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Gale J, Aizenman E. The physiological and pathophysiological roles of copper in the nervous system. Eur J Neurosci 2024; 60:3505-3543. [PMID: 38747014 PMCID: PMC11491124 DOI: 10.1111/ejn.16370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 07/06/2024]
Abstract
Copper is a critical trace element in biological systems due the vast number of essential enzymes that require the metal as a cofactor, including cytochrome c oxidase, superoxide dismutase and dopamine-β-hydroxylase. Due its key role in oxidative metabolism, antioxidant defence and neurotransmitter synthesis, copper is particularly important for neuronal development and proper neuronal function. Moreover, increasing evidence suggests that copper also serves important functions in synaptic and network activity, the regulation of circadian rhythms, and arousal. However, it is important to note that because of copper's ability to redox cycle and generate reactive species, cellular levels of the metal must be tightly regulated to meet cellular needs while avoiding copper-induced oxidative stress. Therefore, it is essential that the intricate system of copper transporters, exporters, copper chaperones and copper trafficking proteins function properly and in coordinate fashion. Indeed, disorders of copper metabolism such as Menkes disease and Wilson disease, as well as diseases linked to dysfunction of copper-requiring enzymes, such as SOD1-linked amyotrophic lateral sclerosis, demonstrate the dramatic neurological consequences of altered copper homeostasis. In this review, we explore the physiological importance of copper in the nervous system as well as pathologies related to improper copper handling.
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Affiliation(s)
- Jenna Gale
- Department of Neurobiology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Elias Aizenman
- Department of Neurobiology and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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2
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Fan YG, Wu TY, Zhao LX, Jia RJ, Ren H, Hou WJ, Wang ZY. From zinc homeostasis to disease progression: Unveiling the neurodegenerative puzzle. Pharmacol Res 2024; 199:107039. [PMID: 38123108 DOI: 10.1016/j.phrs.2023.107039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/16/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
Zinc is a crucial trace element in the human body, playing a role in various physiological processes such as oxidative stress, neurotransmission, protein synthesis, and DNA repair. The zinc transporters (ZnTs) family members are responsible for exporting intracellular zinc, while Zrt- and Irt-like proteins (ZIPs) are involved in importing extracellular zinc. These processes are essential for maintaining cellular zinc homeostasis. Imbalances in zinc metabolism have been linked to the development of neurodegenerative diseases. Disruptions in zinc levels can impact the survival and activity of neurons, thereby contributing to the progression of neurodegenerative diseases through mechanisms like cell apoptosis regulation, protein phase separation, ferroptosis, oxidative stress, and neuroinflammation. Therefore, conducting a systematic review of the regulatory network of zinc and investigating the relationship between zinc dysmetabolism and neurodegenerative diseases can enhance our understanding of the pathogenesis of these diseases. Additionally, it may offer new insights and approaches for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Yong-Gang Fan
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China.
| | - Ting-Yao Wu
- First Affiliated Hospital of Jinzhou Medical University, Jinzhou 121000, China
| | - Ling-Xiao Zhao
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Rong-Jun Jia
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Hang Ren
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Wen-Jia Hou
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China
| | - Zhan-You Wang
- Key Laboratory of Medical Cell Biology of Ministry of Education, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China.
