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Asai Y, Yano K, Higashino T, Yoshihara D, Sakiyama H, Eguchi H, Fukushima K, Suzuki K, Fujiwara N. The Ile35 Residue of the ALS-Associated Mutant SOD1 Plays a Crucial Role in the Intracellular Aggregation of the Molecule. Mol Neurobiol 2024:10.1007/s12035-024-04369-0. [PMID: 39060907 DOI: 10.1007/s12035-024-04369-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an unknown pathogenesis. It has been reported that mutations in the gene for Cu/Zn superoxide dismutase (SOD1) cause familial ALS. Mutant SOD1 undergoes aggregation and forms amyloid more easily, and SOD1-immunopositive inclusions have been observed in the spinal cords of ALS patients. Because of this, SOD1 aggregation is thought to be related to the pathogenesis of ALS. Some core regions of amyloid have been identified, but the issue of whether these regions form aggregates in living cells remains unclear, and the mechanism responsible for intracellular SOD1 aggregation also remains unclear. The findings reported in this study indicate that the aggregation of the ALS-linked mutant SOD1-EGFP was significantly enhanced when the BioID2 gene was fused to the N-terminus of the mutant SOD1-EGFP plasmid for cellular expression. Expression of a series of BioID2-(C-terminal deletion peptides of SOD1)-EGFP permitted us to identify 1-35 as a minimal N-terminal sequence and Ile35 as an essential amino acid residue that contributes to the intracellular aggregation of SOD1. The findings also showed that an additional substitution of Ile35 with Ser into the ALS mutant SOD1 resulted in the significant suppression of aggregate formation. The fact that no Ile35 mutations have been reported to date in ALS patients indicates that all ALS mutant SOD1s contain Ile35. Taken together, we propose that Ile35 plays a pivotal role in the aggregation of the ALS-linked SOD1 and that this study will contribute to our understanding of the mechanism responsible for SOD1 aggregation.
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Affiliation(s)
- Yoshiyuki Asai
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Kyoka Yano
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Tomoyuki Higashino
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Daisaku Yoshihara
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
- Labolatory of Biochemistry, School of Pharmacy, Hyogo Medical University, Kobe, Hyogo, 650-8530, Japan
| | - Haruhiko Sakiyama
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
- Faculty of Nutrition, Department of Food and Nutrition, Senri Kinran University, Suita, Osaka, 565-0873, Japan
| | - Hironobu Eguchi
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Kazuaki Fukushima
- Department of Chemistry, School of Medicine, Hyogo Medical University, Nishinomiya, Hyogo, 663-8501, Japan
| | - Keiichiro Suzuki
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan
| | - Noriko Fujiwara
- Department of Biochemistry, School of Medicine, Hyogo Medical University, 1-1 Mukogawa-Cho, Nishinomiya, Hyogo, 663-8501, Japan.
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2
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Tokuda E, Sakashita Y, Tokoro N, Date A, Kosuge Y, Miyasaka T. MS785-MS27 Reactive Misfolded/Non-Native Zn-Deficient SOD1 Species Exhibit Cytotoxicity and Adopt Heterozygous Conformations in Motor Neurons. Int J Mol Sci 2024; 25:5603. [PMID: 38891791 PMCID: PMC11171496 DOI: 10.3390/ijms25115603] [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: 04/04/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Misfolding of superoxide dismutase-1 (SOD1) is a pathological hallmark of amyotrophic lateral sclerosis (ALS) with SOD1 mutations. The development of antibodies specific for misfolded SOD1 deepens our understanding of how the protein participates in ALS pathogenesis. Since the term "misfolding" refers to various disordered conformers other than the natively folded one, which misfolded species are recognized by specific antibodies should be determined. Here, we molecularly characterized the recognition by MS785-MS27, an antibody cocktail experimentally confirmed to recognize over 100 ALS-linked SOD1 mutants. Indirect ELISA revealed that the antibody cocktail recognized Zn-deficient wild-type and mutated SOD1 species. It also recognized conformation-disordered wild-type and mutated SOD1 species, such as unfolded and oligomeric forms, but had less affinity for the aggregated form. Antibody-reactive SOD1 exhibited cytotoxicity to a motor neuron cell model, which was blocked by Zn treatment with Zn-deficient SOD1. Immunohistochemistry revealed antibody-reactive SOD1 mainly in spinal motor neurons of SOD1G93A mice throughout the disease course, and the distribution after symptomatic stages differed from that of other misfolded SOD1 species. This suggests that misfolded/non-native SOD1 species exist as heterogeneous populations. In conclusion, MS785-MS27 recognizes various conformation-disordered SOD1 species lacking the Zn ion.
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Affiliation(s)
- Eiichi Tokuda
- Laboratory of Clinical Medicine, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan
| | - Yume Sakashita
- Laboratory of Clinical Medicine, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan
| | - Naoya Tokoro
- Laboratory of Clinical Medicine, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan
| | - Ayano Date
- Laboratory of Clinical Medicine, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan
| | - Yasuhiro Kosuge
- Laboratory of Pharmacology, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan;
| | - Tomohiro Miyasaka
- Laboratory of Physiology and Anatomy, School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi 274-8555, Chiba, Japan;
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Nordström U, Lang L, Ekhtiari Bidhendi E, Zetterström P, Oliveberg M, Danielsson J, Andersen PM, Marklund SL. Mutant SOD1 aggregates formed in vitro and in cultured cells are polymorphic and differ from those arising in the CNS. J Neurochem 2023; 164:77-93. [PMID: 36326589 PMCID: PMC10099669 DOI: 10.1111/jnc.15718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Mutations in the human Superoxide dismutase 1 (hSOD1) gene are well-established cause of the motor neuron disease ALS. Patients and transgenic (Tg) ALS model mice carrying mutant variants develop hSOD1 aggregates in the CNS. We have identified two hSOD1 aggregate strains, which both transmit spreading template-directed aggregation and premature fatal paralysis when inoculated into adult transgenic mice. This prion-like spread of aggregation could be a primary disease mechanism in SOD1-induced ALS. Human SOD1 aggregation has been studied extensively both in cultured cells and under various conditions in vitro. To determine how the structure of aggregates formed in these model systems related to disease-associated aggregates in the CNS, we used a binary epitope-mapping assay to examine aggregates of hSOD1 variants G93A, G85R, A4V, D90A, and G127X formed in vitro, in four different cell lines and in the CNS of Tg mice. We found considerable variability between replicate sets of in vitro-generated aggregates. In contrast, there was a high similarity between replicates of a given hSOD1 mutant in a given cell line, but pronounced variations between different hSOD1 mutants and different cell lines in both structures and amounts of aggregates formed. The aggregates formed in vitro or in cultured cells did not replicate the aggregate strains that arise in the CNS. Our findings suggest that the distinct aggregate morphologies in the CNS could result from a micro-environment with stringent quality control combined with second-order selection by spreading ability. Explorations of pathogenesis and development of therapeutics should be conducted in models that replicate aggregate structures forming in the CNS.
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Affiliation(s)
- Ulrika Nordström
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Lisa Lang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Elaheh Ekhtiari Bidhendi
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden.,Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden
| | - Per Zetterström
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, Umeå, Sweden
| | - Stefan L Marklund
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden
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4
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Deol HK, Broom HR, Sienbeneichler B, Lee B, Leonenko Z, Meiering EM. Immature ALS-associated mutant superoxide dismutases form variable aggregate structures through distinct oligomerization processes. Biophys Chem 2022; 288:106844. [DOI: 10.1016/j.bpc.2022.106844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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Hsueh SCC, Nijland M, Peng X, Hilton B, Plotkin SS. First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants. Front Mol Biosci 2022; 9:845013. [PMID: 35402516 PMCID: PMC8988244 DOI: 10.3389/fmolb.2022.845013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
Cu,Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the stability of the protein. Monomerization increases the likelihood of SOD1 misfolding into conformations associated with aggregation, cellular toxicity, and neuronal death in familial amyotrophic lateral sclerosis (fALS). The ubiquity of disease-associated mutations throughout the primary sequence of SOD1 suggests an important role of physicochemical processes, including monomerization of SOD1, in the pathology of the disease. Herein, we use a first-principles statistical mechanics method to systematically calculate the free energy of dimer binding for SOD1 using molecular dynamics, which involves sequentially computing conformational, orientational, and separation distance contributions to the binding free energy. We consider the effects of two ALS-associated mutations in SOD1 protein on dimer stability, A4V and D101N, as well as the role of metal binding and disulfide bond formation. We find that the penalty for dimer formation arising from the conformational entropy of disordered loops in SOD1 is significantly larger than that for other protein-protein interactions previously considered. In the case of the disulfide-reduced protein, this leads to a bound complex whose formation is energetically disfavored. Somewhat surprisingly, the loop free energy penalty upon dimerization is still significant for the holoprotein, despite the increased structural order induced by the bound metal cations. This resulted in a surprisingly modest increase in dimer binding free energy of only about 1.5 kcal/mol upon metalation of the protein, suggesting that the most significant stabilizing effects of metalation are on folding stability rather than dimer binding stability. The mutant A4V has an unstable dimer due to weakened monomer-monomer interactions, which are manifested in the calculation by a separation free energy surface with a lower barrier. The mutant D101N has a stable dimer partially due to an unusually rigid β-barrel in the free monomer. D101N also exhibits anticooperativity in loop folding upon dimerization. These computational calculations are, to our knowledge, the most quantitatively accurate calculations of dimer binding stability in SOD1 to date.
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Affiliation(s)
- Shawn C. C. Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Mark Nijland
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, Netherlands
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, China
| | - Benjamin Hilton
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Imperial College London, London, United Kingdom
| | - Steven S. Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
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6
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McAlary L, Shephard VK, Wright GSA, Yerbury JJ. A copper chaperone-mimetic polytherapy for SOD1-associated amyotrophic lateral sclerosis. J Biol Chem 2022; 298:101612. [PMID: 35065969 PMCID: PMC8885447 DOI: 10.1016/j.jbc.2022.101612] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/20/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease in which motor neurons progressively and rapidly degenerate, eventually leading to death. The first protein found to contain ALS-associated mutations was copper/zinc superoxide dismutase 1 (SOD1), which is conformationally stable when it contains its metal ligands and has formed its native intramolecular disulfide. Mutations in SOD1 reduce protein folding stability via disruption of metal binding and/or disulfide formation, resulting in misfolding, aggregation, and ultimately cellular toxicity. A great deal of effort has focused on preventing the misfolding and aggregation of SOD1 as a potential therapy for ALS; however, the results have been mixed. Here, we utilize a small-molecule polytherapy of diacetylbis(N(4)-methylthiosemicarbazonato)copper(II) (CuATSM) and ebselen to mimic the metal delivery and disulfide bond promoting activity of the cellular chaperone of SOD1, the “copper chaperone for SOD1.” Using microscopy with automated image analysis, we find that polytherapy using CuATSM and ebselen is highly effective and acts in synergy to reduce inclusion formation in a cell model of SOD1 aggregation for multiple ALS-associated mutants. Polytherapy reduces mutant SOD1-associated cell death, as measured by live-cell microscopy. Measuring dismutase activity via zymography and immunoblotting for disulfide formation showed that polytherapy promoted more effective maturation of transfected SOD1 variants beyond either compound alone. Our data suggest that a polytherapy of CuATSM and ebselen may merit more study as an effective method of treating SOD1-associated ALS.
