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Mohite SV, Sharma KK. Gut microbial metalloproteins and its role in xenobiotics degradation and ROS scavenging. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:495-538. [PMID: 38960484 DOI: 10.1016/bs.apcsb.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The gut microbial metalloenzymes play an important role in maintaining the balance between gut microbial ecosystem, human physiologically processes and immune system. The metals coordinated into active site contribute in various detoxification and defense strategies to avoid unfavourable environment and ensure bacterial survival in human gut. Metallo-β-lactamase is a potent degrader of antibiotics present in periplasmic space of both commensals and pathogenic bacteria. The resistance to anti-microbial agents developed in this enzyme is one of the global threats for human health. The organophosphorus eliminator, organophosphorus hydrolases have evolved over a course of time to hydrolyze toxic organophosphorus compounds and decrease its effect on human health. Further, the redox stress responders namely superoxide dismutase and catalase are key metalloenzymes in reducing both endogenous and exogenous oxidative stress. They hold a great importance for pathogens as they contribute in pathogenesis in human gut along with reduction of oxidative stress. The in-silico study on these enzymes reveals the importance of point mutation for the evolution of these enzymes in order to enhance their enzyme activity and stability. Various mutation studies were conducted to investigate the catalytic activity of these enzymes. By using the "directed evolution" method, the enzymes involved in detoxification and defense system can be engineered to produce new variants with enhance catalytic features, which may be used to predict the severity due to multi-drug resistance and degradation pattern of organophosphorus compounds in human gut.
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Affiliation(s)
- Shreya Vishwas Mohite
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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Sánchez JM, López-Laguna H, Parladé E, Somma AD, Livieri AL, Álamo P, Mangues R, Unzueta U, Villaverde A, Vázquez E. Structural Stabilization of Clinically Oriented Oligomeric Proteins During their Transit through Synthetic Secretory Amyloids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309427. [PMID: 38501900 DOI: 10.1002/advs.202309427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Indexed: 03/20/2024]
Abstract
Developing time-sustained drug delivery systems is a main goal in innovative medicines. Inspired by the architecture of secretory granules from the mammalian endocrine system it has generated non-toxic microscale amyloid materials through the coordination between divalent metals and poly-histidine stretches. Like their natural counterparts that keep the functionalities of the assembled protein, those synthetic structures release biologically active proteins during a slow self-disintegration process occurring in vitro and upon in vivo administration. Being these granules formed by a single pure protein species and therefore, chemically homogenous, they act as highly promising time-sustained drug delivery systems. Despite their enormous clinical potential, the nature of the clustering process and the quality of the released protein have been so far neglected issues. By using diverse polypeptide species and their protein-only oligomeric nanoscale versions as convenient models, a conformational rearrangement and a stabilization of the building blocks during their transit through the secretory granules, being the released material structurally distinguishable from the original source is proved here. This fact indicates a dynamic nature of secretory amyloids that act as conformational arrangers rather than as plain, inert protein-recruiting/protein-releasing granular depots.
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Affiliation(s)
- Julieta M Sánchez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET-Universidad Nacional de Córdoba), ICTA, FCEFyN, UNC, Av. Velez Sarsfield 1611, Córdoba, X5016GCA, Argentina
| | - Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Angela Di Somma
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Department of Chemical Sciences, University of Naples "Federico II", Vicinale Cupa Cintia 26, Naples, 20126, Italy
- CEINGE Advanced Biotechnologies, Via Gaetano Salvatore 486, Naples, 80131, Italy
| | - Andrea L Livieri
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
| | - Patricia Álamo
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, 08025, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
- Institut de Recerca Sant Pau (IR SANT PAU), Sant Quintí 77-79, Barcelona, 08041, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, 08025, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Plaça Cívica s/n, Bellaterra, Barcelona, 08193, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, 08024, Spain
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3
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Qiu F, Liu Y, Liu Z. The Role of Protein S-Nitrosylation in Mitochondrial Quality Control in Central Nervous System Diseases. Aging Dis 2024:AD.2024.0099. [PMID: 38739938 DOI: 10.14336/ad.2024.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/25/2024] [Indexed: 05/16/2024] Open
Abstract
S-Nitrosylation is a reversible covalent post-translational modification. Under physiological conditions, S-nitrosylation plays a dynamic role in a wide range of biological processes by regulating the function of substrate proteins. Like other post-translational modifications, S-nitrosylation can affect protein conformation, activity, localization, aggregation, and protein interactions. Aberrant S-nitrosylation can lead to protein misfolding, mitochondrial fragmentation, synaptic damage, and autophagy. Mitochondria are essential organelles in energy production, metabolite biosynthesis, cell death, and immune responses, among other processes. Mitochondrial dysfunction can result in cell death and has been implicated in the development of many human diseases. Recent evidence suggests that S-nitrosylation and mitochondrial dysfunction are important modulators of the progression of several diseases. In this review, we highlight recent findings regarding the aberrant S- nitrosylation of mitochondrial proteins that regulate mitochondrial biosynthesis, fission and fusion, and autophagy. Specifically, we discuss the mechanisms by which S-nitrosylated mitochondrial proteins exercise mitochondrial quality control under pathological conditions, thereby influencing disease. A better understanding of these pathological events may provide novel therapeutic targets to mitigate the development of neurological diseases.
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Affiliation(s)
- Fang Qiu
- Department of Burn and Plastic Surgery, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yuqiang Liu
- Department of Anesthesiology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhiheng Liu
- Department of Anesthesiology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, China
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Qassim HM, Seyedalipour B, Baziyar P, Ahamady-Asbchin S. Polyphenolic flavonoid compounds act as the inhibitory potential of aggregation process: Implications for the prevention and therapeutics against FALS-associated D101G SOD1 mutant. Comput Biol Chem 2023; 107:107967. [PMID: 37844376 DOI: 10.1016/j.compbiolchem.2023.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Aggregation of proteins is a biological phenomenon caused by misfolded proteins. Human superoxide dismutase (hSOD1) misfolding and aggregation underlie the neurological illness amyotrophic lateral sclerosis (ALS). The most significant contributing factor to ALS is genetic point mutations in SOD1. particularly, D101G mutant is the most harmful because it significantly reduces the life expectancy of patients. Subsequently, the use of natural polyphenolic flavonoids is strongly recommended to reduce the amyloidogenic behavior of protopathic proteins. In this study, using computational parameters such as protein-ligand interaction and molecular dynamics (MD) simulation analyses, we are trying to identify a pharmacodynamically promising flavonoid compound that can effectively inhibit the pathogenic behavior of the D101G mutant. Epigallocatechin-gallate (EGCG), Hesperidin, Isorhamnetin, and Diosmetin were identified as potential leads in a preliminary screening of flavonoids to anti-amyloid action. The results of MD showed that the binding of flavonoids to D101G mutant caused changes in stability, hydrophobicity of protein, and flexibility, as well as significantly led to the restoration of lost hydrogen bonds. Secondary structure analysis showed that protein destabilization and the increased propensity of β-sheet caused by the mutation were restored to the wild-type state upon binding of flavonoids. Besides, to differentiate aggregation, we elucidated alterations in the free energy landscape (FEL) and dynamic cross-correlation matrix (DCCM) of WT-SOD1 and mutant (unbound /bound) states. Among flavonoids, Epigallocatechin-gallate and Hesperidin had the most therapeutic efficacy against the D101G mutant. Therefore, Epigallocatechin-gallate and Hesperidin promise considerable therapeutic potential to develop highly effective inhibitors in reducing fatal and irreversible ALS.