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3
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Lim L, Kang J, Song J. Extreme diversity of 12 cations in folding ALS-linked hSOD1 unveils novel hSOD1-dependent mechanisms for Fe 2+/Cu 2+-induced cytotoxicity. Sci Rep 2023; 13:19868. [PMID: 37964005 PMCID: PMC10645853 DOI: 10.1038/s41598-023-47338-8] [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: 09/04/2023] [Accepted: 11/12/2023] [Indexed: 11/16/2023] Open
Abstract
153-Residue copper-zinc superoxide dismutase 1 (hSOD1) is the first gene whose mutation was linked to FALS. To date, > 180 ALS-causing mutations have been identified within hSOD1, yet the underlying mechanism still remains mysterious. Mature hSOD1 is exceptionally stable constrained by a disulfide bridge to adopt a Greek-key β-barrel fold that accommodates copper/zinc cofactors. Conversely, nascent hSOD1 is unfolded and susceptible to aggregation and amyloid formation, requiring Zn2+ to initiate folding to a coexistence of folded and unfolded states. Recent studies demonstrate mutations that disrupt Zn2+-binding correlate with their ability to form toxic aggregates. Therefore, to decode the role of cations in hSOD1 folding provides not only mechanistic insights, but may bear therapeutic implications for hSOD1-linked ALS. Here by NMR, we visualized the effect of 12 cations: 8 essential for humans (Na+, K+, Ca2+, Zn2+, Mg2+, Mn2+, Cu2+, Fe2+), 3 mimicking zinc (Ni2+, Cd2+, Co2+), and environmentally abundant Al3+. Surprisingly, most cations, including Zn2+-mimics, showed negligible binding or induction for folding of nascent hSOD1. Cu2+ exhibited extensive binding to the unfolded state but led to severe aggregation. Unexpectedly, for the first time Fe2+ was deciphered to have Zn2+-like folding-inducing capacity. Zn2+ was unable to induce folding of H80S/D83S-hSOD1, while Fe2+ could. In contrast, Zn2+ could trigger folding of G93A-hSOD1, but Fe2+ failed. Notably, pre-existing Fe2+ disrupted the Zn2+-induced folding of G93A-hSOD1. Comparing with the ATP-induced folded state, our findings delineate that hSOD1 maturation requires: (1) intrinsic folding capacity encoded by the sequence; (2) specific Zn2+-coordination; (3) disulfide formation and Cu-load catalyzed by hCCS. This study unveils a previously-unknown interplay of cations in governing the initial folding of hSOD1, emphasizing the pivotal role of Zn2+ in hSOD1-related ALS and implying new hSOD1-dependent mechanisms for Cu2+/Fe2+-induced cytotoxicity, likely relevant to aging and other diseases.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jian Kang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 119260, Republic of Singapore.
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4
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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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Wang Z, Jin D, Zhou S, Dong N, Ji Y, An P, Wang J, Luo Y, Luo J. Regulatory roles of copper metabolism and cuproptosis in human cancers. Front Oncol 2023; 13:1123420. [PMID: 37035162 PMCID: PMC10076572 DOI: 10.3389/fonc.2023.1123420] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Copper is an essential micronutrient for human body and plays a vital role in various biological processes including cellular respiration and free radical detoxification. Generally, copper metabolism in the body is in a stable state, and there are specific mechanisms to regulate copper metabolism and maintain copper homeostasis. Dysregulation of copper metabolism may have a great connection with various types of diseases, such as Wilson disease causing copper overload and Menkes disease causing copper deficiency. Cancer presents high mortality rates in the world due to the unlimited proliferation potential, apoptosis escape and immune escape properties to induce organ failure. Copper is thought to have a great connection with cancer, such as elevated levels in cancer tissue and serum. Copper also affects tumor progression by affecting angiogenesis, metastasis and other processes. Notably, cuproptosis is a novel form of cell death that may provide novel targeting strategies for developing cancer therapy. Copper chelators and copper ionophores are two copper coordinating compounds for the treatment of cancer. This review will explore the relationship between copper metabolism and cancers, and clarify copper metabolism and cuproptosis for cancer targeted therapy.