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Affiliation(s)
- L McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, NSW, Australia.
| | - V K Shephard
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, NSW, Australia
| | - G S A Wright
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - J J Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia; Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, NSW, Australia.
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7
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Keskin I, Ekhtiari Bidhendi E, Marklund M, Andersen PM, Brännström T, Marklund SL, Nordström U. Peripheral administration of SOD1 aggregates does not transmit pathogenic aggregation to the CNS of SOD1 transgenic mice. Acta Neuropathol Commun 2021; 9:111. [PMID: 34158126 PMCID: PMC8220797 DOI: 10.1186/s40478-021-01211-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
The deposition of aggregated proteins is a common neuropathological denominator for neurodegenerative disorders. Experimental evidence suggests that disease propagation involves prion-like mechanisms that cause the spreading of template-directed aggregation of specific disease-associated proteins. In transgenic (Tg) mouse models of superoxide dismutase-1 (SOD1)-linked amyotrophic lateral sclerosis (ALS), inoculation of minute amounts of human SOD1 (hSOD1) aggregates into the spinal cord or peripheral nerves induces premature ALS-like disease and template-directed hSOD1 aggregation that spreads along the neuroaxis. This infectious nature of spreading pathogenic aggregates might have implications for the safety of laboratory and medical staff, recipients of donated blood or tissue, or possibly close relatives and caregivers. Here we investigate whether transmission of ALS-like disease is unique to the spinal cord and peripheral nerve inoculations or if hSOD1 aggregation might spread from the periphery into the central nervous system (CNS). We inoculated hSOD1 aggregate seeds into the peritoneal cavity, hindlimb skeletal muscle or spinal cord of adult Tg mice expressing mutant hSOD1. Although we used up to 8000 times higher dose—compared to the lowest dose transmitting disease in spinal cord inoculations—the peripheral inoculations did not transmit seeded aggregation to the CNS or premature ALS-like disease in hSOD1 Tg mice. Nor was any hSOD1 aggregation detected in the liver, kidney, skeletal muscle or sciatic nerve. To explore potential reasons for the lack of disease transmission, we examined the stability of hSOD1 aggregates and found them to be highly vulnerable to both proteases and detergent. Our findings suggest that exposed individuals and personnel handling samples from ALS patients are at low risk of any potential transmission of seeded hSOD1 aggregation.
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8
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Wells NGM, Tillinghast GA, O'Neil AL, Smith CA. Free energy calculations of ALS-causing SOD1 mutants reveal common perturbations to stability and dynamics along the maturation pathway. Protein Sci 2021; 30:1804-1817. [PMID: 34076319 DOI: 10.1002/pro.4132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 01/25/2023]
Abstract
With over 150 heritable mutations identified as disease-causative, superoxide dismutase 1 (SOD1) has been a main target of amyotrophic lateral sclerosis (ALS) research and therapeutic efforts. However, recent evidence has suggested that neither loss of function nor protein aggregation is responsible for promoting neurotoxicity. Furthermore, there is no clear pattern to the nature or the location of these mutations that could suggest a molecular mechanism behind SOD1-linked ALS. Here, we utilize reliable and accurate computational techniques to predict the perturbations of 10 such mutations to the free energy changes of SOD1 as it matures from apo monomer to metallated dimer. We find that the free energy perturbations caused by these mutations strongly depend on maturational progress, indicating the need for state-specific therapeutic targeting. We also find that many mutations exhibit similar patterns of perturbation to native and non-native maturation, indicating strong thermodynamic coupling between the dynamics at various sites of maturation within SOD1. These results suggest the presence of an allosteric network in SOD1 which is vulnerable to disruption by these mutations. Analysis of these perturbations may contribute to uncovering a unifying molecular mechanism which explains SOD1-linked ALS and help to guide future therapeutic efforts.
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Affiliation(s)
- Nicholas G M Wells
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Grant A Tillinghast
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA.,Department of Biomedical Engineering, Columbia University, New York, New York City, USA
| | - Alison L O'Neil
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
| | - Colin A Smith
- Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA
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9
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Abstract
Protein aggregation is a widespread phenomenon with important implications in many scientific areas. Although amyloid formation is typically considered as detrimental, functional amyloids that perform physiological roles have been identified in all kingdoms of life. Despite their functional and pathological relevance, the structural details of the majority of molecular species involved in the amyloidogenic process remains elusive. Here, we explore the application of AlphaFold, a highly accurate protein structure predictor, in the field of protein aggregation. While we envision a straightforward application of AlphaFold in assisting the design of globular proteins with improved solubility for biomedical and industrial purposes, the use of this algorithm for predicting the structure of aggregated species seems far from trivial. First, in amyloid diseases, the presence of multiple amyloid polymorphs and the heterogeneity of aggregation intermediates challenges the "one sequence, one structure" paradigm, inherent to sequence-based predictions. Second, aberrant aggregation is not the subject of positive selective pressure, precluding the use of evolutionary-based approaches, which are the core of the AlphaFold pipeline. Instead, amyloid polymorphism seems to be constrained by the need for a defined structure-activity relationship in functional amyloids. They may thus provide a starting point for the application of AlphaFold in the amyloid landscape.
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10
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A Metal-Free, Disulfide Oxidized Form of Superoxide Dismutase 1 as a Primary Misfolded Species with Prion-Like Properties in the Extracellular Environments Surrounding Motor Neuron-Like Cells. Int J Mol Sci 2021; 22:ijms22084155. [PMID: 33923808 PMCID: PMC8074096 DOI: 10.3390/ijms22084155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022] Open
Abstract
Superoxide dismutase 1 (SOD1) is a metalloenzyme with high structural stability, but a lack of Cu and Zn ions decreases its stability and enhances the likelihood of misfolding, which is a pathological hallmark of amyotrophic lateral sclerosis (ALS). A growing body of evidence has demonstrated that misfolded SOD1 has prion-like properties such as transmissibility between cells and intracellular propagation of misfolding of natively folded SOD1. Recently, we found that SOD1 is misfolded in the cerebrospinal fluid of sporadic ALS patients, providing a route by which misfolded SOD1 spreads via the extracellular environment of the central nervous system. Unlike intracellular misfolded SOD1, it is unknown which extracellular misfolded species is most relevant to prion-like properties. Here, we determined a conformational feature of extracellular misfolded SOD1 that is linked to prion-like properties. Using culture media from motor neuron-like cells, NSC-34, extracellular misfolded wild-type, and four ALS-causing SOD1 mutants were characterized as a metal-free, disulfide oxidized form of SOD1 (apo-SOD1S-S). Extracellular misfolded apo-SOD1S-S exhibited cell-to-cell transmission from the culture medium to recipient cells as well as intracellular propagation of SOD1 misfolding in recipient cells. Furthermore, culture medium containing misfolded apo-SOD1S-S exerted cytotoxicity to motor neuron-like cells, which was blocked by removal of misfolded apo-SOD1S-S from the medium. We conclude that misfolded apo-SOD1S-S is a primary extracellular species that is linked to prion-like properties.
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11
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Butler KE, Takinami Y, Rainczuk A, Baker ES, Roberts BR. Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase. Front Chem 2021; 9:614595. [PMID: 33634076 PMCID: PMC7900566 DOI: 10.3389/fchem.2021.614595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/08/2021] [Indexed: 11/30/2022] Open
Abstract
Native mass spectrometry has emerged as a powerful tool for structural biology as it enables the evaluation of molecules as they occur in their physiological conditions. Ion mobility spectrometry-mass spectrometry (IMS-MS) has shown essential in these analyses as it allows the measurement of the shape of a molecule, denoted as its collision cross section (CCS), and mass. The structural information garnered from native IMS-MS provides insight into the tertiary and quaternary structure of proteins and can be used to validate NMR or crystallographic X-ray structures. Additionally, due to the rapid nature (millisecond measurements) and ability of IMS-MS to analyze heterogeneous solutions, it can be used to address structural questions not possible with traditional structural approaches. Herein, we applied multiple solution conditions to systematically denature bovine Cu/Zn-superoxide dismutase (SOD1) and assess its unfolding pathway from the holo-dimer to the holo-monomer, single-metal monomer, and apo-monomer. Additionally, we compared and noted 1–2% agreement between CCS values from both drift tube IMS and trapped IMS for the SOD1 holo-monomer and holo-dimer. The observed CCS values were in excellent agreement with computational CCS values predicted from the homo-dimer crystal structure, showcasing the ability to use both IMS-MS platforms to provide valuable structural information for molecular modeling of protein interactions and structural assessments.
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Affiliation(s)
- Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | | | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Blaine R Roberts
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States.,Department of Neuroscience, Emory University School of Medicine, Atlanta, GA, United States
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12
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McAlary L, Chew YL, Lum JS, Geraghty NJ, Yerbury JJ, Cashman NR. Amyotrophic Lateral Sclerosis: Proteins, Proteostasis, Prions, and Promises. Front Cell Neurosci 2020; 14:581907. [PMID: 33328890 PMCID: PMC7671971 DOI: 10.3389/fncel.2020.581907] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of the motor neurons that innervate muscle, resulting in gradual paralysis and culminating in the inability to breathe or swallow. This neuronal degeneration occurs in a spatiotemporal manner from a point of onset in the central nervous system (CNS), suggesting that there is a molecule that spreads from cell-to-cell. There is strong evidence that the onset and progression of ALS pathology is a consequence of protein misfolding and aggregation. In line with this, a hallmark pathology of ALS is protein deposition and inclusion formation within motor neurons and surrounding glia of the proteins TAR DNA-binding protein 43, superoxide dismutase-1, or fused in sarcoma. Collectively, the observed protein aggregation, in conjunction with the spatiotemporal spread of symptoms, strongly suggests a prion-like propagation of protein aggregation occurs in ALS. In this review, we discuss the role of protein aggregation in ALS concerning protein homeostasis (proteostasis) mechanisms and prion-like propagation. Furthermore, we examine the experimental models used to investigate these processes, including in vitro assays, cultured cells, invertebrate models, and murine models. Finally, we evaluate the therapeutics that may best prevent the onset or spread of pathology in ALS and discuss what lies on the horizon for treating this currently incurable disease.