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Affiliation(s)
- Hussein Maitham Qassim
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Salman Ahamady-Asbchin
- Department of Microbiology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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Noorbakhsh Varnosfaderani SM, Sadat Haeri M, Arian AS, Yousefi Rad A, Yazdanpour M, Mojahedian F, Yaghoubzad-Maleki M, Zalpoor H, Baziyar P, Nabi-Afjadi M. Fighting against amyotrophic lateral sclerosis (ALS) with flavonoids: a computational approach to inhibit superoxide dismutase (SOD1) mutant aggregation. J Biomol Struct Dyn 2023:1-18. [PMID: 37975411 DOI: 10.1080/07391102.2023.2281641] [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: 08/07/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
Protein aggregation is a biological process that occurs when proteins misfold. Misfolding and aggregation of human superoxide dismutase (hSOD1) cause a neurodegenerative disease called amyotrophic lateral sclerosis (ALS). Among the mutations occurring, targeting the E21K mutation could be a good choice to understand the pathological mechanism of SOD1 in ALS, whereof it significantly reduces life hopefulness in patients. Naturally occurring polyphenolic flavonoids have been suggested as a way to alleviate the amyloidogenic behavior of proteins. In this study, computational tools were used to identify promising flavonoid compounds that effectively inhibit the pathogenic behavior of the E21K mutant. Initial screening identified Pelargonidin, Curcumin, and Silybin as promising leads. Molecular dynamics (MD) simulations showed that the binding of flavonoids to the mutated SOD1 caused changes in the protein stability, hydrophobicity, flexibility, and restoration of lost hydrogen bonds. Secondary structure analysis indicated that the protein destabilization and the increased propensity of β-sheet caused by the mutation were restored to the wild-type state upon binding of flavonoids. Free energy landscape (FEL) analysis was also used to differentiate aggregation, and results showed that Silybin followed by Pelargonidin had the most therapeutic efficacy against the E21K mutant SOD1. Therefore, these flavonoids hold great potential as highly effective inhibitors in mitigating ALS's fatal and insuperable effects.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Melika Sadat Haeri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ali Sam Arian
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Yousefi Rad
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Mohammad Yazdanpour
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Mojahedian
- Department of Biochemistry, Faculty of Biological Sciences, University of Tarbiat Modares, Tehran, Iran
| | - Mohammad Yaghoubzad-Maleki
- Division of Biochemistry, Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, University of Tarbiat Modares, Tehran, Iran
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Sim KS, Inoue T. Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1. Acta Crystallogr F Struct Biol Commun 2023; 79:169-179. [PMID: 37358501 PMCID: PMC10327573 DOI: 10.1107/s2053230x2300523x] [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: 04/02/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.
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Affiliation(s)
- Kee-Shin Sim
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan
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Zaji HD, Seyedalipour B, Hanun HM, Baziyar P, Hosseinkhani S, Akhlaghi M. Computational insight into in silico analysis and molecular dynamics simulation of the dimer interface residues of ALS-linked hSOD1 forms in apo/holo states: a combined experimental and bioinformatic perspective. 3 Biotech 2023; 13:92. [PMID: 36845075 PMCID: PMC9944573 DOI: 10.1007/s13205-023-03514-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023] Open
Abstract
The aggregation of misfolded SOD1 proteins in neurodegenerative illnesses is a key pathological hallmark in amyotrophic lateral sclerosis (ALS). SOD1 is stabilized and enzymatically activated after binding to Cu/Zn and forming intramolecular disulfide. SOD1 aggregation/oligomerization is triggered by the dissociation of Cu and/or Zn ions. Therefore, we compared the possible effects of ALS-associated point mutations of the holo/apo forms of WT/I149T/V148G SOD1 variants located at the dimer interface to determine structural characterization using spectroscopic methods, computational approaches as well as molecular dynamics (MD) simulations. Predictive results of computational analysis of single-nucleotide polymorphisms (SNPs) suggested that mutant SOD1 has a deleterious effect on activity and structure destabilization. MD data analysis indicated that changes in flexibility, stability, hydrophobicity of the protein as well as increased intramolecular interactions of apo-SOD1 were more than holo-SOD1. Furthermore, a decrease in enzymatic activity in apo-SOD1 was observed compared to holo-SOD1. Comparative intrinsic and ANS fluorescence results of holo/apo-WT-hSOD1 and mutants indicated structural alterations in the local environment of tryptophan residue and hydrophobic patches, respectively. Experimental and MD data supported that substitution effect and metal deficiency of mutants (apo forms) in the dimer interface may promote the tendency to protein mis-folding and aggregation, consequently disrupting the dimer-monomer equilibrium and increased propensity to dissociation dimer into SOD-monomer ultimately leading to loss of stability and function. Overall, data analysis of apo/holo SOD1 forms on protein structure and function using computational and experimental studies will contribute to a better understanding of ALS pathogenicity.
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Affiliation(s)
- Hamza Dakhil Zaji
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Haider Munzer Hanun
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Payam Baziyar
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mona Akhlaghi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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Sharma S, Tomar VR, Jayaraj A, Deep S. A computational strategy for therapeutic development against superoxide dismutase (SOD1) amyloid formation: effect of polyphenols on the various events in the aggregation pathway. Phys Chem Chem Phys 2023; 25:6232-6246. [PMID: 36756854 DOI: 10.1039/d2cp05537f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pathology of superoxide dismutase 1 (SOD1) aggregation is linked to a neurodegenerative disease known as amyotrophic lateral sclerosis (ALS). Without suitable post-translational modifications (PTMs), the protein structure tends to become aggregation-prone. Understanding the role of PTMs and targeting the aggregation-prone SOD1 with small molecules can be used to design a strategy to inhibit its aggregation. Microsecond long molecular dynamics (MD) simulations followed by free energy surface (FES) analyses show that the loss of structure in the apo monomer happens locally and stepwise. Removing the disulfide bond from apoprotein leads to further instability in the zinc-binding loop, giving rise to non-native protein conformations. Further, it was found that these non-native conformations have a higher propensity to form a non-native dimer. We chose three structurally similar polyphenols based on their binding energies and investigated their impact on SOD1 aggregation kinetics. MD simulations of apo-SOD1SH/corkscrew fibril-polyphenol complexes were also carried out. The effect of polyphenols was seen on fibril elongation as well. Based on the experiments and MD simulation results, it can be inferred that the choice of inhibitors is influenced not only by the binding energy but also by dimer interface stabilization, the proclivity to form non-native dimers, the propensity to break fibrils, and the propensity to decrease the rate of elongation. The polyphenols with 3' and 4' hydroxyl groups are better inhibitors of SOD1 aggregation.
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Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.
| | - Vijay Raj Tomar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.
| | - Abhilash Jayaraj
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India, 110016.
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Wang TW, Wuu J, Cooley A, Yeh TS, Benatar M, Weisskopf M. Occupational lead exposure and survival with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:100-107. [PMID: 35400246 PMCID: PMC9547984 DOI: 10.1080/21678421.2022.2059379] [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: 08/31/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 01/26/2023]
Abstract
Objective: Lead exposure has been hypothesized to increase the risk of ALS, but only two studies have examined the association with ALS survival, and with inconsistent results. The use of occupational history to assess lead exposure can avoid reverse causation that may occur in epidemiologic analyses that use biomarkers of lead exposure collected after ALS onset.Methods: We evaluated the relationship of occupational lead exposure to ALS survival among 135 cases from an international ALS cohort that included deep phenotyping, careful follow-up, and questionnaires to quantify participants' occupation history. ALS patients were recruited in 2015-2019. We determined occupational lead exposure using a job-exposure matrix. We estimated hazard ratios (HR) and 95% confidence intervals (CI) for survival using Cox proportional hazard analysis with adjustment for covariates.Results: A total of 135 ALS patients completed the environmental questionnaires, among whom 38 reached a survival endpoint (death or permanent assisted ventilation). The median survival was 48.3 months (25th-75th percentile, 30.9-74.1). Older patients and those with initial symptom other than limb onset had shorter survival time. There were 36 ALS cases with occupational lead exposure. After adjusting for age, sex, site of onset, smoking, and military service, lead exposure was associated with an HR of 3.26 (95%CI 1.28-8.28). Results with adjustment for subsets of these covariates were similar.Conclusions: These results suggest that lead exposure prior to onset of ALS is associated with shorter survival following onset of ALS, and this association is independent of other prognostic factors.
