N-terminal acetylation promotes general protein misfolding, a redeployment of chaperones to these substrates, and a corresponding stress response. These proteostasis changes, combined with the decreased stability of unacetylated Sup35 amyloid, reduce the size of prion aggregates and reverse their phenotypic consequences. Thus, loss of N-terminal acetylation, and its previously unanticipated role in protein biogenesis, globally resculpts the proteome to create a unique phenotype.
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Affiliation(s)
- William M Holmes
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
| | - Brian K Mannakee
- Graduate Interdisciplinary Program in Statistics, University of Arizona, 1548 East Drachman Street, Tucson, Arizona 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, 1007 East Lowell Street, Tucson, Arizona 85721, USA
| | - Tricia R Serio
- 1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA [2]
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37
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Reddy JG, Hosur RV. A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 59:199-210. [PMID: 24854885 DOI: 10.1007/s10858-014-9839-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/08/2014] [Indexed: 05/21/2023]
Abstract
Resonance assignment in intrinsically disordered proteins poses a great challenge because of poor chemical shift dispersion in most of the nuclei that are commonly monitored. Reduced dimensionality (RD) experiments where more than one nuclei are co-evolved simultaneously along one of the time axes of a multi-dimensional NMR experiment help to resolve this problem partially, and one can conceive of different combinations of nuclei for co-evolution depending upon the magnetization transfer pathways and the desired information content in the spectrum. Here, we present a RD experiment, (4,3)D-hNCOCAnH, which uses a combination of CO and CA chemical shifts along one of the axes of the 3-dimensional spectrum, to improve spectral dispersion on one hand, and provide information on four backbone atoms of every residue-HN, N, CA and CO chemical shifts-from a single experiment, on the other. The experiment provides multiple unidirectional sequential (i → i - 1) amide (1)H correlations along different planes of the spectrum enabling easy assignment of most nuclei along the protein backbone. Occasional ambiguities that may arise due to degeneracy of amide proton chemical shifts are proposed to be resolved using the HNN experiment described previously (Panchal et al. in J Biomol NMR 20:135-147, 2001). Applications of the experiment and the assignment protocol have been demonstrated using intrinsically disordered α-synuclein (140 aa) protein.
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Affiliation(s)
- Jithender G Reddy
- Department of Chemical Sciences, Tata Institute of Fundamental Research (TIFR), 1, Homi Bhabha Road, Colaba, 400005, Mumbai, India
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38
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Moriarty GM, Minetti CASA, Remeta DP, Baum J. A Revised Picture of the Cu(II)−α-Synuclein Complex: The Role of N-Terminal Acetylation. Biochemistry 2014; 53:2815-7. [DOI: 10.1021/bi5003025] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Gina M. Moriarty
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Conceição A. S. A. Minetti
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - David P. Remeta
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jean Baum
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
- BioMaPS
Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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Auburger G, Gispert S, Jendrach M. Mitochondrial acetylation and genetic models of Parkinson's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:155-82. [PMID: 25149217 DOI: 10.1016/b978-0-12-394625-6.00006-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) is frequent at old age, leading to atrophy of specific neurons and to early death. Lifespan and healthy aging of organisms depend on growth factor/nutrient signaling and on bioenergetics via mitochondria, all of which regulate downstream nuclear functions through FOXO and SIR proteins. Mammalian SIRtuins include the mitochondrial deacetylase SIRT3, and recently mitochondrial lysine acetylation (AcLys) was found to initiate mitochondrial degradation by autophagy. This mitophagy process is closely regulated by PINK1 and Parkin, two interacting proteins which relocalize to mitochondria with deficient proton gradients, and whose mutations cause autosomal recessive variants of PD. Strong generalized deacetylation of mitochondrial proteins and altered SIRT3 levels occur in rodent models of PD before the onset of toxic aggregate formation. We propose that the development of site-specific AcLys-antibodies and their characterization in patients will have medical value.
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Affiliation(s)
- Georg Auburger
- Experimental Neurology, Goethe University Medical School, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, Frankfurt am Main, Germany
| | - Marina Jendrach
- Experimental Neurology, Goethe University Medical School, Frankfurt am Main, Germany
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