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Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Yee Lian Chew
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Jeremy Stephen Lum
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Nicholas John Geraghty
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Justin John Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R. Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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Yerbury JJ, Cashman NR. Selenium-based compounds: Emerging players in the ever-unfolding story of SOD1 in amyotrophic lateral sclerosis. EBioMedicine 2020; 59:102997. [PMID: 32891934 PMCID: PMC7479490 DOI: 10.1016/j.ebiom.2020.102997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Justin J Yerbury
- Illawarra Health and Medical Research Institute, and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
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14
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Dantas LS, Viviani LG, Inague A, Piccirillo E, Rezende LD, Ronsein GE, Augusto O, Medeiros MHG, Amaral ATD, Miyamoto S. Lipid aldehyde hydrophobicity affects apo-SOD1 modification and aggregation. Free Radic Biol Med 2020; 156:157-167. [PMID: 32598986 DOI: 10.1016/j.freeradbiomed.2020.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
Unsaturated lipids are oxidized by reactive oxygen species and enzymes, leading to the increased formation of lipid hydroperoxides and several electrophilic products. Lipid-derived electrophiles can modify macromolecules, such as proteins, resulting in the loss of function and/or aggregation. The accumulation of Cu,Zn-superoxide dismutase (SOD1) aggregates has been associated with familial cases of amyotrophic lateral sclerosis (ALS). The protein aggregation mechanisms in motor neurons remain unclear, although recent studies have shown that lipids and oxidized lipid derivatives may play roles in this process. Here, we aimed to compare the effects of different lipid aldehydes on the induction of SOD1 modifications and aggregation, in vitro. Human recombinant apo-SOD1 was incubated with 4-hydroxy-2-hexenal (HHE), 4-hydroxy-2-nonenal (HNE), 2-hexen-1-al (HEX), 2,4-nonadienal (NON), 2,4-decadienal (DEC), or secosterol aldehydes (SECO-A or SECO-B). High-molecular-weight apo-SOD1 aggregates dramatically increased in the presence of highly hydrophobic aldehydes (LogPcalc > 3). Notably, several Lys residues were modified by exposure to all aldehydes. The observed modifications were primarily observed on Lys residues located near the dimer interface (K3 and K9) and at the electrostatic loop (K122, K128, and K136). Moreover, HHE and HNE induced extensive apo-SOD1 modifications, by forming Schiff bases or Michael adducts with Lys, His, and Cys residues. However, these aldehydes were unable to induce large protein aggregates. Overall, our data shed light on the importance of lipid aldehyde hydrophobicity on the induction of apo-SOD1 aggregation and identified preferential sites of lipid aldehyde-induced modifications.
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Affiliation(s)
- Lucas S Dantas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Lucas G Viviani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Inague
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erika Piccirillo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil; Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Leandro de Rezende
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Graziella E Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marisa H G Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Antonia T do Amaral
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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15
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Tompa DR, Muthusamy S, Srikanth S, Kadhirvel S. Molecular dynamics of far positioned surface mutations of Cu/Zn SOD1 promotes altered structural stability and metal-binding site: Structural clues to the pathogenesis of amyotrophic lateral sclerosis. J Mol Graph Model 2020; 100:107678. [PMID: 32768728 DOI: 10.1016/j.jmgm.2020.107678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/18/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) mutations are associated to the motor neuron disorder, amyotrophic lateral sclerosis (ALS), which is characterized by aggregates of the misfolded proteins. The distribution of mutations all over the three-dimensional structure of SOD1 makes it complex to determine the exact molecular mechanism underlying SOD1 destabilization and the associated ALS pathology. In this study, we have examined structure and dynamics of SOD1 protein upon two ALS associated point mutations at the surface residue Glu100 (E100G and E100K), which is located far from the Cu and Zn sites and dimer interface. The molecular dynamics simulations were performed for these mutants for 50ns using GROMACS package. Our results indicate that the mutations result in structural destabilization by affecting the gate keeping role of Glu100 and loss of electrostatic interactions on the protein surface which stabilizes the β-barrel structure of the native form. Further, these mutations could increase the fluctuations in the zinc-binding loop (loop IV), primarily due to loss of hydrogen bond between Asp101 and Arg79. The relaxed conformation of Arg79 further affects the native conformation of His80 and Asp83, that results in altered zinc site geometry and the structure of the substrate channel. Our results clearly suggest that, similar to the mutations located at metal sites/dimer interface/disulfide regions, the mutations at the far positioned site (Glu100) also induce significant conformational changes that could affect the metallation and structure of SOD1 molecule, resulting in formation of toxic intermediate species that cause ALS.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Sureshan Muthusamy
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Srimari Srikanth
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India.
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16
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Crown A, McAlary L, Fagerli E, Brown H, Yerbury JJ, Galaleldeen A, Cashman NR, Borchelt DR, Ayers JI. Tryptophan residue 32 in human Cu-Zn superoxide dismutase modulates prion-like propagation and strain selection. PLoS One 2020; 15:e0227655. [PMID: 31999698 PMCID: PMC6991973 DOI: 10.1371/journal.pone.0227655] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/21/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in Cu/Zn superoxide dismutase 1 (SOD1) associated with familial amyotrophic lateral sclerosis cause the protein to aggregate via a prion-like process in which soluble molecules are recruited to aggregates by conformational templating. These misfolded SOD1 proteins can propagate aggregation-inducing conformations across cellular membranes. Prior studies demonstrated that mutation of a Trp (W) residue at position 32 to Ser (S) suppresses the propagation of misfolded conformations between cells, whereas other studies have shown that mutation of Trp 32 to Phe (F), or Cys 111 to Ser, can act in cis to attenuate aggregation of mutant SOD1. By expressing mutant SOD1 fused with yellow fluorescent protein (YFP), we compared the relative ability of these mutations to modulate the formation of inclusions by ALS-mutant SOD1 (G93A and G85R). Only mutation of Trp 32 to Ser persistently reduced the formation of the amorphous inclusions that form in these cells, consistent with the idea that a Ser at position 32 inhibits templated propagation of aggregation prone conformations. To further test this idea, we produced aggregated fibrils of recombinant SOD1-W32S in vitro and injected them into the spinal cords of newborn mice expressing G85R-SOD1: YFP. The injected mice developed an earlier onset paralysis with a frequency similar to mice injected with WT SOD1 fibrils, generating a strain of misfolded SOD1 that produced highly fibrillar inclusion pathology. These findings suggest that the effect of Trp 32 in modulating the propagation of misfolded SOD1 conformations may be dependent upon the “strain” of the conformer that is propagating.
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Affiliation(s)
- Anthony Crown
- Center for Translational Research in Neurodegenerative Disease, SantaFe HealthCare Alzheimer’s Disease Research Center, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Luke McAlary
- Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, New South Wales, Australia
- Illawarra Health and Medical Research Institute, School of Chemistry & Molecular Bioscience, University of Wollongong, New South Wales, Australia
| | - Eric Fagerli
- Center for Translational Research in Neurodegenerative Disease, SantaFe HealthCare Alzheimer’s Disease Research Center, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Hilda Brown
- Center for Translational Research in Neurodegenerative Disease, SantaFe HealthCare Alzheimer’s Disease Research Center, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Justin J. Yerbury
- Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, New South Wales, Australia
- Illawarra Health and Medical Research Institute, School of Chemistry & Molecular Bioscience, University of Wollongong, New South Wales, Australia
| | - Ahmad Galaleldeen
- Department of Biological Sciences, St. Mary’s University, San Antonio, Texas, United States of America
| | - Neil R. Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - David R. Borchelt
- Center for Translational Research in Neurodegenerative Disease, SantaFe HealthCare Alzheimer’s Disease Research Center, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jacob I. Ayers
- Center for Translational Research in Neurodegenerative Disease, SantaFe HealthCare Alzheimer’s Disease Research Center, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
- Institute for Neurodegenerative Disease, University of California, San Francisco, California, United States of America
- * E-mail:
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17
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McAlary L, Harrison JA, Aquilina JA, Fitzgerald SP, Kelso C, Benesch JL, Yerbury JJ. Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt Bridge Formation. Anal Chem 2019; 92:1702-1711. [DOI: 10.1021/acs.analchem.9b01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Julian A. Harrison
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J. Andrew Aquilina
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | | | - Celine Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Department, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
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18
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Khan MAI, Weininger U, Kjellström S, Deep S, Akke M. Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils. Protein Eng Des Sel 2019; 32:77-85. [PMID: 31832682 DOI: 10.1093/protein/gzz033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 11/12/2022] Open
Abstract
Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.
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Affiliation(s)
- Mohammad Ashhar I Khan
- Biophysical Chemistry, Department of Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 221 00, Lund, Sweden.,Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ulrich Weininger
- Biophysical Chemistry, Department of Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Sven Kjellström
- Biochemistry and Structural Biology, Department of Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Mikael Akke
- Biophysical Chemistry, Department of Chemistry, Center for Molecular Protein Science, Lund University, P.O. Box 124, 221 00, Lund, Sweden
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19
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Abstract
Few proteins have come under such intense scrutiny as superoxide dismutase-1 (SOD1). For almost a century, scientists have dissected its form, function and then later its malfunction in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). We now know SOD1 is a zinc and copper metalloenzyme that clears superoxide as part of our antioxidant defence and respiratory regulation systems. The possibility of reduced structural integrity was suggested by the first crystal structures of human SOD1 even before deleterious mutations in the sod1 gene were linked to the ALS. This concept evolved in the intervening years as an impressive array of biophysical studies examined the characteristics of mutant SOD1 in great detail. We now recognise how ALS-related mutations perturb the SOD1 maturation processes, reduce its ability to fold and reduce its thermal stability and half-life. Mutant SOD1 is therefore predisposed to monomerisation, non-canonical self-interactions, the formation of small misfolded oligomers and ultimately accumulation in the tell-tale insoluble inclusions found within the neurons of ALS patients. We have also seen that several post-translational modifications could push wild-type SOD1 down this toxic pathway. Recently we have come to view ALS as a prion-like disease where both the symptoms, and indeed SOD1 misfolding itself, are transmitted to neighbouring cells. This raises the possibility of intervention after the initial disease presentation. Several small-molecule and biologic-based strategies have been devised which directly target the SOD1 molecule to change the behaviour thought to be responsible for ALS. Here we provide a comprehensive review of the many biophysical advances that sculpted our view of SOD1 biology and the recent work that aims to apply this knowledge for therapeutic outcomes in ALS.