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Affiliation(s)
- Te-Wei Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Joanne Wuu
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Anne Cooley
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Tian-Shin Yeh
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Michael Benatar
- Department of Neurology, Miller Schoof of Medicine, University of Miami, Miami, FL, USA
| | - Marc Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
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10
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Shakerinasab N, Azizi M, Mansourian M, Sadeghi H, Salaminia S, Abbasi R, Shahaboddin ME, Doustimotlagh AH. Empagliflozin Exhibits Hepatoprotective Effects Against Bile Duct Ligation-induced Liver Injury in Rats: A Combined Molecular Docking Approach to In Vivo Studies. Curr Pharm Des 2022; 28:3313-3323. [PMID: 36305136 DOI: 10.2174/1381612829666221027112239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/22/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND Cholestatic liver damage is a chronic disease caused by dysfunction of the hepaticbiliary system. Oxidative stress and inflammation are essential factors in the pathogenesis of cholestasis. Thus, the current study was designed to examine the effect of empagliflozin on bile duct ligation-induced liver damage in rats. METHODS This study was done on male Wistar rats, which were randomly assigned to the four experimental groups: sham control (SC), bile duct ligation (BDL), SC plus empagliflozin (SC+EMPA) (receiving 10 mg of EMPA orally for 7 days), BDL plus empagliflozin 10 mg/kg (BDL+ EMPA). At the end of the study, the rats were sacrificed, and serum and tissue samples were collected to analyze biochemical parameters, biomarkers of oxidative stress, inflammatory markers, and histopathological changes. The molecular docking technique was performed to elucidate the interaction of EMPA and Cu/Zn-superoxide dismutase (SOD1). RESULTS The results showed that BDL elevated the serum activity of ALT, AST, ALP, and levels of TBIL and TPro. BDL also intensifies the oxidative stress state in rats, which was confirmed by augmenting lipid peroxidation (MDA), protein oxidation (PCO), and altering antioxidant defense parameters through decreased SOD, catalase (CAT), and glutathione peroxidase (GPX) levels. Furthermore, the histopathological changes in the liver demonstrated the aggravation of inflammation and oxidative stress. In contrast, treatment with EMPA has shown anti-inflammatory and anti-oxidant effects by reducing TNF-α and IL-6 pro-inflammatory marker proteins, restoring the antioxidant status (increased SOD and GPX), reducing ALT, AST, ALP, TBIL levels, and protein oxidation, and improving the histopathological alterations through reducing bile duct proliferation, fibrosis, focal and portal inflammation. According to the attained findings, the SOD1 activity can be regulated by the EMPA. Our documentation presents direct evidence at the molecular level related to the ability of EMPA to exert its antioxidant performance through certain measures in a particular molecular route. CONCLUSION The results showed EMPA to have hepatic protective effects in rats against cholestatic liver injury, an effect mediated by its antioxidant and anti-inflammatory properties.
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Affiliation(s)
- Nasrin Shakerinasab
- Department of Biochemistry, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Mahdokht Azizi
- Department of Pharmacology, Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Mahboubeh Mansourian
- Department of Pharmacology, Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Hossein Sadeghi
- Department of Pharmacology, Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Shirvan Salaminia
- Department of Cardiac Surgery, Yasuj University of Medical Science, Yasuj, Iran
| | - Reza Abbasi
- Department of Pediatrics, Yasuj University of Medical Science, Yasuj, Iran
| | | | - Amir Hossein Doustimotlagh
- Department of Pharmacology, Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Department of Clinical Biochemistry, Faculty of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran
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11
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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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12
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Bian X, Zhuang X, Zheng Z, Liu S, Liu Z, Song F. Unfolding and aggregation of oxidized metal-deficient superoxide dismutase and isoflavone inhibition based on ion mobility mass spectrometry and ThT fluorescence assay. Arch Biochem Biophys 2022; 727:109306. [DOI: 10.1016/j.abb.2022.109306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
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13
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Hnath B, Dokholyan NV. Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS. Biophys J 2022; 121:2084-2095. [PMID: 35505609 DOI: 10.1016/j.bpj.2022.04.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
Accumulation of insoluble amyloid fibrils is widely studied as a critical factor in the pathology of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease. Misfolded Cu, Zn superoxide dismutase (SOD1) was the first protein linked to ALS, and non-native SOD1 trimeric oligomers were recently linked to cytotoxicity, while larger oligomers were protective to cells. The balance between trimers and larger aggregates in the process of SOD1 aggregation is, thus, a critical determinant of potential therapeutic approaches to treat ALS. Yet, it is unknown whether these trimeric oligomers are a necessary intermediate for larger aggregate formation or a distinct off-pathway species competing with fibril formation. Depending on the on- or off-pathway scenario of trimer formation, we expect drastically different therapeutic approaches. Here, we show that the toxic SOD1 trimer is an off-pathway intermediate competing with protective fibril formation. We design mutant SOD1 constructs that remain in a trimeric state (super stable trimers) and show that stabilizing the trimeric SOD1 prevents formation of fibrils in vitro and in a motor neuron like cell model (NSC-34). Using size exclusion chromatography, we track the aggregation kinetics of purified SOD1 and show direct competition of trimeric SOD1 with larger oligomer and fibril formation. Finally, we show the trimer is structurally independent of both larger soluble oligomers and insoluble fibrils using circular dichroism spectroscopy and limited proteolysis.
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Affiliation(s)
- Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
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14
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Kumari M, Sharma S, Deep S. Tetrabutylammonium based ionic liquids (ILs) inhibit the amyloid aggregation of superoxide dismutase 1 (SOD1). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Nishiko M, Sakamoto T, Mun S, Noh MY, Arakane Y, Kanost MR, Arai K, Tabunoki H. Superoxide dismutase 6 is required during metamorphosis for the development of properly movable legs in Tribolium castaneum. Sci Rep 2022; 12:6900. [PMID: 35477951 PMCID: PMC9046187 DOI: 10.1038/s41598-022-10166-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/04/2022] [Indexed: 11/09/2022] Open
Abstract
The body form of holometabolous insects dramatically transforms from larval to adult stages during metamorphosis that occurs in the pupal stage. The larval disorganization and then new adult tissues are built up at this time. In motoneuron, larval neuronal cells degenerate, and new adult neurons are remodeled. Finally, adult neurons reconnect to new adult muscles. However, the factors that control metamorphosis have not yet been fully elucidated. Here, we show that an antioxidant enzyme, Tribolium castaneum superoxide dismutase 6 (TcSOD6), is secreted into the haemolymph and is required for proper movable legs during metamorphosis. TcSOD6 has a unique domain architecture and is mainly expressed in the pupal stage. The depletion of TcSOD6 expression in the pupa inhibits normal axon development and results in adults that display dysfunctional leg motions, suggesting that SOD6 expression is required for the development of properly movable legs. Therefore, we speculate that TcSOD6 might participate in some of the processes for larval neurons to be remodelled to new adult functions in the legs during metamorphosis, providing new insight into the evolution of SOD functions.
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Affiliation(s)
- Maaya Nishiko
- Department of United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuma Sakamoto
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Seulgi Mun
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Department of Forest Resources, AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61186, South Korea
| | - Yasuyuki Arakane
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141Chalmers Hall, Manhattan, KS, 66506-3702, USA
| | - Katsuhiko Arai
- Department of Tissue Physiology, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroko Tabunoki
- Department of United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
- Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
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16
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Srinivasan E, Chandrasekhar G, Chandrasekar P, Anbarasu K, Vickram AS, Tayubi IA, Rajasekaran R, Karunakaran R. Decoding Conformational Imprint of Convoluted Molecular Interactions Between Prenylflavonoids and Aggregated Amyloid-Beta42 Peptide Causing Alzheimer's Disease. Front Chem 2022; 9:753146. [PMID: 34988060 PMCID: PMC8720757 DOI: 10.3389/fchem.2021.753146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Protein misfolding occurs due to the loss of native protein structure and adopts an abnormal structure, wherein the misfolded proteins accumulate and form aggregates, which result in the formation of amyloid fibrils that are associated with neurodegenerative diseases. Amyloid beta (Aβ42) aggregation or amyloidosis is contemplated as a unique hallmark characteristic of Alzheimer’s disease (AD). Due to aberrant accrual and aggregation of Aβ42 in extracellular space, the formation of senile plaques is found in AD patients. These senile plaques occur usually in the cognitive and memory region of the brain, enfeebles neurodegeneration, hinders the signaling between synapse, and disrupts neuronal functioning. In recent years, herbal compounds are identified and characterized for their potential as Aβ42 inhibitors. Thus, understanding their structure and molecular mechanics can provide an incredible finding in AD therapeutics. To describe the structure-based molecular studies in the rational designing of drugs against amyloid fibrils, we examined various herbal compounds that belong to prenylflavonoids. The present study characterizes the trends we identified at molecular docking studies and dynamics simulation where we observed stronger binding orientation of bavachalcone, bavachin, and neobavaisoflavone with the amyloid-beta (Aβ42) fibril structure. Hence, we could postulate that these herbal compounds could be potential inhibitors of Aβ42 fibrils; these anti-aggregation agents need to be considered in treating AD.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India.,Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - G Chandrasekhar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - P Chandrasekar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Iftikhar Aslam Tayubi
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Bedong, Malaysia
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17
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Wen X, Zhu W, Xia NL, Li Q, Di L, Zhang S, Chen H, Lu Y, Wang M, Xu M, Wang S, Shen XM, Lu J, Da Y. Missense Mutations of Codon 116 in the SOD1 Gene Cause Rapid Progressive Familial ALS and Predict Short Viability With PMA Phenotype. Front Genet 2021; 12:776831. [PMID: 34868265 PMCID: PMC8638083 DOI: 10.3389/fgene.2021.776831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/14/2021] [Indexed: 11/25/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron disease, characterized by a great variety of both clinical presentations and genetic causes. Previous studies had identified two different missense mutations in SOD1 (p.R116C and p.R116G) causing familial ALS. In this study, we report a novel heterozygous missense mutation in the SOD1 gene (p.R116S) in a family with inherited ALS manifested as fast-deteriorating pure lower motor neuron symptoms. The patient displayed similar clinical picture and prognostic value to previous reported cases with different R116 substitution mutations. Modeling of all R116 substitutions in the resolved SOD1 protein structure revealed a shared mechanism with destroyed hydrogen bonds between R116 and other two residues, which might lead to protein unfolding and oligomer formation, ultimately conferring neurotoxicity.