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Affiliation(s)
- Zhe Wang
- Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Dekui Jin
- Department of General Practice, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Shuaishuai Zhou
- Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Niujing Dong
- China Astronaut Research and Training Center, Beijing, China
| | - Yuting Ji
- Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Peng An
- Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Jiaping Wang
- China Astronaut Research and Training Center, Beijing, China
- *Correspondence: Jiaping Wang, ; Yongting Luo, ; Junjie Luo,
| | - Yongting Luo
- Department of Nutrition and Health, China Agricultural University, Beijing, China
- *Correspondence: Jiaping Wang, ; Yongting Luo, ; Junjie Luo,
| | - Junjie Luo
- Department of Nutrition and Health, China Agricultural University, Beijing, China
- *Correspondence: Jiaping Wang, ; Yongting Luo, ; Junjie Luo,
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Basith S, Manavalan B, Lee G. Amyotrophic lateral sclerosis disease-related mutations disrupt the dimerization of superoxide dismutase 1 - A comparative molecular dynamics simulation study. Comput Biol Med 2022; 151:106319. [PMID: 36446187 DOI: 10.1016/j.compbiomed.2022.106319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/31/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022]
Abstract
More than 150 genes are involved in amyotrophic lateral sclerosis (ALS), with superoxide dismutase 1 (SOD1) being one of the most studied. Mutations in SOD1 gene, which encodes the enzyme SOD1 is the second most prevalent and studied cause of familial ALS. SOD1 is a ubiquitous, homodimeric metalloenzyme that forms a critical component of the cellular defense against reactive oxygen species. Several mutations in the SOD1 enzyme cause misfolding, dimerization instability, and increased aggregate formation in ALS. However, there is a lack of information on the dimerization of SOD1 monomers and the mechanistic underpinnings on how the pathogenic mutations disrupt the dimerization mechanism. Here, we presented microsecond-scale molecular dynamics (MD) simulations to unravel how interface-based mutations compromise SOD1 dimerization and provide mechanistic understanding into the corresponding process using WT and three interface-based mutant systems (A4V, T54R, and I113T). Structural stability analysis showed that the mutant systems displayed disparate variations in the catalytic sites which may directly alter the stability and activity of the SOD1 enzyme. Based on the dynamic network analysis and principal component analysis, it has been identified that the mutations weakened the correlated motions along the dimer interface and altered the protein conformational behavior, thus weakening the stability of dimer formation. Moreover, the simulation results identified crucial residues such as G51, D52, G114, I151, and Q153 in establishing the dimerization interaction network, which were weakened or absent in the presence of interfacial mutants. Surface potential analysis on mutant systems also displayed changes in the dimerization potential, thus showing the unfavorable dimer formation. Furthermore, network analysis identified the hotspot residues necessary for SOD1 signal transduction which were surprisingly found in the catalytic sites rather than the anticipated dimerization interface.
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Affiliation(s)
- Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Balachandran Manavalan
- Computational Biology and Bioinformatics Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea.
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7
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Obukhova LM, Evdokimov II, Medyanik IA, Orlinskaya NY, Grishin AS, Babintsev VE, Barinov YA, Kontorshchikov MM, Gorshkova TN, Lazukin VF. Prospects for the use of blood elemental status to assess the molecular genetic profile of gliomas. Klin Lab Diagn 2022; 67:497-503. [PMID: 36099457 DOI: 10.51620/0869-2084-2022-67-9-497-503] [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] [Indexed: 06/15/2023]
Abstract
It has been established that blood element homeostasis is related to gliomagenesis which increases the attractiveness of the analysis of its components as a promising preoperative mediated characteristics of the molecular genetic profile of gliomas. The aim of this work is to analyze the relationship between mineral metabolism parameters and immunohistochemical characteristics of glial tumors and evaluate the clinical significance of blood element homeostasis analysis for preoperative assessment of the molecular profile of gliomas. The levels of cancer specific markers MGMT, Ki-67, p-53, IDH1 were determined immunohistochemically using the corresponding antibody clones. Micronutrient levels were analyzed by inductively coupled plasma atomic emission spectrometry recalculating the results per 1 g of protein which was determined by the Lowry method. The data on cancer-specific marker levels obtained in primary brain tumors (20) and in blood plasma of gliomas patients (20) and practically healthy subjects (5) were compared using a number of statistical programs. We found significant differences in the levels of sodium, potassium, zinc and copper depending on the value of the mitotic index Ki-67 and IDH1 isocitrate dehydrogenase gene mutation. For the first time, a significant correlation showing the consistency between the level of glial tumor cancer-specific markers and blood mineral metabolism was observed. The revealed correlations provide new insights into understanding of gliomagenesis mechanisms and can be used as a predictive preoperative assessment of molecular genetic markers of gliomas.