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20
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Effect of Mutations in SOD1 and C9orf72 Genes on Autophagy in Lymphomonocytes in Myotrophic Lateral Sclerosis. Bull Exp Biol Med 2019; 167:667-670. [PMID: 31625064 DOI: 10.1007/s10517-019-04595-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 12/13/2022]
Abstract
Insoluble protein inclusions accumulate in somatic cells in amyotrophic lateral sclerosis. The most common gene mutations associated with this pathology are SOD1 and C9orf72. Protein aggregates can be removed from cells by autophagy. We studied the relationship between the presence of genetic abnormalities in the SOD1 and C9orf72 genes and changes in autophagy in lymphomonocytes in amyotrophic lateral sclerosis. The study included 85 patients with amyotrophic lateral sclerosis and 15 healthy volunteers. Genetic analysis for the presence of mutations in the SOD1 and C9orf72 genes and detection of autophagy marker LC3 in lymphomonocytes were performed. In amyotrophic lateral sclerosis, autophagy activation in lymphomonocytes was found. We also obtained evidence that protein product of the mutant C9orf72 gene can disturb the late stages of autophagy.
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21
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Manjula R, Unni S, Wright GSA, Bharath M M S, Padmanabhan B. Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis. J Biomol Struct Dyn 2019; 37:3936-3946. [PMID: 30286701 DOI: 10.1080/07391102.2018.1531787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
Abstract
Formation of Cu, Zn superoxide dismutase 1 (SOD1) protein inclusions within motor neurons is one of the principal characteristics of SOD1-related amyotrophic lateral sclerosis (ALS). A hypothesis as to the nature of SOD1 aggregation implicates oxidative damage to a solvent-exposed tryptophan as causative. Here, we chart the discovery of a phenanthridinone based compound (Lig9) from the NCI Diversity Set III by rational methods by in silico screening and crystallographic validation. The crystal structure of the complex with SOD1, refined to 2.5 Å, revealed that Lig9 binds the SOD1 β-barrel in the β-strand 2 and 3 region which is known to scaffold SOD1 fibrillation. The phenanthridinone moiety makes a substantial π-π interaction with Trp32 of SOD1. The compound possesses a significant binding affinity for SOD1 and inhibits oxidation of Trp32; a critical residue for SOD1 aggregation. Thus, Lig9 is a good candidate from which to develop a new library of SOD1 aggregation inhibitors through protection of Trp32 oxidation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramu Manjula
- a Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS) , Bangalore , India
| | - Sruthi Unni
- a Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS) , Bangalore , India
| | - Gareth S A Wright
- b Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool , Liverpool , UK
| | - Srinivas Bharath M M
- c Department of Neurochemistry, National Institute of Mental Health and Neurosciences (NIMHANS) , Bangalore , India
- d Neurotoxicology Laboratory, Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS) , Bangalore , India
| | - Balasundaram Padmanabhan
- a Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS) , Bangalore , India
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22
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Tompa DR, Kadhirvel S. Far positioned ALS associated mutants of Cu/Zn SOD forms partially metallated, destabilized misfolding intermediates. Biochem Biophys Res Commun 2019; 516:494-499. [PMID: 31230748 DOI: 10.1016/j.bbrc.2019.06.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 11/18/2022]
Abstract
Loss of stability of proteins is associated with their misfolding and aggregation which results in disease. Despite of the higher stability of Cu/Zn superoxide dismutase (SOD1), the point mutations destabilize its structure, results in oligomerization and the aggregation of SOD1 which is closely associated with the motor neuron disorder, amyotrophic lateral sclerosis. In the present study, we analyzed the role of two SOD1 mutants V14G and E100G which are located far away from the metal sites, dimer interface and disulfide region. The SOD1 mutants were recombinantly produced and their activity, structure and stability were investigated using biochemical methods, CD and DSC methods. In comparison with wild-type SOD1, the mutants exhibited reduced activity and the CD data showed comparable secondary structures composition. However, the stability studies using chemical and thermal denaturation methods showed the mutants are destabilized. Interestingly, our DSC data strongly suggested the destabilization of the mutants is due to the partial metalation of Cu/Zn ions. This observation emphasizes that although the mutations V14G and E100G are located away from the metal sites, they could affect the metal binding similar to metal binding region mutants, which are more susceptible to misfold and aggregate.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India.
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23
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Farrawell NE, Yerbury MR, Plotkin SS, McAlary L, Yerbury JJ. CuATSM Protects Against the In Vitro Cytotoxicity of Wild-Type-Like Copper-Zinc Superoxide Dismutase Mutants but not Mutants That Disrupt Metal Binding. ACS Chem Neurosci 2019; 10:1555-1564. [PMID: 30462490 DOI: 10.1021/acschemneuro.8b00527] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations in the SOD1 gene are associated with some forms of familial amyotrophic lateral sclerosis (fALS). There are more than 150 different mutations in the SOD1 gene that have various effects on the copper-zinc superoxide dismutase (SOD1) enzyme structure, including the loss of metal binding and a decrease in dimer affinity. The copper-based therapeutic CuATSM has been proven to be effective at rescuing neuronal cells from SOD1 mutant toxicity and has also increased the life expectancy of mice expressing the human transgenes SOD1G93A and SOD1G37R. Furthermore, CuATSM is currently the subject of a phase I/II clinical trial in Australia as a treatment for ALS. To determine if CuATSM protects against a broad variety of SOD1 mutations, we used a well-established cell culture model of SOD1-fALS. NSC-34 cells expressing SOD1-EGFP constructs were treated with CuATSM and examined by time-lapse microscopy. Our results show a concentration-dependent protection of cells expressing mutant SOD1A4V over the experimental time period. We tested the efficacy of CuATSM on 10 SOD1-fALS mutants and found that while protection was observed in cells expressing pathogenic wild-type-like mutants, cells expressing a truncation mutant or metal binding region mutants were not. We also show that CuATSM rescue is associated with an increase in human SOD1 activity and a decrease in the level of SOD1 aggregation in vitro. In conclusion, CuATSM has shown to be a promising therapeutic for SOD1-associated ALS; however, our in vitro results suggest that the protection afforded varies depending on the SOD1 variant, including negligible protection to mutants with deficient copper binding.
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Affiliation(s)
- Natalie E. Farrawell
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Biological Sciences, Centre of Medicine and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Maddison R. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Biological Sciences, Centre of Medicine and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Steven S. Plotkin
- Department of Physics & Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
- Genome Sciences and Technology Program, The University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - Luke McAlary
- Department of Physics & Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Biological Sciences, Centre of Medicine and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
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24
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Polykretis P, Cencetti F, Donati C, Luchinat E, Banci L. Cadmium effects on superoxide dismutase 1 in human cells revealed by NMR. Redox Biol 2019; 21:101102. [PMID: 30654299 PMCID: PMC6348768 DOI: 10.1016/j.redox.2019.101102] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 11/24/2022] Open
Abstract
Cadmium is a toxic pollutant that in recent decades has become more widespread in the environment due to anthropogenic activities, significantly increasing the risk of exposure. Concurrently, a continually growing body of research has begun to enumerate the harmful effects that this heavy metal has on human health. Consequently, additional research is required to better understand the mechanism and effects of cadmium at the molecular level. The main mechanism of cadmium toxicity is based on the indirect induction of severe oxidative stress, through several processes that unbalance the anti-oxidant cellular defence system, including the displacement of metals such as zinc from its native binding sites. Such mechanism was thought to alter the in vivo enzymatic activity of SOD1, one of the main antioxidant proteins of many tissues, including the central nervous system. SOD1 misfolding and aggregation is correlated with cytotoxicity in neurodegenerative diseases such as amyotrophic lateral sclerosis. We assessed the effect of cadmium on SOD1 folding and maturation pathway directly in human cells through in-cell NMR. Cadmium does not directly bind intracellular SOD1, instead causes the formation of its intramolecular disulfide bond in the zinc-bound form. Metallothionein overexpression is strongly induced by cadmium, reaching NMR-detectable levels. The intracellular availability of zinc modulates both SOD1 oxidation and metallothionein overexpression, strengthening the notion that zinc-loaded metallothioneins help maintaining the redox balance under cadmium-induced acute stress. Cadmium does not bind to superoxide dismutase 1 (SOD1) in human cells. In defect of zinc, cadmium causes the premature oxidation of SOD1. Cadmium induces the overexpression of metallothioneins to levels detectable by NMR. Zinc modulates metallothionein expression and attenuates SOD1 oxidation.
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Affiliation(s)
- Panagis Polykretis
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Cencetti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Chiara Donati
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy
| | - Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale Morgagni 50, 50134 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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25
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Peng X, Cashman NR, Plotkin SS. Prediction of Misfolding-Specific Epitopes in SOD1 Using Collective Coordinates. J Phys Chem B 2018; 122:11662-11676. [PMID: 30351123 DOI: 10.1021/acs.jpcb.8b07680] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We introduce a global, collective coordinate bias into molecular dynamics simulations that partially unfolds a protein, in order to predict misfolding-specific epitopes based on the regions that locally unfold. Several metrics are used to measure local disorder, including solvent exposed surface area (SASA), native contacts ( Q), and root mean squared fluctuations (RMSF). The method is applied to Cu, Zn superoxide dismutase (SOD1). For this protein, the processes of monomerization, metal loss, and conformational unfolding due to microenvironmental stresses are all separately taken into account. Several misfolding-specific epitopes are predicted, and consensus epitopes are calculated. These predicted epitopes are consistent with the "lower-resolution" peptide sequences used to raise disease-specific antibodies, but the epitopes derived from collective coordinates contain shorter, more refined sequences for the key residues constituting the epitope.
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Affiliation(s)
- Xubiao Peng
- Department of Physics and Astronomy , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada.,Center for Quantum Technology Research, School of Physics , Beijing Institute of Technology , Haidian, Beijing 100081 , China
| | - Neil R Cashman
- Brain Research Centre , University of British Columbia , Vancouver , British Columbia V6T 2B5 , Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, and Genome Sciences and Technology Program , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
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26
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Abstract
Abstract
Metal ions are essential cofactors required by the proteome of organisms from any kingdom of life to correctly exert their functions. Dedicated cellular import, transport and homeostasis systems assure that the needed metal ion is correctly delivered and inserted into the target proteins and avoid the presence of free metal ions in the cell, preventing oxidative damaging. Among metal ions, in eukaryotic organisms copper and iron are required by proteins involved in absolutely essential functions, such as respiration, oxidative stress protection, catalysis, gene expression regulation. Copper and iron binding proteins are localized in essentially all cellular compartments. Copper is physiologically present mainly as individual metal ion. Iron can be present both as individual metal ion or as part of cofactors, such as hemes and iron-sulfur (Fe-S) clusters. Both metal ions are characterized by the ability to cycle between different oxidation states, which enable them to catalyze redox reactions and to participate in electron transfer processes. Here we describe in detail the main processes responsible for the trafficking of copper and iron sulfur clusters, with particular interest for the structural aspects of the maturation of copper and iron-sulfur-binding proteins.