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Affiliation(s)
- Xinmei Wen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Wenjia Zhu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Nan L Xia
- Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qianwen Li
- Department of Radiology and Nuclear Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Magnetic Resonance Imaging and Brain Informatics, Beijing, China
| | - Li Di
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shu Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hai Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yan Lu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Min Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Min Xu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Suobin Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN, United States
| | - Jie Lu
- Department of Radiology and Nuclear Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Magnetic Resonance Imaging and Brain Informatics, Beijing, China
| | - Yuwei Da
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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18
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Timucin AC, Cinaroglu SS, Sezerman OU, Timucin E. Bridging the Bridging Imidazolate in the Bimetallic Center of the Cu/Zn SOD1 and ALS. Front Chem 2021; 9:716438. [PMID: 34540798 PMCID: PMC8446448 DOI: 10.3389/fchem.2021.716438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/10/2021] [Indexed: 12/24/2022] Open
Abstract
Metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis (ALS). All of the amino acids found in the bimetallic center have been associated with ALS except for two positions. H63 which forms the bridging imidazolate ion in the bimetallic center and K136 which is not directly involved in coordination but located in the bimetallic center were not reported to be mutated in any of the identified ALS cases. In this study, we investigated the structure and flexibility of five SOD1 variants by using classical molecular dynamics simulations. These variants include three substitutions on the non-ALS-linked positions; H63A, H63R, K136A and ALS-linked positions; G37R, H46R/H48D. We have generated four systems for each variant differing in metallation and presence of the intramolecular disulfide bond. Overall, a total of 24 different dimers including the wild-type were generated and simulated at two temperatures, 298 and 400 K. We have monitored backbone mobility, fluctuations and compactness of the dimer structures to assess whether the hypothetical mutations would behave similar to the ALS-linked variants. Results showed that particularly two mutants, H63R and K136A, drastically affected the dimer dynamics by increasing the fluctuations of the metal binding loops compared with the control mutations. Further, these variants resulted in demetallation of the dimers, highlighting probable ALS toxicity that could be elicited by the SOD1 variants of H63R and K136A. Overall, this study bridges two putative SOD1 positions in the metallic center and ALS, underlining the potential use of atomistic simulations for studying disease variants.
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Affiliation(s)
- Ahmet Can Timucin
- Department of Molecular Biology and Genetics, Acibadem MAA University, Istanbul, Turkey
| | | | - Osman Ugur Sezerman
- Department of Medical Informatics and Biostatistics, School of Medicine, Acibadem MAA University, Istanbul, Turkey
| | - Emel Timucin
- Department of Medical Informatics and Biostatistics, School of Medicine, Acibadem MAA University, Istanbul, Turkey
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19
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2021; 60:9215-9246. [PMID: 32144830 PMCID: PMC8247289 DOI: 10.1002/anie.202000451] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 12/11/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.
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Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
| | - James B. Hilton
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
- School of BioSciencesThe University of MelbourneParkvilleVictoria3052Australia
- Atomic Medicine InitiativeThe University of Technology SydneyBroadwayNew South Wales2007Australia
| | - Peter J. Crouch
- Department of Pharmacology and TherapeuticsThe University of MelbourneParkvilleVictoria3052Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of PharmacologyThe University of Sydney, CamperdownSydneyNew South Wales2050Australia
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20
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Bovio F, Sciandrone B, Urani C, Fusi P, Forcella M, Regonesi ME. Superoxide dismutase 1 (SOD1) and cadmium: A three models approach to the comprehension of its neurotoxic effects. Neurotoxicology 2021; 84:125-135. [PMID: 33774064 DOI: 10.1016/j.neuro.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
Cadmium (Cd) is a widespread toxic environmental contaminant, released by anthropogenic activities. It interferes with essential metal ions homeostasis and affects protein structures and functions by substituting zinc, copper and iron. In this study, the effect of cadmium on SOD1, a CuZn metalloenzyme catalyzing superoxide conversion into hydrogen peroxide, has been investigated in three different biological models. We first evaluated the effects of cadmium combined with copper and/or zinc on the recombinant GST-SOD1, expressed in E. coli BL21. The enzyme activity and expression were investigated in the presence of fixed copper and/or zinc doses with different cadmium concentrations, in the cellular medium. Cadmium caused a dose-dependent reduction in SOD1 activity, while the expression remains constant. Similar results were obtained in the cellular model represented by the human SH-SY5Y neuronal cell line. After cadmium treatment for 24 and 48 h, SOD1 enzymatic activity decreased in a dose- and time-dependent way, while the protein expression remained constant. Finally, a 16 h cadmium treatment caused a 25 % reduction of CuZn-SOD activity without affecting the protein expression in the Caenorhabditis elegans model. Taken together our results show an inhibitory effect of cadmium on SOD1 enzymatic activity, without affecting the protein expression, in all the biological models used, suggesting that cadmium can displace zinc from the enzyme catalytic site.
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Affiliation(s)
- Federica Bovio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy
| | - Barbara Sciandrone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy
| | - Chiara Urani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL), Interuniversity Research Center, Italy
| | - Paola Fusi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL), Interuniversity Research Center, Italy.
| | - Matilde Forcella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy.
| | - Maria Elena Regonesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126, Milan, Italy; Milan Center of Neuroscience (NeuroMI), 20126, Milan, Italy
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21
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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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22
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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23
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Simien JM, Haglund E. Topological Twists in Nature. Trends Biochem Sci 2021; 46:461-471. [PMID: 33419636 DOI: 10.1016/j.tibs.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
The first entangled protein was observed about 30 years ago, resulting in an increased interest for uncovering the biological functions and biophysical properties of these complex topologies. Recently, the Pierced Lasso Topology (PLT) was discovered in which a covalent bond forms an intramolecular loop, leaving one or both termini free to pierce the loop. This topology is related to knots and other entanglements. PLTs exist in many well-researched systems where the PLTs have previously been unnoticed. PLTs represents 18% of all disulfide containing proteins across all kingdoms of life. In this review, we investigate the biological implications of this specific topology in which the PLT-forming disulfide may act as a molecular switch for protein function and consequently human health.
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Affiliation(s)
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA.
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24
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Eleutherio ECA, Silva Magalhães RS, de Araújo Brasil A, Monteiro Neto JR, de Holanda Paranhos L. SOD1, more than just an antioxidant. Arch Biochem Biophys 2020; 697:108701. [PMID: 33259795 DOI: 10.1016/j.abb.2020.108701] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
During cellular respiration, radicals, such as superoxide, are produced, and in a large concentration, they may cause cell damage. To combat this threat, the cell employs the enzyme Cu/Zn Superoxide Dismutase (SOD1), which converts the radical superoxide into molecular oxygen and hydrogen peroxide, through redox reactions. Although this is its main function, recent studies have shown that the SOD1 has other functions that deviates from its original one including activation of nuclear gene transcription or as an RNA binding protein. This comprehensive review looks at the most important aspects of human SOD1 (hSOD1), including the structure, properties, and characteristics as well as transcriptional and post-translational modifications (PTM) that the enzyme can receive and their effects, and its many functions. We also discuss the strategies currently used to analyze it to better understand its participation in diseases linked to hSOD1 including Amyotrophic Lateral Sclerosis (ALS), cancer, and Parkinson.