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Affiliation(s)
- Larisa Mikhailovna Obukhova
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - I I Evdokimov
- Federal Budgetary Scientific Institution G.G. Devyatykh Institute of Chemistry High-Purity Chemistry of the Russian Academy of Sciences
| | - I A Medyanik
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - N Yu Orlinskaya
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - A S Grishin
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - V E Babintsev
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - Yu A Barinov
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - M M Kontorshchikov
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
| | - T N Gorshkova
- Federal State-Funded Healthcare Institution "Privolzhsky District Medical Center" of Federal and Biological Agency of Russia
| | - V F Lazukin
- Federal State Budgetary Educational Institution of Higher Educational "Privolzhsky Research Medical University" of the Ministry of Health of the Russian Federation
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Wyszkowska J, Borowik A, Zaborowska M, Kucharski J. Mitigation of the Adverse Impact of Copper, Nickel, and Zinc on Soil Microorganisms and Enzymes by Mineral Sorbents. MATERIALS 2022; 15:ma15155198. [PMID: 35955133 PMCID: PMC9369485 DOI: 10.3390/ma15155198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 02/02/2023]
Abstract
Despite numerous studies on the influence of heavy metals on soil health, the search for effective, eco-friendly, and economically viable remediation substances is far from over. This encouraged us to carry out a study under strictly controlled conditions to test the effects of Cu2+, Ni2+, and Zn2+ added to soil in amounts of 150 mg·kg−1 d.m. of soil on the soil microbiome, on the activity of two oxidoreductases and five hydrolases, and on the growth and development of the sunflower Helianthus annunus L. The remediation substances were a molecular sieve, halloysite, sepiolite, expanded clay, zeolite, and biochar. It has been demonstrated that the most severe turbulences in the soil microbiome, its activity, and the growth of Helianthus annunus L. were caused by Ni2+, followed by Cu2+, and the mildest negative effect was produced by Zn2+. The adverse impact of heavy metals on the soil microbiome and its activity was alleviated by the applied sorbents. Their application also contributed to the increased biomass of plants, which is significant for the successful phytoextraction of these metals from soil. Irrespective of which property was analysed, sepiolite can be recommended for the remediation of soil polluted with Ni2+ and zeolite—for soil polluted with Cu2+ and Zn2+. Both sorbents mitigated to the highest degree disturbances caused by the tested metals in the soil environment.
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Garg P, Semmler S, Baudouin C, Velde CV, Plotkin SS. Misfolding-Associated Exposure of Natively Buried Residues in Mutant SOD1 Facilitates Binding to TRAF6. J Mol Biol 2022; 434:167697. [PMID: 35753527 DOI: 10.1016/j.jmb.2022.167697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/14/2022] [Accepted: 06/18/2022] [Indexed: 10/17/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease primarily impacting motor neurons. Mutations in superoxide dismutase 1 (SOD1) are the second most common cause of familial ALS. Several of these mutations lead to misfolding or toxic gain of function in the SOD1 protein. Recently, we reported that misfolded SOD1 interacts with TNF receptor-associated factor 6 (TRAF6) in the SOD1G93A rat model of ALS. Further, we showed in cultured cells that several mutant SOD1 proteins, but not wildtype SOD1 protein, interact with TRAF6 via the MATH domain. Here, we sought to uncover the structural details of this interaction through molecular dynamics (MD) simulations of a dimeric model system, coarse grained using the AWSEM force field. We used direct MD simulations to identify buried residues, and predict binding poses by clustering frames from the trajectories. Metadynamics simulations were also used to deduce preferred binding regions on the protein surfaces from the potential of the mean force in orientation space. Well-folded SOD1 was found to bind TRAF6 via co-option of its native homodimer interface. However, if loops IV and VII of SOD1 were disordered, as typically occurs in the absence of stabilizing Zn2+ ion binding, these disordered loops now participated in novel interactions with TRAF6. On TRAF6, multiple interaction hot-spots were distributed around the equatorial region of the MATH domain beta barrel. Expression of TRAF6 variants with mutations in this region in cultured cells demonstrated that TRAF6T475 facilitates interaction with different SOD1 mutants. These findings contribute to our understanding of the disease mechanism and uncover potential targets for the development of therapeutics.
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Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sabrina Semmler
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada; Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada
| | - Charlotte Baudouin
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada; Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada; Department of Neurosciences, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.