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27
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Pokrishevsky E, McAlary L, Farrawell NE, Zhao B, Sher M, Yerbury JJ, Cashman NR. Tryptophan 32-mediated SOD1 aggregation is attenuated by pyrimidine-like compounds in living cells. Sci Rep 2018; 8:15590. [PMID: 30349065 PMCID: PMC6197196 DOI: 10.1038/s41598-018-32835-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022] Open
Abstract
Over 160 mutations in superoxide dismutase 1 (SOD1) are associated with familial amyotrophic lateral sclerosis (fALS), where the main pathological feature is deposition of SOD1 into proteinaceous cytoplasmic inclusions. We previously showed that the tryptophan residue at position 32 (W32) mediates the prion-like propagation of SOD1 misfolding in cells, and that a W32S substitution blocks this phenomenon. Here, we used in vitro protein assays to demonstrate that a W32S substitution in SOD1-fALS mutants significantly diminishes their propensity to aggregate whilst paradoxically decreasing protein stability. We also show SOD1-W32S to be resistant to seeded aggregation, despite its high abundance of unfolded protein. A cell-based aggregation assay demonstrates that W32S substitution significantly mitigates inclusion formation. Furthermore, this assay reveals that W32 in SOD1 is necessary for the formation of a competent seed for aggregation under these experimental conditions. Following the observed importance of W32 for aggregation, we established that treatment of living cells with the W32-interacting 5-Fluorouridine (5-FUrd), and its FDA approved analogue 5-Fluorouracil (5-FU), substantially attenuate inclusion formation similarly to W32S substitution. Altogether, we highlight W32 as a significant contributor to SOD1 aggregation, and propose that 5-FUrd and 5-FU present promising lead drug candidates for the treatment of SOD1-associated ALS.
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Affiliation(s)
- Edward Pokrishevsky
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Luke McAlary
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Natalie E Farrawell
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Beibei Zhao
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Mine Sher
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Justin J Yerbury
- Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, 2522, Australia. .,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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28
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Luchinat E, Banci L. In-Cell NMR in Human Cells: Direct Protein Expression Allows Structural Studies of Protein Folding and Maturation. Acc Chem Res 2018; 51:1550-1557. [PMID: 29869502 DOI: 10.1021/acs.accounts.8b00147] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cellular structural biology methods are needed to characterize biological processes at atomic resolution in the physiological environment of the cell. Toward this goal, solution in-cell NMR is a powerful approach because it provides structural and dynamic data on macromolecules inside living cells. Several approaches have been developed for in-cell NMR in cultured human cells, which are needed to study processes related to human diseases that rely on the delivery of exogenous macromolecules to the cells. Such strategies, however, may not be applicable to proteins that are sensitive to the external environment or prone to aggregate and can introduce artifacts during protein purification or delivery. As a complementary approach, direct protein expression for in-cell NMR in human cells was developed. This strategy is especially useful when studying processes like protein folding, maturation, and post-translational modification, starting right after protein synthesis. Compared with the protein expression techniques in mammalian cells commonly used in cellular biology, the low sensitivity of NMR requires higher protein levels. Among the cell lines used for high-yield protein expression, the HEK293T cell line was chosen, as it can be efficiently transfected with a cost-effective reagent. A vector originally designed for secreted proteins allows high-level cytosolic protein expression. For isotopic labeling, commercially available or homemade labeled media are employed. Uniform or amino acid type-selective labeling strategies are possible. Protein expression can be targeted to specific organelles (e.g., mitochondria), allowing for in organello NMR applications. A variant of the approach was developed that allows the sequential expression of two or more proteins, with only one selectively labeled. Protein expression in HEK293T cells was applied to recapitulate the maturation steps of intracellular superoxide dismutase 1 (SOD1) and to study the effect of mutations linked to familial amyotrophic lateral sclerosis (fALS) by in-cell NMR. Intracellular wild-type SOD1 spontaneously binds zinc, while it needs the copper chaperone for superoxide dismutase (CCS) for copper delivery and disulfide bond formation. Some fALS-linked mutations impair zinc binding and cause SOD1 to irreversibly unfold, likely forming the precursor of cytotoxic aggregates. The SOD-like domain of CCS acts as a molecular chaperone toward mutant SOD1, stabilizing its folding and allowing zinc binding and correct maturation. Changes in protein redox state distributions can also be investigated by in-cell NMR. Mitochondrial proteins require the redox-regulating partners glutaredoxin 1 (Grx1) and thioredoxin (Trx) to remain in the reduced, import-competent state in the cytosol, whereas SOD1 requires CCS for disulfide bond formation. In both cases, the proteins do not equilibrate with the cytosolic redox pool. Cysteine oxidation in response to oxidative stress can also be monitored. In the near future, in-cell NMR in human cells will likely benefit from technological advancements in NMR hardware, the development of bioreactor systems for increased sample lifetime, the application of paramagnetic NMR to obtain structural restraints, and advanced tools for genome engineering and should be increasingly integrated with advanced cellular imaging techniques.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center - CERM, University of Florence, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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29
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Therapeutic strategies for targeting neurodegenerative protein misfolding disorders. Curr Opin Chem Biol 2018; 44:66-74. [PMID: 29902695 DOI: 10.1016/j.cbpa.2018.05.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/25/2018] [Indexed: 12/14/2022]
Abstract
Neurodegenerative diseases can arise from a multitude of different pathological drivers, however protein misfolding appears to be a common molecular feature central to several disorders. Protein folding, and attainment of correct secondary and tertiary structure, is essential for proper protein function. Protein misfolding gives rise to structural perturbations that can result in loss of protein function or a gain of toxic function, such as through aggregation, either of which can initiate and propagate biological responses that are deleterious to cells. Several neurodegenerative diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease and Parkinson's disease, each have identified molecular components in which protein misfolding perturbs cellular systems that ultimately lead to cell death, and this predominately occurs in neurons. Current efforts focused on developing therapies for protein misfolding disorders have employed diverse strategies; inhibiting the production of disease-relevant proteins prone to misfolding, inhibiting the aggregation of misfolded proteins, removing and preventing spread of aggregated misfolded proteins and manipulating cellular systems to mitigate the toxic effects of misfolded proteins. Each of these strategies has yielded therapeutic agents that have transitioned from preclinical proof of concept studies into human clinical testing. These approaches and therapies are described herein.
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30
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Goyal VD, Magliery TJ. Phylogenetic spread of sequence data affects fitness of SOD1 consensus enzymes: Insights from sequence statistics and structural analyses. Proteins 2018; 86:609-620. [PMID: 29490429 DOI: 10.1002/prot.25486] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 01/25/2018] [Accepted: 02/24/2018] [Indexed: 12/19/2022]
Abstract
Non-natural protein sequences with native-like structures and functions can be constructed successfully using consensus design. This design strategy is relatively well understood in repeat proteins with simple binding function, however detailed studies are lacking in globular enzymes. The SOD1 family is a good model for such studies due to the availability of large amount of sequence and structure data motivated by involvement of human SOD1 in the fatal motor neuron disease amyotrophic lateral sclerosis (ALS). We constructed two consensus SOD1 enzymes from multiple sequence alignments from all organisms and eukaryotic organisms. A significant difference in their catalytic activities shows that the phylogenetic spread of the sequences used affects the fitness of the construct obtained. A mutation in an electrostatic loop and overall design incompatibilities between bacterial and eukaryotic sequences were implicated in this disparity. Based on this analysis, a bioinformatics approach was used to classify mutations thought to cause familial ALS providing a unique high level view of the physical basis of disease-causing aggregation of human SOD1.
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Affiliation(s)
- Venuka Durani Goyal
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210.,Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Thomas J Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, 43210
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31
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Leighton PLA, Allison WT. Protein Misfolding in Prion and Prion-Like Diseases: Reconsidering a Required Role for Protein Loss-of-Function. J Alzheimers Dis 2018; 54:3-29. [PMID: 27392869 DOI: 10.3233/jad-160361] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prion disease research has contributed much toward understanding other neurodegenerative diseases, including recent demonstrations that Alzheimer's disease (AD) and other neurodegenerative diseases are prion-like. Prion-like diseases involve the spread of degeneration between individuals and/or among cells or tissues via template directed misfolding, wherein misfolded protein conformers propagate disease by causing normal proteins to misfold. Here we use the premise that AD, amyotrophic lateral sclerosis, Huntington's disease, and other similar diseases are prion-like and ask: Can we apply knowledge gained from studies of these prion-like diseases to resolve debates about classical prion diseases? We focus on controversies about what role(s) protein loss-of-function might have in prion diseases because this has therapeutic implications, including for AD. We examine which loss-of-function events are recognizable in prion-like diseases by considering the normal functions of the proteins before their misfolding and aggregation. We then delineate scenarios wherein gain-of-function and/or loss-of-function would be necessary or sufficient for neurodegeneration. We consider roles of PrPC loss-of-function in prion diseases and in AD, and conclude that the conventional wisdom that prion diseases are 'toxic gain-of-function diseases' has limitations. While prion diseases certainly have required gain-of-function components, we propose that disease phenotypes are predominantly caused by deficits in the normal physiology of PrPC and its interaction partners as PrPC converts to PrPSc. In this model, gain-of-function serves mainly to spread disease, and loss-of-function directly mediates neuron dysfunction. We propose experiments and predictions to assess our conclusion. Further study on the normal physiological roles of these key proteins is warranted.