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25
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Trist BG, Hilton JB, Hare DJ, Crouch PJ, Double KL. Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Benjamin G. Trist
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
| | - James B. Hilton
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Dominic J. Hare
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
- School of BioSciences The University of Melbourne Parkville Victoria 3052 Australia
- Atomic Medicine Initiative The University of Technology Sydney Broadway New South Wales 2007 Australia
| | - Peter J. Crouch
- Department of Pharmacology and Therapeutics The University of Melbourne Parkville Victoria 3052 Australia
| | - Kay L. Double
- Brain and Mind Centre and Discipline of Pharmacology The University of Sydney, Camperdown Sydney New South Wales 2050 Australia
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26
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Bonaccorsi M, Knight MJ, Le Marchand T, Dannatt HRW, Schubeis T, Salmon L, Felli IC, Emsley L, Pierattelli R, Pintacuda G. Multimodal Response to Copper Binding in Superoxide Dismutase Dynamics. J Am Chem Soc 2020; 142:19660-19667. [PMID: 33166153 DOI: 10.1021/jacs.0c09242] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copper/zinc superoxide dismutase (SOD) is a homodimeric metalloenzyme that has been extensively studied as a benchmark for structure-function relationships in proteins, in particular because of its implication in the familial form of the neurodegenerative disease amyotrophic lateral sclerosis. Here, we investigate microcrystalline preparations of two differently metalated forms of SOD, namely, the fully mature functional Cu,Zn state and the E,Zn-SOD state in which the Cu site is empty. By using solid-state NMR with fast magic-angle spinning (MAS) at high magnetic fields (1H Larmor frequency of 800-1000 MHz), we quantify motions spanning a dynamic range from ns to ms. We determine that metal ion uptake does not act as a rigidification element but as a switch redistributing motional processes on different time scales, with coupling of the dynamics of histidine side chains and those of remote key backbone elements of the protein.
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Affiliation(s)
- Marta Bonaccorsi
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Michael J Knight
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Hugh R W Dannatt
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Laboratory of Magnetic Resonance, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and CERM, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, FRE 2034 (CNRS/Université Claude Bernard Lyon 1/Ecole Normale Supérieure de Lyon), University of Lyon, 69100 Villeurbanne, France
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27
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Niu B, Mackness BC, Zitzewitz JA, Matthews CR, Gross ML. Trifluoroethanol Partially Unfolds G93A SOD1 Leading to Protein Aggregation: A Study by Native Mass Spectrometry and FPOP Protein Footprinting. Biochemistry 2020; 59:3650-3659. [PMID: 32924445 DOI: 10.1021/acs.biochem.0c00425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolding of Cu, Zn superoxide dismutase (SOD1) variants may lead to protein aggregation and ultimately amyotrophic lateral sclerosis (ALS). The mechanism and protein conformational changes during this process are complex and remain unclear. To study SOD1 variant aggregation at the molecular level and in solution, we chemically induced aggregation of a mutant variant (G93A SOD1) with trifluoroethanol (TFE) and used both native mass spectrometry (MS) to analyze the intact protein and fast photochemical oxidation of proteins (FPOP) to characterize the structural changes induced by TFE. We found partially unfolded G93A SOD1 monomers prior to oligomerization and identified regions of the N-terminus, C-terminus, and strands β5, β6 accountable for the partial unfolding. We propose that exposure of hydrophobic interfaces of these unstructured regions serves as a precursor to aggregation. Our results provide a possible mechanism and molecular basis for ALS-linked SOD1 misfolding and aggregation.
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Affiliation(s)
- Ben Niu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Brian C Mackness
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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28
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Schneider S, Shakeri F, Trötschel C, Arévalo L, Kruse A, Buness A, Poetsch A, Steger K, Schorle H. Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. Cells 2020; 9:E1789. [PMID: 32727081 PMCID: PMC7463811 DOI: 10.3390/cells9081789] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 12/24/2022] Open
Abstract
Protamines are the safeguards of the paternal sperm genome. They replace most of the histones during spermiogenesis, resulting in DNA hypercondensation, thereby protecting its genome from environmental noxa. Impaired protamination has been linked to male infertility in mice and humans in many studies. Apart from impaired DNA integrity, protamine-deficient human and murine sperm show multiple secondary effects, including decreased motility and aberrant head morphology. In this study, we use a Protamine-2 (Prm2)-deficient mouse model in combination with label-free quantitative proteomics to decipher the underlying molecular processes of these effects. We show that loss of the sperm's antioxidant capacity, indicated by downregulation of key proteins like Superoxide dismutase type 1 (SOD1) and Peroxiredoxin 5 (PRDX5), ultimately initiates an oxidative stress-mediated destruction cascade during epididymal sperm maturation. This is confirmed by an increased level of 8-OHdG in epididymal sperm, a biomarker for oxidative stress-mediated DNA damage. Prm2-deficient testicular sperm are not affected and initiate the proper development of blastocyst stage preimplantation embryos in vitro upon intracytoplasmic sperm injection (ICSI) into oocytes. Our results provide new insight into the role of Prm2 and its downstream molecular effects on sperm function and present an important contribution to the investigation of new treatment regimens for infertile men with impaired protamination.
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Affiliation(s)
- Simon Schneider
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (S.S.); (L.A.)
| | - Farhad Shakeri
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (F.S.); (A.B.)
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Christian Trötschel
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (C.T.); (A.P.)
| | - Lena Arévalo
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (S.S.); (L.A.)
| | - Alexander Kruse
- Department of Urology, Pediatric Urology and Andrology, Section Molecular Andrology, Biomedical Research Center of the Justus-Liebig University Gießen, 35392 Gießen, Germany; (A.K.); (K.S.)
| | - Andreas Buness
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, 53127 Bonn, Germany; (F.S.); (A.B.)
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany; (C.T.); (A.P.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Klaus Steger
- Department of Urology, Pediatric Urology and Andrology, Section Molecular Andrology, Biomedical Research Center of the Justus-Liebig University Gießen, 35392 Gießen, Germany; (A.K.); (K.S.)
| | - Hubert Schorle
- Department of Developmental Pathology, Institute of Pathology, University Hospital Bonn, 53127 Bonn, Germany; (S.S.); (L.A.)
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29
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Jahan I, Nayeem SM. Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study. RSC Adv 2020; 10:27598-27614. [PMID: 35516947 PMCID: PMC9055598 DOI: 10.1039/d0ra02151b] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/25/2020] [Indexed: 11/23/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the misfolding of Cu, Zn superoxide dismutase (SOD1). Several earlier studies have shown that monomeric apo SOD1 undergoes significant local unfolding dynamics and is the predecessor for aggregation. Here, we have employed atomistic molecular dynamics (MD) simulations to study the structure and dynamics of monomeric apo and holo SOD1 in water, aqueous urea and aqueous urea-TMAO (trimethylamine oxide) solutions. Loop IV (zinc-binding loop) and loop VII (electrostatic loop) of holo SOD1 are considered as functionally important loops as they are responsible for the structural stability of holo SOD1. We found larger local unfolding of loop IV and VII of apo SOD1 as compared to holo SOD1 in water. Urea induced more unfolding in holo SOD1 than apo SOD1, whereas the stabilization of both the form of SOD1 was observed in ternary solution (i.e. water/urea/TMAO solution) but the extent of stabilization was higher in holo SOD1 than apo SOD1. The partially unfolded structures of apo SOD1 in water, urea and holo SOD1 in urea were identified by the exposure of the hydrophobic cores, which are highly dynamic and these may be the initial events of aggregation in SOD1. Our simulation studies support the formation of aggregates by means of the local unfolding of monomeric apo SOD1 as compared to holo SOD1 in water.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University Aligarh-202002 U.P. India +91-9412527078
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University Aligarh-202002 U.P. India +91-9412527078
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30
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Timr S, Gnutt D, Ebbinghaus S, Sterpone F. The Unfolding Journey of Superoxide Dismutase 1 Barrels under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions with Crowders. J Phys Chem Lett 2020; 11:4206-4212. [PMID: 32364389 DOI: 10.1021/acs.jpclett.0c00699] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The thermal stability of the superoxide dismutase 1 protein in a crowded solution is investigated by performing enhanced sampling molecular simulations. By complementing thermal unfolding experiments done close to physiological conditions (200 mg/mL), we provide evidence that the presence of the protein crowder bovine serum albumin in different packing states has only a minor, and essentially destabilizing, effect. The finding that quinary interactions counteract the pure stabilization contribution stemming from excluded volume is rationalized here by exploring the SOD1 unfolding mechanism in microscopic detail. In agreement with recent experiments, we unveil the importance of intermediate unfolded states as well as the correlation between protein conformations and local packing with the crowders. This link helps us to elucidate why certain SOD1 mutations involved in the ALS disease reverse the stability effect of the intracellular environment.
