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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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Sarkar A, Gasic AG, Cheung MS, Morrison G. Effects of Protein Crowders and Charge on the Folding of Superoxide Dismutase 1 Variants: A Computational Study. J Phys Chem B 2022; 126:4458-4471. [PMID: 35686856 DOI: 10.1021/acs.jpcb.2c00819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The neurodegenerative disease amyotrophic lateral sclerosis (ALS) is associated with the misfolding and aggregation of the metalloenzyme protein superoxide dismutase 1 (SOD1) via mutations that destabilize the monomer-dimer interface. In a cellular environment, crowding and electrostatic screening play essential roles in the folding and aggregation of the SOD1 monomers. Despite numerous studies on the effects of mutations on SOD1 folding, a clear understanding of the interplay between crowding, folding, and aggregation in vivo remains lacking. Using a structure-based minimal model for molecular dynamics simulations, we investigate the role of self-crowding and charge on the folding stability of SOD1 and the G41D mutant where experimentalists were intrigued by an alteration of the folding mechanism by a single point mutation from glycine to charged aspartic acid. We show that unfolded SOD1 configurations are significantly affected by charge and crowding, a finding that would be extremely costly to achieve with all-atom simulations, while the native state is not significantly altered. The mutation at residue 41 alters the interactions between proteins in the unfolded states instead of those within a protein. This paper suggests electrostatics may play an important role in the folding pathway of SOD1 and modifying the charge via mutation and ion concentration may change the dominant interactions between proteins, with potential impacts for aggregation of the mutants. This work provides a plausible reason for the alteration of the unfolded states to address why the mutant G41D causes the changes to the folding mechanism of SOD1 that have intrigued experimentalists.
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Affiliation(s)
- Atrayee Sarkar
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Andrei G Gasic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Pacific Northwest National Laboratory, Seattle Research Center, Seattle, Washington 98109, United States
| | - Greg Morrison
- Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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Iwakawa N, Morimoto D, Walinda E, Leeb S, Shirakawa M, Danielsson J, Sugase K. Transient Diffusive Interactions with a Protein Crowder Affect Aggregation Processes of Superoxide Dismutase 1 β-Barrel. J Phys Chem B 2021; 125:2521-2532. [PMID: 33657322 DOI: 10.1021/acs.jpcb.0c11162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aggregate formation of superoxide dismutase 1 (SOD1) inside motor neurons is known as a major factor in onset of amyotrophic lateral sclerosis. The thermodynamic stability of the SOD1 β-barrel has been shown to decrease in crowded environments such as inside a cell, but it remains unclear how the thermodynamics of crowding-induced protein destabilization relate to SOD1 aggregation. Here we have examined the effects of a protein crowder, lysozyme, on fibril aggregate formation of the SOD1 β-barrel. We found that aggregate formation of SOD1 is decelerated even in mildly crowded solutions. Intriguingly, transient diffusive interactions with lysozyme do not significantly affect the static structure of the SOD1 β-barrel but stabilize an alternative excited "invisible" state. The net effect of crowding is to favor species off the aggregation pathway, thereby explaining the decelerated aggregation in the crowded environment. Our observations suggest that the intracellular environment may have a similar negative (inhibitory) effect on fibril formation of other amyloidogenic proteins in living cells. Deciphering how crowded intracellular environments affect aggregation and fibril formation of such disease-associated proteins will probably become central in understanding the exact role of aggregation in the etiology of these enigmatic diseases.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sarah Leeb
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Yu Y, Grazioli G, Unhelkar MH, Martin RW, Butts CT. Network Hamiltonian models reveal pathways to amyloid fibril formation. Sci Rep 2020; 10:15668. [PMID: 32973286 PMCID: PMC7515878 DOI: 10.1038/s41598-020-72260-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/27/2020] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibril formation is central to the etiology of a wide range of serious human diseases, such as Alzheimer's disease and prion diseases. Despite an ever growing collection of amyloid fibril structures found in the Protein Data Bank (PDB) and numerous clinical trials, therapeutic strategies remain elusive. One contributing factor to the lack of progress on this challenging problem is incomplete understanding of the mechanisms by which these locally ordered protein aggregates self-assemble in solution. Many current models of amyloid deposition diseases posit that the most toxic species are oligomers that form either along the pathway to forming fibrils or in competition with their formation, making it even more critical to understand the kinetics of fibrillization. A recently introduced topological model for aggregation based on network Hamiltonians is capable of recapitulating the entire process of amyloid fibril formation, beginning with thousands of free monomers and ending with kinetically accessible and thermodynamically stable amyloid fibril structures. The model can be parameterized to match the five topological classes encompassing all amyloid fibril structures so far discovered in the PDB. This paper introduces a set of network statistical and topological metrics for quantitative analysis and characterization of the fibrillization mechanisms predicted by the network Hamiltonian model. The results not only provide insight into different mechanisms leading to similar fibril structures, but also offer targets for future experimental exploration into the mechanisms by which fibrils form.
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Affiliation(s)
- Yue Yu
- Department of Computer Science, University of California, Irvine, CA, 92697, USA
| | - Gianmarc Grazioli
- Department of Chemistry, San José State University, San Jose, CA, 95192, USA
| | - Megha H Unhelkar
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Rachel W Martin
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Carter T Butts
- Department of Computer Science, University of California, Irvine, CA, 92697, USA. .,California Institute for Telecommunications and Information Technology, University of California, Irvine, CA, 92697, USA. .,Departments of Sociology, Statistics, and EECS, University of California, Irvine, CA, 92697, USA.
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