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Affiliation(s)
- Patricia L A Leighton
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - W Ted Allison
- Centre for Prions & Protein Folding Disease, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
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32
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Luchinat E, Barbieri L, Banci L. A molecular chaperone activity of CCS restores the maturation of SOD1 fALS mutants. Sci Rep 2017; 7:17433. [PMID: 29234142 PMCID: PMC5727297 DOI: 10.1038/s41598-017-17815-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
Superoxide dismutase 1 (SOD1) is an important metalloprotein for cellular oxidative stress defence, that is mutated in familiar variants of Amyotrophic Lateral Sclerosis (fALS). Some mutations destabilize the apo protein, leading to the formation of misfolded, toxic species. The Copper Chaperone for SOD1 (CCS) transiently interacts with SOD1 and promotes its correct maturation by transferring copper and catalyzing disulfide bond formation. By in vitro and in-cell NMR, we investigated the role of the SOD-like domain of CCS (CCS-D2). We showed that CCS-D2 forms a stable complex with zinc-bound SOD1 in human cells, that has a twofold stabilizing effect: it both prevents the accumulation of unstructured mutant SOD1 and promotes zinc binding. We further showed that CCS-D2 interacts with apo-SOD1 in vitro, suggesting that in cells CCS stabilizes mutant apo-SOD1 prior to zinc binding. Such molecular chaperone function of CCS-D2 is novel and its implications in SOD-linked fALS deserve further investigation.
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Affiliation(s)
- Enrico Luchinat
- Magnetic Resonance Centre (CERM), University of Florence, 50019, Sesto Fiorentino, Italy.,Department of Biomedical, Clinical and Experimental Sciences, University of Florence, 50134, Florence, Italy
| | - Letizia Barbieri
- Magnetic Resonance Centre (CERM), University of Florence, 50019, Sesto Fiorentino, Italy.,Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), 50019, Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Centre (CERM), University of Florence, 50019, Sesto Fiorentino, Italy. .,Department of Chemistry, University of Florence, 50019, Sesto Fiorentino, Florence, Italy.
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33
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Tompa DR, Kadhirvel S. Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior. J Biomol Struct Dyn 2017; 36:4085-4098. [PMID: 29157189 DOI: 10.1080/07391102.2017.1407675] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human superoxide dismutase (Cu/Zn SOD1) is a homodimeric enzyme. Mutations in Cu/Zn SOD1 causes a familial form of amyotrophic lateral sclerosis (fALS), and aggregation of mutant SOD1 has been proposed to play a role in neurodegeneration. Though a majority of the mutations are point substitutions, there are a few changes that result in amino acid deletions or truncations of the polypeptide. These pathogenic mutations are scattered throughout the three-dimensional structure of the dimeric enzyme, which creates a puzzling pattern to investigate the molecular determinants of fALS. The most common hypothesis proposed that the misfolding of SOD1 mutants are primarily triggered by decreased affinity for metal ions. However, this hypothesis is challenging, as a significant number of disease-causing mutations are located far away from the metal-binding site and dimer interface. So in the present study, we have investigated the influence of such a far positioned pathogenic mutation, V14M, in altering the stability and folding of the Cu/Zn SOD1. Though the location of Val14 is far positioned, it has a vital role in the stability of SOD1 by preserving its hydrophobic cluster at one end of the β barrel domain. We have performed MD simulations of the V14M mutant for 80 ns timescale. The results reveal the fact that irrespective of its location, V14M mutation triggers a conformational change that is more similar to that of the metal-deficient holo form and could resemble an intermediate state in the folding reaction which results in protein misfolding and aggregation.
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Affiliation(s)
- Dharma Rao Tompa
- a Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613 401 , India
| | - Saraboji Kadhirvel
- a Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thanjavur 613 401 , India
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34
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Zeineddine R, Farrawell NE, Lambert-Smith IA, Yerbury JJ. Addition of exogenous SOD1 aggregates causes TDP-43 mislocalisation and aggregation. Cell Stress Chaperones 2017; 22:893-902. [PMID: 28560609 PMCID: PMC5655364 DOI: 10.1007/s12192-017-0804-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 12/11/2022] Open
Abstract
ALS is characterised by a focal onset of motor neuron loss, followed by contiguous outward spreading of pathology throughout the nervous system, resulting in paralysis and death generally within a few years after diagnosis. The aberrant release and uptake of toxic proteins including SOD1 and TDP-43 and their subsequent propagation, accumulation and deposition in motor neurons may explain such a pattern of pathology. Previous work has suggested that the internalization of aggregates triggers stress granule formation. Given the close association of stress granules and TDP-43, we wondered whether internalisation of SOD1 aggregates stimulated TDP-43 cytosolic aggregate structures. Addition of recombinant mutant G93A SOD1 aggregates to NSC-34 cells was found to trigger a rapid shift of TDP-43 to the cytoplasm where it was still accumulated after 48 h. In addition, SOD1 aggregates also triggered cleavage of TDP-43 into fragments including a 25 kDa fragment. Collectively, this study suggests a role for protein aggregate uptake in TDP-43 pathology.
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Affiliation(s)
- Rafaa Zeineddine
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Biological Sciences, Science Medicine and Health Faculty, University of Wollongong, Wollongong, NSW, Australia
| | - Natalie E Farrawell
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Biological Sciences, Science Medicine and Health Faculty, University of Wollongong, Wollongong, NSW, Australia
| | - Isabella A Lambert-Smith
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Biological Sciences, Science Medicine and Health Faculty, University of Wollongong, Wollongong, NSW, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia.
- School of Biological Sciences, Science Medicine and Health Faculty, University of Wollongong, Wollongong, NSW, Australia.
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35
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Khan MAI, Respondek M, Kjellström S, Deep S, Linse S, Akke M. Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant. ACS Chem Neurosci 2017; 8:2019-2026. [PMID: 28585802 DOI: 10.1021/acschemneuro.7b00162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cu/Zn superoxide dismutase (SOD1) forms intracellular aggregates that are pathological indicators of amyotrophic lateral sclerosis. A large body of research indicates that the entry point to aggregate formation is a monomeric, metal-ion free (apo), and disulfide-reduced species. Fibril formation by SOD1 in vitro has typically been reported only for harsh solvent conditions or mechanical agitation. Here we show that monomeric apo-SOD1 in the disulfide-reduced state forms fibrillar aggregates under near-physiological quiescent conditions. Monomeric apo-SOD1 with an intact intramolecular disulfide bond is highly resistant to aggregation under the same conditions. A cysteine-free variant of SOD1 exhibits fibrillization behavior and fibril morphology identical to those of disulfide-reduced SOD1, firmly establishing that intermolecular disulfide bonds or intramolecular disulfide shuffling are not required for aggregation and fibril formation. The decreased lag time for fibril formation resulting from reduction of the intramolecular disulfide bond thus primarily reflects the decreased stability of the folded state relative to partially unfolded states, rather than an active role of free sulfhydryl groups in mediating aggregation. Addition of urea to increase the amount of fully unfolded SOD1 increases the lag time for fibril formation, indicating that the population of this species does not dominate over other factors in determining the onset of aggregation. Our results contrast with previous results obtained for agitated samples, in which case amyloid formation was accelerated by denaturant. We reconcile these observations by suggesting that denaturants destabilize monomeric and aggregated species to different extents and thus affect nucleation and growth.
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Affiliation(s)
- M. Ashhar I. Khan
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
- Department
of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Michal Respondek
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Sven Kjellström
- Biochemistry and Structural
Biology,
Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Shashank Deep
- Department
of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sara Linse
- Biochemistry and Structural
Biology,
Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Mikael Akke
- Biophysical
Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00 Lund, Sweden
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36
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Kumar V, Rahman S, Choudhry H, Zamzami MA, Sarwar Jamal M, Islam A, Ahmad F, Hassan MI. Computing disease-linked SOD1 mutations: deciphering protein stability and patient-phenotype relations. Sci Rep 2017; 7:4678. [PMID: 28680046 PMCID: PMC5498623 DOI: 10.1038/s41598-017-04950-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
Protein stability is a requisite in the field of biotechnology, cell biology and drug design. To understand effects of amino acid substitutions, computational models are preferred to save time and expenses. As a systemically important, highly abundant, stable protein, the knowledge of Cu/Zn Superoxide dismutase1 (SOD1) is important, making it a suitable test case for genotype-phenotype correlation in understanding ALS. Here, we report performance of eight protein stability calculators (PoPMuSiC 3.1, I-Mutant 2.0, I-Mutant 3.0, CUPSAT, FoldX, mCSM, BeatMusic and ENCoM) against 54 experimental stability changes due to mutations of SOD1. Four different high-resolution structures were used to test structure sensitivity that may affect protein calculations. Bland-Altman plot was also used to assess agreement between stability analyses. Overall, PoPMuSiC and FoldX emerge as the best methods in this benchmark. The relative performance of all the eight methods was very much structure independent, and also displayed less structural sensitivity. We also analyzed patient's data in relation to experimental and computed protein stabilities for mutations of human SOD1. Correlation between disease phenotypes and stability changes suggest that the changes in SOD1 stability correlate with ALS patient survival times. Thus, the results clearly demonstrate the importance of protein stability in SOD1 pathogenicity.
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Affiliation(s)
- Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, 712-749, South Korea
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Center of Innovation in Personalized Medicine, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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37
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Tachu BJ, Wüsten KA, Garza MC, Wille H, Tamgüney G. An easy method for bacterial expression and purification of wild-type and mutant superoxide dismutase 1 (SOD1). Protein Expr Purif 2017; 134:63-71. [DOI: 10.1016/j.pep.2017.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/06/2017] [Accepted: 04/01/2017] [Indexed: 12/13/2022]
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38
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Towards understanding cellular structure biology: In-cell NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:547-557. [PMID: 28257994 DOI: 10.1016/j.bbapap.2017.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/20/2022]
Abstract
To watch biological macromolecules perform their functions inside the living cells is the dream of any biologists. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that can be used to observe the structures, interactions and dynamics of these molecules in the living cells at atomic level. In principle, in-cell NMR can be applied to different cellular systems to achieve biologically relevant structural and functional information. In this review, we summarize the existing approaches in this field and discuss its applications in protein interactions, folding, stability and post-translational modifications. We hope this review will emphasize the effectiveness of in-cell NMR for studies of intricate biological processes and for structural analysis in cellular environments.
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39
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Anzai I, Tokuda E, Mukaiyama A, Akiyama S, Endo F, Yamanaka K, Misawa H, Furukawa Y. A misfolded dimer of Cu/Zn-superoxide dismutase leading to pathological oligomerization in amyotrophic lateral sclerosis. Protein Sci 2017; 26:484-496. [PMID: 27977888 DOI: 10.1002/pro.3094] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
Misfolding of mutant Cu/Zn-superoxide dismutase (SOD1) is a pathological hallmark in a familial form of amyotrophic lateral sclerosis. Pathogenic mutations have been proposed to monomerize SOD1 normally adopting a homodimeric configuration and then trigger abnormal oligomerization of SOD1 proteins. Despite this, a misfolded conformation of SOD1 leading to the oligomerization at physiological conditions still remains ambiguous. Here, we show that, around the body temperature (∼37°C), mutant SOD1 maintains a dimeric configuration but lacks most of its secondary structures. Also, such an abnormal SOD1 dimer with significant structural disorder was prone to irreversibly forming the oligomers crosslinked via disulfide bonds. The disulfide-crosslinked oligomers of SOD1 were detected in the spinal cords of the diseased mice expressing mutant SOD1. We hence propose an alternative pathway of mutant SOD1 misfolding that is responsible for oligomerization in the pathologies of the disease.