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Affiliation(s)
- Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, F-75005 Paris, France
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, Technical University Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Department of Physical Chemistry II, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, Technical University Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
- Department of Physical Chemistry II, Ruhr University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, F-75005 Paris, France
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31
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Bhatia NK, Modi P, Sharma S, Deep S. Quercetin and Baicalein Act as Potent Antiamyloidogenic and Fibril Destabilizing Agents for SOD1 Fibrils. ACS Chem Neurosci 2020; 11:1129-1138. [PMID: 32208672 DOI: 10.1021/acschemneuro.9b00677] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that has been associated with the deposition of aggregates of superoxide dismutase 1 (SOD1). Effective therapeutics against SOD1 fibrillation is still an area of active research. Herein, we demonstrate the potential of two naturally occurring flavonoids (quercetin and baicalein) to inhibit fibrillation of wild-type SOD1 with the aid of a series of biophysical techniques. Our seeding experiments reveal that both of these flavonoids significantly affect the fibril elongation. Interestingly, our ThT binding assay, TEM, and SDS-PAGE experiments suggest that these flavonoids also disintegrate the fibrils into shorter fragments but do not completely depolymerize them into monomers. Binding parameters obtained from the analysis of UV-vis spectra suggest that these flavonoids bind moderately to native SOD1 dimer and have different binding sites. Docking of these flavonoids with a non-native monomer, non-native trimer, and oligomer derived from the 11-residue segment of SOD1 indicates that both quercetin and baicalein can bind to these species and thus can arrest the elongation of fibrils by blocking the fibrillar core regions on the intermediate species formed during aggregation of SOD1. MTT assay data revealed that both the flavonoids reduced the cytotoxicity of SOD1 fibrils. Experimental data also show the antiamyloidogenic potential of both flavonoids against A4V SOD1 mutant fibrillation. Thus, our findings may provide a direction for designing effective therapeutic agents against ALS which can act as promising antiamyloidogenic and fibril destabilizing agents.
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Affiliation(s)
- Nidhi K. Bhatia
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
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32
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Anzai I, Tokuda E, Handa S, Misawa H, Akiyama S, Furukawa Y. Oxidative misfolding of Cu/Zn-superoxide dismutase triggered by non-canonical intramolecular disulfide formation. Free Radic Biol Med 2020; 147:187-199. [PMID: 31863908 DOI: 10.1016/j.freeradbiomed.2019.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Misfolded Cu/Zn-superoxide dismutase (SOD1) is a pathological species in a subset of amyotrophic lateral sclerosis (ALS). Oxidative stress is known to increase in affected spinal cords of ALS and is thus considered to cause damages on SOD1 leading to the misfolding and aggregation. Despite this, it still remains elusive what triggers misfolding of SOD1 under oxidizing environment. Here, we show that a thiol group of Cys111 in SOD1 is oxidized to a sulfenic acid with hydrogen peroxide and reveal that further dissociation of the bound metal ions from the oxidized SOD1 allows another free Cys residue (Cys6) to nucleophilically attack the sulfenylated Cys111. As a result, an intra-molecular disulfide bond forms between Cys6 and Cys111. Such an abnormal SOD1 with the non-canonical disulfide bond was conformationally extended with significant cytotoxicity as well as high propensity to aggregate. Taken together, we propose a new model of SOD1 misfolding under oxidizing environment, in which formation of the non-canonical intramolecular disulfide bond plays a pivotal role.
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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
| | - Sumika Handa
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan
| | - Hidemi Misawa
- Division of Pharmacology, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan; Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, 444-8585, Japan
| | - Yoshiaki Furukawa
- Department of Chemistry, Keio University, Yokohama, 223-8522, Japan.
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33
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Mouro PR, Povinelli APR, Leite VBP, Chahine J. Exploring Folding Aspects of Monomeric Superoxide Dismutase. J Phys Chem B 2020; 124:650-661. [DOI: 10.1021/acs.jpcb.9b09640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paulo R. Mouro
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
| | - Vitor B. P. Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto 15054-000, Brazil
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34
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Souza PT, Thallmair S, Marrink SJ, Mera-Adasme R. An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. J Phys Chem Lett 2019; 10:7740-7744. [PMID: 31747286 PMCID: PMC6926953 DOI: 10.1021/acs.jpclett.9b02868] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/20/2019] [Indexed: 05/29/2023]
Abstract
Several different mutations of the protein copper, zinc superoxide dismutase (SOD1) produce the neurodegenerative disorder amyotrophic lateral sclerosis (ALS). The molecular mechanism by which the diverse mutations converge to a similar pathology is currently unknown. The electrostatic loop (EL) of SOD1 is known to be affected in all of the studied ALS-linked mutations of SOD1. In this work, we employ a multiscale simulation approach to show that this perturbation corresponds to an increased probability of the EL detaching from its native position, exposing the metal site of the protein to water. From extensive atomistic and coarse-grained molecular dynamics (MD) simulations, we identify an allosteric pathway that explains the action of the distant G93A mutation on the EL. Finally, we employ quantum mechanics/molecular mechanics MD simulations to show that the opening of the EL decreases the Zn(II) affinity of the protein. As the loss of Zn(II) is at the center of several proposed pathogenic mechanisms in SOD1-linked ALS, the structural effect identified here not only is in agreement with the experimental data but also places the opening of the electrostatic loop as the possible main pathogenic effect for a significant number of ALS-linked SOD1 mutations.
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Affiliation(s)
- Paulo
C. T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Raúl Mera-Adasme
- Departamento
de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Av. Libertador Bernardo O’Higgins
3363, 9170022 Estacion
Central, Chile
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35
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Proctor EA, Mowrey DD, Dokholyan NV. β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology. PLoS Comput Biol 2019; 15:e1007225. [PMID: 31323035 PMCID: PMC6668853 DOI: 10.1371/journal.pcbi.1007225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/31/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
Exposure to the environmental toxin β-methylamino-L-alanine (BMAA) is linked to amyotrophic lateral sclerosis (ALS), but its disease-promoting mechanism remains unknown. We propose that incorporation of BMAA into the ALS-linked protein Cu,Zn superoxide dismutase (SOD1) upon translation promotes protein misfolding and aggregation, which has been linked to ALS onset and progression. Using molecular simulation and predictive energetic computation, we demonstrate that substituting any serine with BMAA in SOD1 results in structural destabilization and aberrant dynamics, promoting neurotoxic SOD1 aggregation. We propose that translational incorporation of BMAA into SOD1 is directly responsible for its toxicity in neurodegeneration, and BMAA modification of SOD1 may serve as a biomarker of ALS.