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Affiliation(s)
- Itsuki Anzai
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Eiichi Tokuda
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Atsushi Mukaiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, NINS, Okazaki, 444-8585, Japan.,Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, NINS, Okazaki, 444-8585, Japan.,Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Fumito Endo
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
| | - Hidemi Misawa
- Division of Pharmacology, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan
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Petrozziello T, Secondo A, Tedeschi V, Esposito A, Sisalli M, Scorziello A, Di Renzo G, Annunziato L. ApoSOD1 lacking dismutase activity neuroprotects motor neurons exposed to beta-methylamino-L-alanine through the Ca 2+/Akt/ERK1/2 prosurvival pathway. Cell Death Differ 2017; 24:511-522. [PMID: 28085149 PMCID: PMC5344211 DOI: 10.1038/cdd.2016.154] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/04/2016] [Accepted: 11/24/2016] [Indexed: 01/05/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a severe human adult-onset neurodegenerative disease affecting lower and upper motor neurons. In >20% of cases, the familial form of ALS is caused by mutations in the gene encoding Cu,Zn-superoxide dismutase (SOD1). Interestingly, administration of wild-type SOD1 to SOD1G93A transgenic rats ameliorates motor symptoms through an unknown mechanism. Here we investigated whether the neuroprotective effects of SOD1 are due to the Ca2+-dependent activation of such prosurvival signaling pathway and not to its catalytic activity. To this aim, we also examined the mechanism of neuroprotective action of ApoSOD1, the metal-depleted state of SOD1 that lacks dismutase activity, in differentiated motor neuron-like NSC-34 cells and in primary motor neurons exposed to the cycad neurotoxin beta-methylamino-L-alanine (L-BMAA). Preincubation of ApoSOD1 and SOD1, but not of human recombinant SOD1G93A, prevented cell death in motor neurons exposed to L-BMAA. Moreover, ApoSOD1 elicited ERK1/2 and Akt phosphorylation in motor neurons through an early increase of intracellular Ca2+ concentration ([Ca2+]i). Accordingly, inhibition of ERK1/2 by siMEK1 and PD98059 counteracted ApoSOD1- and SOD1-induced neuroprotection. Similarly, transfection of the dominant-negative form of Akt in NSC-34 motor neurons and treatment with the selective PI3K inhibitor LY294002 prevented ApoSOD1- and SOD1-mediated neuroprotective effects in L-BMAA-treated motor neurons. Furthermore, ApoSOD1 and SOD1 prevented the expression of the two markers of L-BMAA-induced ER stress GRP78 and caspase-12. Collectively, our data indicate that ApoSOD1, which is devoid of any catalytic dismutase activity, exerts a neuroprotective effect through an early activation of Ca2+/Akt/ERK1/2 pro-survival pathway that, in turn, prevents ER stress in a neurotoxic model of ALS.
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Affiliation(s)
- Tiziana Petrozziello
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Agnese Secondo
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Valentina Tedeschi
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Alba Esposito
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - MariaJosè Sisalli
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Antonella Scorziello
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Gianfranco Di Renzo
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy
| | - Lucio Annunziato
- Division of Pharmacology, Department of Neuroscience, Reproductive and Odontostomatological Sciences, School of Medicine, "Federico II" University of Naples, Via Sergio Pansini 5, Naples, Italy.,Fondazione IRCCS SDN, Naples, Italy
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41
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McAlary L, Aquilina JA, Yerbury JJ. Susceptibility of Mutant SOD1 to Form a Destabilized Monomer Predicts Cellular Aggregation and Toxicity but Not In vitro Aggregation Propensity. Front Neurosci 2016; 10:499. [PMID: 27867347 PMCID: PMC5095133 DOI: 10.3389/fnins.2016.00499] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the rapid and progressive degeneration of upper and lower motor neurons in the spinal cord, brain stem and motor cortex. The first gene linked to ALS was the gene encoding the free radical scavenging enzyme superoxide dismutase-1 (SOD1) that currently has over 180, mostly missense, ALS-associated mutations identified. SOD1-associated fALS patients show remarkably broad mean survival times (<1 year to ~17 years death post-diagnosis) that are mutation dependent. A hallmark of SOD1-associated ALS is the deposition of SOD1 into large insoluble aggregates in motor neurons. This is thought to be a consequence of mutation induced structural destabilization and/or oxidative damage leading to the misfolding and aggregation of SOD1 into a neurotoxic species. Here we aim to understand the relationship between SOD1 variant toxicity, structural stability, and aggregation propensity using a combination of cell culture and purified protein assays. Cell based assays indicated that aggregation of SOD1 variants correlate closely to cellular toxicity. However, the relationship between cellular toxicity and disease severity was less clear. We next utilized mass spectrometry to interrogate the structural consequences of metal loss and disulfide reduction on fALS-associated SOD1 variant structure. All variants showed evidence of unfolded, intermediate, and compact conformations, with SOD1G37R, SOD1G93A and SOD1V148G having the greatest abundance of intermediate and unfolded SOD1. SOD1G37R was an informative outlier as it had a high propensity to unfold and form oligomeric aggregates, but it did not aggregate to the same extent as SOD1G93A and SOD1V148G in in vitro aggregation assays. Furthermore, seeding the aggregation of DTT/EDTA-treated SOD1G37R with preformed SOD1G93A fibrils elicited minimal aggregation response, suggesting that the arginine substitution at position-37 blocks the templating of SOD1 onto preformed fibrils. We propose that this difference may be explained by multiple strains of SOD1 aggregate and this may also help explain the slow disease progression observed in patients with SOD1G37R.
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Affiliation(s)
- Luke McAlary
- Lab 210, Illawarra Health and Medical Research InstituteWollongong, NSW, Australia; Science Medicine and Health Faculty, School of Biological Sciences, University of WollongongWollongong, NSW, Australia
| | - J Andrew Aquilina
- Science Medicine and Health Faculty, School of Biological Sciences, University of Wollongong Wollongong, NSW, Australia
| | - Justin J Yerbury
- Lab 210, Illawarra Health and Medical Research InstituteWollongong, NSW, Australia; Science Medicine and Health Faculty, School of Biological Sciences, University of WollongongWollongong, NSW, Australia
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42
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Karamanos TK, Pashley CL, Kalverda AP, Thompson GS, Mayzel M, Orekhov VY, Radford SE. A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity. J Am Chem Soc 2016; 138:6271-80. [PMID: 27117876 PMCID: PMC4922733 DOI: 10.1021/jacs.6b02464] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The balance between protein folding and misfolding is a crucial determinant of amyloid assembly. Transient intermediates that are sparsely populated during protein folding have been identified as key players in amyloid aggregation. However, due to their ephemeral nature, structural characterization of these species remains challenging. Here, using the power of nonuniformly sampled NMR methods we investigate the folding pathway of amyloidogenic and nonamyloidogenic variants of β2-microglobulin (β2m) in atomic detail. Despite folding via common intermediate states, we show that the decreased population of the aggregation-prone ITrans state and population of a less stable, more dynamic species ablate amyloid formation by increasing the energy barrier for amyloid assembly. The results show that subtle changes in conformational dynamics can have a dramatic effect in determining whether a protein is amyloidogenic, without perturbation of the mechanism of protein folding.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Clare L Pashley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
| | - Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg , Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y Orekhov
- The Swedish NMR Centre, University of Gothenburg , Box 465, 40530 Göteborg, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg , Box 465, 40530 Göteborg, Sweden
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
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43
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Petrov D, Daura X, Zagrovic B. Effect of Oxidative Damage on the Stability and Dimerization of Superoxide Dismutase 1. Biophys J 2016; 110:1499-1509. [PMID: 27074676 PMCID: PMC4833831 DOI: 10.1016/j.bpj.2016.02.037] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 02/07/2016] [Accepted: 02/10/2016] [Indexed: 12/13/2022] Open
Abstract
During their life cycle, proteins are subject to different modifications involving reactive oxygen species. Such oxidative damage to proteins may lead to the formation of insoluble aggregates and cytotoxicity and is associated with age-related disorders including neurodegenerative diseases, cancer, and diabetes. Superoxide dismutase 1 (SOD1), a key antioxidant enzyme in human cells, is particularly susceptible to such modifications. Moreover, this homodimeric metalloenzyme has been directly linked to both familial and sporadic amyotrophic lateral sclerosis (ALS), a devastating, late-onset motor neuronal disease, with more than 150 ALS-related mutations in the SOD1 gene. Importantly, oxidatively damaged SOD1 aggregates have been observed in both familial and sporadic forms of the disease. However, the molecular mechanisms as well as potential implications of oxidative stress in SOD1-induced cytotoxicity remain elusive. In this study, we examine the effects of oxidative modification on SOD1 monomer and homodimer stability, the key molecular properties related to SOD1 aggregation. We use molecular dynamics simulations in combination with thermodynamic integration to study microscopic-level site-specific effects of oxidative "mutations" at the dimer interface, including lysine, arginine, proline and threonine carbonylation, and cysteine oxidation. Our results show that oxidative damage of even single residues at the interface may drastically destabilize the SOD1 homodimer, with several modifications exhibiting a comparable effect to that of the most drastic ALS-causing mutations known. Additionally, we show that the SOD1 monomer stability decreases upon oxidative stress, which may lead to partial local unfolding and consequently to increased aggregation propensity. Importantly, these results suggest that oxidative stress may play a key role in development of ALS, with the mutations in the SOD1 gene being an additional factor.
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Affiliation(s)
- Drazen Petrov
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
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44
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Doyle CM, Rumfeldt JA, Broom HR, Sekhar A, Kay LE, Meiering EM. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts. Biochemistry 2016; 55:1346-61. [PMID: 26849066 DOI: 10.1021/acs.biochem.5b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.
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Affiliation(s)
| | | | | | | | - Lewis E Kay
- Program in Molecular Structure and Function, Hospital for Sick Children , Toronto, Canada
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45
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Zeineddine R, Pundavela JF, Corcoran L, Stewart EM, Do-Ha D, Bax M, Guillemin G, Vine KL, Hatters DM, Ecroyd H, Dobson CM, Turner BJ, Ooi L, Wilson MR, Cashman NR, Yerbury JJ. SOD1 protein aggregates stimulate macropinocytosis in neurons to facilitate their propagation. Mol Neurodegener 2015; 10:57. [PMID: 26520394 PMCID: PMC4628302 DOI: 10.1186/s13024-015-0053-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 10/23/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Amyotrophic Lateral Sclerosis is characterized by a focal onset of symptoms followed by a progressive spread of pathology that has been likened to transmission of infectious prions. Cell-to-cell transmission of SOD1 protein aggregates is dependent on fluid-phase endocytosis pathways, although the precise molecular mechanisms remain to be elucidated. RESULTS We demonstrate in this paper that SOD1 aggregates interact with the cell surface triggering activation of Rac1 and subsequent membrane ruffling permitting aggregate uptake via stimulated macropinocytosis. In addition, other protein aggregates, including those associated with neurodegenerative diseases (TDP-43, Httex146Q, α-synuclein) also trigger membrane ruffling to gain entry into the cell. Aggregates are able to rupture unstructured macropinosomes to enter the cytosol allowing propagation of aggregation to proceed. CONCLUSION Thus, we conclude that in addition to basic proteostasis mechanisms, pathways involved in the activation of macropinocytosis are key determinants in the spread of pathology in these misfolding diseases.
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Affiliation(s)
- Rafaa Zeineddine
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Jay F Pundavela
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Lisa Corcoran
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Elise M Stewart
- Intelligent Polymer Research Institute, University of Wollongong, Wollongong, Australia, 2522.
| | - Dzung Do-Ha
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Monique Bax
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Gilles Guillemin
- Australian School for Advanced Medicine, Macquarie University, Sydney, Australia, 2109.
| | - Kara L Vine
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia, 3010.
| | - Heath Ecroyd
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | | | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia, 3010.
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Mark R Wilson
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
| | - Neil R Cashman
- Department of Medicine (Neurology), University of British Columbia and Vancouver Coastal Health Research Institute, Brain Research Centre, University of British Columbia, Vancouver, Canada, V6T 2B5.
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, Australia, 2522.
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, Australia, 2522.
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46
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Leal SS, Cristóvão JS, Biesemeier A, Cardoso I, Gomes CM. Aberrant zinc binding to immature conformers of metal-free copper-zinc superoxide dismutase triggers amorphous aggregation. Metallomics 2015; 7:333-46. [PMID: 25554447 DOI: 10.1039/c4mt00278d] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Superoxide dismutase 1 (SOD1) is a Cu/Zn metalloenzyme that aggregates in amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. Correct metal insertion during SOD1 biosynthesis is critical to prevent misfolding; however Zn(2+) can bind to the copper-site leading to an aberrantly metallated protein. These effects of Zn(2+) misligation on SOD1 aggregation remain to be explored, even though Zn(2+) levels are upregulated in ALS motor neurons. Here we use complementary biophysical methods to investigate Zn(2+) binding and its effects on the aggregation of three immature metal-free SOD1 conformers that represent biogenesis intermediates: dimeric, monomeric and reduced monomeric SOD1. Using isothermal titration calorimetry we determined that Zn(2+) binds to all conformers both at the zinc- as well as to the copper-site; however Zn(2+) binding mechanisms to the zinc-site have distinct characteristics across immature conformers. We show that this 'zinc overload' of immature SOD1 promotes intermolecular interactions, as evidenced by dynamic light scattering and ThT fluorescence kinetic studies. Analysis of aged zinc-induced aggregates by energy-dispersive X-ray and electron energy-loss spectroscopy shows that aggregates integrate some Zn(2+). In addition, electron diffraction analysis identifies nano-scaled crystalline materials and amyloid fibril-like reflections. Transmission electron microscopy reveals that Zn(2+) diverts the SOD1 aggregation pathway from fibrils to amorphous aggregate, and electrophoretic analysis evidences an increase in insoluble materials. Overall, we provide evidence that aberrant zinc coordination to immature conformers broadens the population of SOD1 misfolded species at early aggregation stages and provide evidence for a high structural polymorphism and heterogeneity of SOD1 aggregates.
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Affiliation(s)
- Sónia S Leal
- Instituto Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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47
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Ida M, Ando M, Adachi M, Tanaka A, Machida K, Hongo K, Mizobata T, Yamakawa MY, Watanabe Y, Nakashima K, Kawata Y. Structural basis of Cu, Zn-superoxide dismutase amyloid fibril formation involves interaction of multiple peptide core regions. J Biochem 2015; 159:247-60. [PMID: 26319711 DOI: 10.1093/jb/mvv091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/24/2015] [Indexed: 12/29/2022] Open
Abstract
Cu, Zn-superoxide dismutase (SOD1), an enzyme implicated in the progression of familial amyotrophic lateral sclerosis (fALS), forms amyloid fibrils under certain experimental conditions. As part of our efforts to understand ALS pathogenesis, in this study we found that reduction of the intramolecular disulfide bond destabilized the tertiary structure of metal free wild-type SOD1 and greatly enhanced fibril formation in vitro. We also identified fibril core peptides that are resistant to protease digestion by using mass spectroscopy and Edman degradation analyses. Three regions dispersed throughout the sequence were detected as fibril core sequences of SOD1. Interestingly, by using three synthetic peptides that correspond to these identified regions, we determined that each region was capable of fibril formation, either alone or in a mixture containing multiple peptides. It was also revealed that by reducing the disulfide bond and causing a decrease in the structural stability, the amyloid fibril formation of a familial mutant SOD1 G93A was accelerated even under physiological conditions. These results demonstrate that by destabilizing the structure of SOD1 by removing metal ions and breaking the intramolecular disulfide bridge, multiple fibril-forming core regions are exposed, which then interact with each another and form amyloid fibrils under physiological conditions.
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Affiliation(s)
- Masataka Ida
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Mizuho Ando
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Masayuki Adachi
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Asumi Tanaka
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Kodai Machida
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Miho Yoshida Yamakawa
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yasuhiro Watanabe
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Kenji Nakashima
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
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48
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Keerthana SP, Kolandaivel P. Interaction between dimer interface residues of native and mutated SOD1 protein: a theoretical study. J Biol Inorg Chem 2015; 20:509-22. [PMID: 25578810 DOI: 10.1007/s00775-014-1235-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/27/2014] [Indexed: 01/01/2023]
Abstract
Cu-Zn superoxide dismutase 1 (SOD1) is a highly conserved bimetallic protein enzyme, used for the scavenging the superoxide radicals (O2 (-)) produced due to aerobic metabolism in the mitochondrial respiratory chain. Over 100 mutations have been identified and found to be in the homodimeric structure of SOD1. The enzyme has to be maintained in its dimeric state for the structural stability and enzymatic activity. From our investigation, we found that the mutations apart from the dimer interface residues are found to affect the dimer stability of protein and hence enhancing the aggregation and misfolding tendency of mutated protein. The homodimeric state of SOD1 is found to be held together by the non-covalent interactions. The molecular dynamics simulation has been used to study the hydrogen bond interactions between the dimer interface residues of the monomers in native and mutated forms of SOD1 in apo- and holo-states. The results obtained by this analysis reveal the fact that the loss of hydrogen bond interactions between the monomers of the dimer is responsible for the reduced stability of the apo- and holo-mutant forms of SOD1. The conformers with dimer interface residues in native and mutated protein obtained by the molecular dynamics simulation is subjected to quantum mechanical study using M052X/6-31G(d) level of theory. The charge transfer between N-H···O interactions in the dimer interface residues were studied. The weak interaction between the monomers of the dimer accounts for the reduced dimerization and enhanced deformation energy in the mutated SOD1 protein.
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Affiliation(s)
- S P Keerthana
- Department of Physics, Bharathiar University, Coimbatore, 641 046, India
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49
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Hennig J, Andrésen C, Museth AK, Lundström P, Tibell LAE, Jonsson BH. Local Destabilization of the Metal-Binding Region in Human Copper–Zinc Superoxide Dismutase by Remote Mutations Is a Possible Determinant for Progression of ALS. Biochemistry 2015; 54:323-33. [DOI: 10.1021/bi500606j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Janosch Hennig
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
- Institute
of Structural Biology, Helmholtz Zentrum München GmbH, DE-85764 Neuherberg, Germany
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, DE-85748 Garching, Germany
| | - Cecilia Andrésen
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - A. Katrine Museth
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Patrik Lundström
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Lena A. E. Tibell
- Department
of Science and Technology, Linköping University, SE-601 74, Norrköping, Sweden
| | - Bengt-Harald Jonsson
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
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Szpryngiel S, Oliveberg M, Mäler L. Diffuse binding of Zn(2+) to the denatured ensemble of Cu/Zn superoxide dismutase 1. FEBS Open Bio 2015; 5:56-63. [PMID: 25685664 PMCID: PMC4309841 DOI: 10.1016/j.fob.2014.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/30/2014] [Accepted: 12/30/2014] [Indexed: 11/24/2022] Open
Abstract
Nearly complete backbone assignments for monomeric SOD1 were obtained. Monomeric SOD1 is unstructured in 9 M urea. Zn2+-binding to monomeric SOD1 occurs through diffuse coordination to most His residues. The binding geometry of Zn2+ is different than in the native, folded SOD1.
The stability and structural properties of the metalloprotein superoxide dismutase 1 (SOD1) are found to depend critically on metal ions. Native SOD1 monomers coordinate one structural Zn2+ and one redox-active Cu2+/1+ to the active site. To do this, the Zn2+ ions need to interact with the SOD1 protein on the denatured side of the folding barrier, prior to the formation of the folding nucleus. In this study, we have examined at residue level the nature of this early Zn2+ binding by NMR studies on the urea denatured-state of SOD1. Nearly complete backbone chemical shift assignments were obtained in 9 M urea at physiological pH, conditions at which NMR studies are scarce. Our results demonstrate that SOD1 is predominantly unstructured under these conditions. Chemical-shift changes upon Zn2+ titration show that denatured SOD1 retains a significant affinity to Zn2+ ions, even in 9 M urea. However, the Zn2+ interactions are not limited to the native metal-binding ligands in the two binding sites, but are seen for all His residues. Moreover, the native Cu2+/1+ ligand H46 seems not to bind as well as the other His residues, while the nearby non-native H43 does bind, indicating that the binding geometry is relaxed. The result suggests that the Zn2+-binding observed to catalyze folding of SOD1 in physiological buffer is initiated by diffuse, non-specific coordination to the coil, which subsequently funnels by ligand exchange into the native coordination geometry of the folded monomer. Altogether, this diffuse binding is a result with fundamental implications for folding of metalloproteins in general.
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Affiliation(s)
- Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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