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Affiliation(s)
- Elizabeth A. Proctor
- Departments of Neurosurgery, Pharmacology, and Biomedical Engineering, The Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - David D. Mowrey
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nikolay V. Dokholyan
- Departments of Pharmacology, Biochemistry & Molecular Biology, Chemistry, and Biomedical Engineering, The Pennsylvania State University, Hershey, Pennsylvania, United States of America
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36
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Tiwari MK, Hägglund PM, Møller IM, Davies MJ, Bjerrum MJ. Copper ion / H 2O 2 oxidation of Cu/Zn-Superoxide dismutase: Implications for enzymatic activity and antioxidant action. Redox Biol 2019; 26:101262. [PMID: 31284117 PMCID: PMC6614508 DOI: 10.1016/j.redox.2019.101262] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 01/25/2023] Open
Abstract
Copper ion-catalyzed oxidation of yeast SOD1 (ySOD1) was examined to determine early oxidative modifications, including oxidation of a crucial disulfide bond, and the structural and functional repercussions of these events. The study used distinct oxidative conditions: Cu2+/H2O2, Cu2+/H2O2/AscH− and Cu2+/H2O2/glucose. Capillary electrophoresis experiments and quantification of protein carbonyls indicate that ySOD1 is highly susceptible to oxidative modification and that changes can be detected within 0.1 min of the initiation of the reaction. Oxidation-induced structural perturbations, characterized by circular dichroism, revealed the formation of partially-unfolded ySOD1 species in a dose-dependent manner. Consistent with these structural changes, pyrogallol assay indicates a partial loss of enzymatic activity. ESI-MS analyses showed seven distinct oxidized ySOD1 species under mild oxidation within 0.1 min. LC/MS analysis after proteolytic digestion demonstrated that the copper-coordinating active site histidine residues, His47 and His49, were converted into 2-oxo-histidine. Furthermore, the Cu and Zn bridging residue, His64 is converted into aspartate/asparagine. Importantly, the disulfide-bond Cys58-Cys147 which is critical for the structural and functional integrity of ySOD1 was detected as being oxidized at Cys147. We propose, based on LC/MS analyses, that disulfide-bond oxidation occurs without disulfide bond cleavage. Modifications were also detected at Met85 and five surface-exposed Lys residues. Based on these data we propose that the Cys58-Cys147 bond may act as a sacrificial target for oxidants and protect ySOD1 from oxidative inactivation arising from exposure to Cu2+/H2O2 and auto-inactivation during extended enzymatic turnover. Oxidation of yeast superoxide dismutase (ySOD1) by Cu2+/H2O2 is examined. Rapid modification of His, Met, Cys and Lys residues detected by LC-MS methods. Oxidation of active site His residues and partial protein unfolding are early events. The Cys58-Cys147 disulfide bond is oxidized and may act as a sacrificial target. Excess exogenous Cu2+ decreases protein damage and can reverse loss of activity.
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Affiliation(s)
- Manish K Tiwari
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Per M Hägglund
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
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Computational Investigation on Electrostatic Loop Mutants Instigating Destabilization and Aggregation on Human SOD1 Protein Causing Amyotrophic Lateral Sclerosis. Protein J 2019; 38:37-49. [PMID: 30701485 DOI: 10.1007/s10930-018-09809-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mutations in the gene encoding Cu/Zn Superoxide Dismutase 1 (SOD1) protein are contemplated to be a protruding reason for Amyotrophic lateral sclerosis (ALS), which leads towards protein aggregation, misfolding and destabilization. Thus, we investigated the systematic action of entire mutations reported on electrostatic loop of SOD1 protein through thermodynamical and discrete molecular dynamics (DMD) studies. Accordingly, we analyzed the outcomes distinctly for screening the mutant structures having both, deleterious and destabilizing effect. Progressively, the impacts of those mutations on SOD1 were studied using DMD program. Surprisingly, our results predicted that the mutants viz., L126S, N139H and G141A to be the most destabilizing, misfolded and disease-causing compared to other mutants. Besides, the outcomes from secondary structural propensities and free energy landscapes, together assertively suggested that L126S, N139H and G141A tend to increase the formation of aggregates in SOD1 relative to other mutants. Hence, this study could provide an insight into the sprouting neurodegenerative disorder distressing the humans.
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38
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Jia L, Wang W, Sang J, Wei W, Zhao W, Lu F, Liu F. Amyloidogenicity and Cytotoxicity of a Recombinant C-Terminal His 6-Tagged Aβ 1-42. ACS Chem Neurosci 2019; 10:1251-1262. [PMID: 30537813 DOI: 10.1021/acschemneuro.8b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aggregation of amyloid β peptide (Aβ) is closely associated with the occurrence and development of Alzheimer's disease (AD). Reproducible and detailed studies on the aggregation kinetics and structure of various aggregates have been conducted using recombinant Aβ peptides. While the His6-tag is commonly used in the purification of recombinant proteins due to its great simplicity and affinity, there is little information on the aggregation of His6-tagged Aβ and its corresponding cytotoxicity. Moreover, it is also unclear whether there is an effect of the His6-tag on the amyloidogenicity and cytotoxicity of recombinant Aβ1-42. Herein, a method to express and purify a mutant C-terminally His6-tagged Aβ1-42 (named as Aβ1-42-His6) from Escherichia coli was described. Aβ1-42-His6 aggregated into β-sheet-rich fibrils as shown by thioflavin T fluorescence, atomic force microscopy and circular dichroism spectroscopy. Moreover, the fibrillar recombinant Aβ1-42-His6 showed strong toxicity toward PC12 cells in vitro. Molecular dynamics simulations revealed that the His6-tag contributed little to the secondary structure and intermolecular interactions, including hydrophobic interactions, salt bridges, and hydrogen bonding of the fibrillar pentamer of Aβ1-42. This highlights the biological importance of modification on the molecular structure of Aβ. Thus, the easily purified high-quality Aβ1-42-His6 offers great advantages for screening aggregation inhibitors or in vitro confirmation of rationally designed drugs for the treatment of AD.
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Affiliation(s)
- Longgang Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenjuan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jingcheng Sang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wei Wei
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenping Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fuping Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Fufeng Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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39
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Bille A, Jensen KS, Mohanty S, Akke M, Irbäck A. Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders. J Phys Chem B 2019; 123:1920-1930. [PMID: 30753785 DOI: 10.1021/acs.jpcb.8b10774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Using NMR and Monte Carlo (MC) methods, we investigate the stability and dynamics of superoxide dismutase 1 (SOD1) in homogeneous crowding environments, where either bovine pancreatic trypsin inhibitor (BPTI) or the B1 domain of streptococcal protein G (PGB1) serves as a crowding agent. By NMR, we show that both crowders, and especially BPTI, cause a drastic loss in the overall stability of SOD1 in its apo monomeric form. Additionally, we determine chemical shift perturbations indicating that SOD1 interacts with the crowder proteins in a residue-specific manner that further depends on the identity of the crowding protein. Furthermore, the specificity of SOD1-crowder interactions is reciprocal: chemical shift perturbations on BPTI and PGB1 identify regions that interact preferentially with SOD1. By MC simulations, we investigate the local unfolding of SOD1 in the absence and presence of the crowders. We find that the crowders primarily interact with the long flexible loops of the folded SOD1 monomer. The basic mechanisms by which the SOD1 β-barrel core unfolds remain unchanged when adding the crowders. In particular, both with and without the crowders, the second β-sheet of the barrel is more dynamic and unfolding-prone than the first. Notably, the MC simulations (exploring the early stages of SOD1 unfolding) and the NMR experiments (under equilibrium conditions) identify largely the same set of PGB1 and BPTI residues as prone to form SOD1 contacts. Thus, contacts stabilizing the unfolded state of SOD1 in many cases appear to form early in the unfolding reaction.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics , Lund University , Sölvegatan 14A , SE-223 62 Lund , Sweden
| | - Kristine Steen Jensen
- Department of Biophysical Chemistry, Center for Molecular Protein Science , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre , Forschungszentrum Jülich , D-52425 Jülich , Germany
| | - Mikael Akke
- Department of Biophysical Chemistry, Center for Molecular Protein Science , Lund University , P.O. Box 124, SE-22100 Lund , Sweden
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics , Lund University , Sölvegatan 14A , SE-223 62 Lund , Sweden
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40
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Srinivasan E, Rajasekaran R. Molecular binding response of naringin and naringenin to H46R mutant SOD1 protein in combating protein aggregation using density functional theory and discrete molecular dynamics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 145:40-51. [PMID: 30543828 DOI: 10.1016/j.pbiomolbio.2018.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/24/2018] [Accepted: 12/06/2018] [Indexed: 10/27/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a calamitous neurodegenerative disorder characterized by denervation of upper and lower motor neurons. Numerous hypotheses suggest that toxic protein misfolding and aggregation cause ALS, similar to that of other neurodegenerative diseases, such as Alzheimers and Parkinsons. Protruding causes of familial ALS are mutations in the gene encoding Cu/Zn superoxide dismutase-1 (SOD1), which decrease protein stability and endorse protein aggregation. Thus, the interference concerning aggregate formation and destabilization in SOD1 is considered to be an impending therapeutic strategy. In this work, we utilized computational chemistry methods to initially study the effect of substitution mutation, His46Arg on SOD1 protein. Further, we described the interaction of two naturally occurring polyphenol compounds, naringin and naringenin with mutant SOD1 that is regarded to hinder the protein aggregation. Subsequently, the use of quantum chemical and molecular mechanics calculations speculated that naringin had a strong binding affinity with mutant SOD1 and impeded the formation of toxic aggregates than that of naringenin. Ultimately, we could conjecture that ingesting of polyphenol-rich foods in ALS patients may be regarded to improvise their living. Moreover, the findings from our study could pave a way in the field of structure-based drug design in developing potential anti-aggregation inhibitors against incurable ALS, affecting the human population.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT (Deemed to be University), Vellore, 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT (Deemed to be University), Vellore, 632014, Tamil Nadu, India.
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41
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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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Srinivasan E, Rajasekaran R. Comparative binding of kaempferol and kaempferide on inhibiting the aggregate formation of mutant (G85R) SOD1 protein in familial amyotrophic lateral sclerosis: A quantum chemical and molecular mechanics study. Biofactors 2018; 44:431-442. [PMID: 30260512 DOI: 10.1002/biof.1441] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/21/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
Abstract
Mutation in Cu/Zn superoxide dismutase (SOD1) at position 85 from glycine to arginine was found to be a prominent cause of aggregation characterized by an increased content of β-sheets in familial amyotrophic lateral sclerosis (fALS). Various literatures reported that natural polyphenols could act as a β-sheet breaker and therefore, treated as a potential therapeutics against various aggregated proteins involved in neurodegenerative disorders. Through computational perspective, molecular docking, quantum chemical studies, and discrete molecular dynamics were implemented to study the binding and structural effect of natural polyphenols, kaempferol, and kaempferide on mutant SOD1. Kaempferol exhibited significant binding and greater residual energy contribution with mutant SOD1 than kaempferide. More interestingly, kaempferol was found to reduce the β-sheet content augmenting the mutant conformational stability and flexibility relative to that of kaempferide. Hence, the inhibition of mutant SOD1 aggregation by kaempferol was explored, thereby suggesting kaempferol could act as a drug candidate for the design of the natural therapeutics against fALS. © 2018 BioFactors, 44(5):431-442, 2018.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India
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43
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TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies. Biochem J 2018; 475:1701-1719. [DOI: 10.1042/bcj20180085] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/05/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023]
Abstract
Misfolding and aggregation of Cu, Zn Superoxide dismutase (SOD1) is involved in the neurodegenerative disease, amyotrophic lateral sclerosis. Many studies have shown that metal-depleted, monomeric form of SOD1 displays substantial local unfolding dynamics and is the precursor for aggregation. Here, we have studied the structure and dynamics of different apo monomeric SOD1 variants associated with unfolding and aggregation in aqueous trifluoroethanol (TFE) through experiments and simulation. TFE induces partially unfolded β-sheet-rich extended conformations in these SOD1 variants, which subsequently develops aggregates with fibril-like characteristics. Fibrillation was achieved more easily in disulfide-reduced monomeric SOD1 when compared with wild-type and mutant monomeric SOD1. At higher concentrations of TFE, a native-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops were found to unfold first in 20% (v/v) TFE, leading to a partial unfolding of β-strands 4, 5, and 6 which are prone to aggregation. Our results thus shed light on the role of local unfolding and conformational dynamics in SOD1 misfolding and aggregation.
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Alemasov NA, Ivanisenko NV, Ramachandran S, Ivanisenko VA. Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling. BMC STRUCTURAL BIOLOGY 2018; 18:1. [PMID: 29431095 PMCID: PMC5808480 DOI: 10.1186/s12900-018-0080-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background So far, little is known about the molecular mechanisms of amyotrophic lateral sclerosis onset and progression caused by SOD1 mutations. One of the hypotheses is based on SOD1 misfolding resulting from mutations and subsequent deposition of its cytotoxic aggregates. This hypothesis is complicated by the fact that known SOD1 mutations of similar clinical effect could be distributed over the whole protein structure. Results In this work, a measure of hydrogen bond stability in conformational states was studied with elastic network analysis of 35 SOD1 mutants. Twenty-eight hydrogen bonds were detected in nine of 35 mutants with their stability being significantly different from that with the wild-type. These hydrogen bonds were formed by the amino acid residues known from the literature to be located in contact between SOD1 aggregates. Additionally, residues disposed between copper binding sites of both protein subunits were found from the models to form a stiff core, which can be involved in mechanical impulse transduction between these active centres. Conclusions The modelling highlights that both stability of the copper binding site and stability of the dimer can play an important role in ALS progression. Electronic supplementary material The online version of this article (10.1186/s12900-018-0080-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nikolay A Alemasov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.
| | - Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Srinivasan Ramachandran
- Functional Genomics Unit, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi, 110025, India.,Academy of Scientific and Innovative Research, CSIR-IGIB, South Campus, New Delhi, 110025, India
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia
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45
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Kumar V, Prakash A, Lynn AM. Alterations in local stability and dynamics of A4V SOD1 in the presence of trifluoroethanol. Biopolymers 2018; 109:e23102. [DOI: 10.1002/bip.23102] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/26/2017] [Accepted: 01/03/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Amresh Prakash
- School of Computational and Integrative Sciences; Jawaharlal Nehru University; New Delhi 110067 India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences; Jawaharlal Nehru University; New Delhi 110067 India
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46
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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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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Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories. Nat Commun 2017; 8:1881. [PMID: 29192167 PMCID: PMC5709426 DOI: 10.1038/s41467-017-01996-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
Prion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1's propensity for prion-like misfolding and point to possible targets for therapeutic intervention.
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Cysteine to Serine Conversion at 111th Position Renders the Disaggregation and Retains the Stabilization of Detrimental SOD1 A4V Mutant Against Amyotrophic Lateral Sclerosis in Human-A Discrete Molecular Dynamics Study. Cell Biochem Biophys 2017; 76:231-241. [PMID: 28952073 DOI: 10.1007/s12013-017-0830-5] [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] [Received: 06/17/2017] [Accepted: 09/18/2017] [Indexed: 12/11/2022]
Abstract
Protein aggregation is a hallmark of various neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS) in humans. Mutations in Cu/Zn superoxide dismutase (SOD1) protein were found to be a prominent cause behind the majority of the familial ALS cases with abnormal protein aggregates. Herein, we report the biophysical characterization of the beneficial mutation C111S that stabilizes the SOD1 harboring A4V mutation, one of the most lethal diseases causing mutant that leads to protein destabilization and aggregation. In this study, we utilized discrete molecular dynamics (DMD) simulations, which stipulated an outlook over the systematic action of C111S mutation in the A4V mutant that stabilizes the protein and impedes the formation of protein aggregation. Herewith, the findings from our study manifested that the mutation of C111S in SOD1 could aid in regaining the protein structural conformations that protect against the formation of toxic aggregates, thereby hindering the disease pathogenicity subtly. Hence, our study provides a feasible pharmaceutical strategy in developing the treatment for incurable ALS affecting the mankind.
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Srinivasan E, Rajasekaran R. Deciphering the loss of metal binding due to mutation D83G of human SOD1 protein causing FALS disease. Int J Biol Macromol 2017; 107:521-529. [PMID: 28899654 DOI: 10.1016/j.ijbiomac.2017.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 01/23/2023]
Abstract
Mutations in Cu/Zn superoxide dismutase 1 (SOD1) protein are found to be the causative factor, behind the majority of familial amyotrophic later sclerosis (FALS) cases. The mutations particularly on the metal (Zn) binding residues are found to increase the disease onset in the individuals suffering from FALS, while the presence of the metal ion (Zn) is essential for the catalytic activity and retaining the protein stability. Thus in our study, we focused on one such metal binding mutant (D83G) and assessed the impact of the mutation on protein structure and function. The influence of mutation was examined dynamically, using discrete molecular dynamics on both the native and mutant SOD1 protein respectively. Accordingly, the variation in conformational stability, residual flexibility and protein compactness along with the change in conformational free energy were monitored over the entire dynamic period. Moreover, the motion of native and mutant SOD1 was also observed via the essential dynamics. Besides, the disparity in Zn ion binding was inspected through distance analysis and steered molecular dynamics, correspondingly. Therefore, the study provides a better understanding over the profound effect of mutation on SOD1, both structurally and functionally, using computational approaches.
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Affiliation(s)
- E Srinivasan
- Bioinformatics lab, Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore - 632014, Tamil Nadu, India
| | - R Rajasekaran
- Bioinformatics lab, Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore - 632014, Tamil Nadu, India.
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