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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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Baziyar P, Seyedalipour B, Hosseinkhani S. Zinc binding loop mutations of hSOD1 promote amyloid fibrils under physiological conditions: Implications for initiation of amyotrophic lateral sclerosis. Biochimie 2022; 199:170-181. [DOI: 10.1016/j.biochi.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/24/2022] [Accepted: 05/03/2022] [Indexed: 12/25/2022]
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Hsueh SCC, Nijland M, Peng X, Hilton B, Plotkin SS. First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants. Front Mol Biosci 2022; 9:845013. [PMID: 35402516 PMCID: PMC8988244 DOI: 10.3389/fmolb.2022.845013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
Cu,Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the stability of the protein. Monomerization increases the likelihood of SOD1 misfolding into conformations associated with aggregation, cellular toxicity, and neuronal death in familial amyotrophic lateral sclerosis (fALS). The ubiquity of disease-associated mutations throughout the primary sequence of SOD1 suggests an important role of physicochemical processes, including monomerization of SOD1, in the pathology of the disease. Herein, we use a first-principles statistical mechanics method to systematically calculate the free energy of dimer binding for SOD1 using molecular dynamics, which involves sequentially computing conformational, orientational, and separation distance contributions to the binding free energy. We consider the effects of two ALS-associated mutations in SOD1 protein on dimer stability, A4V and D101N, as well as the role of metal binding and disulfide bond formation. We find that the penalty for dimer formation arising from the conformational entropy of disordered loops in SOD1 is significantly larger than that for other protein-protein interactions previously considered. In the case of the disulfide-reduced protein, this leads to a bound complex whose formation is energetically disfavored. Somewhat surprisingly, the loop free energy penalty upon dimerization is still significant for the holoprotein, despite the increased structural order induced by the bound metal cations. This resulted in a surprisingly modest increase in dimer binding free energy of only about 1.5 kcal/mol upon metalation of the protein, suggesting that the most significant stabilizing effects of metalation are on folding stability rather than dimer binding stability. The mutant A4V has an unstable dimer due to weakened monomer-monomer interactions, which are manifested in the calculation by a separation free energy surface with a lower barrier. The mutant D101N has a stable dimer partially due to an unusually rigid β-barrel in the free monomer. D101N also exhibits anticooperativity in loop folding upon dimerization. These computational calculations are, to our knowledge, the most quantitatively accurate calculations of dimer binding stability in SOD1 to date.
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Affiliation(s)
- Shawn C. C. Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Mark Nijland
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, Netherlands
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, China
| | - Benjamin Hilton
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Imperial College London, London, United Kingdom
| | - Steven S. Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
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Folarin OR, Olopade FE, Olopade JO. Essential Metals in the Brain and the Application of Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry for their Detection. Niger J Physiol Sci 2021; 36:123-147. [PMID: 35947740 DOI: 10.54548/njps.v36i2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 06/15/2023]
Abstract
Metals are natural component of the ecosystem present throughout the layers of atmosphere; their abundant expression in the brain indicates their importance in the central nervous system (CNS). Within the brain tissue, their distribution is highly compartmentalized, the pattern of which is determined by their primary roles. Bio-imaging of the brain to reveal spatial distribution of metals within specific regions has provided a unique understanding of brain biochemistry and architecture, linking both the structures and the functions through several metal mediated activities. Bioavailability of essential trace metal is needed for normal brain function. However, disrupted metal homeostasis can influence several biochemical pathways in different fields of metabolism and cause characteristic neurological disorders with a typical disease process usually linked with aberrant metal accumulations. In this review we give a brief overview of roles of key essential metals (Iron, Copper and Zinc) including their molecular mechanisms and bio-distribution in the brain as well as their possible involvement in the pathogenesis of related neurodegenerative diseases. In addition, we also reviewed recent applications of Laser Ablation Inductively Couple Plasma Mass Spectrophotometry (LA-ICP-MS) in the detection of both toxic and essential metal dyshomeostasis in neuroscience research and other related brain diseases.
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14
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Azizian H, Forooghian S, Amanlou A, Pérez-Sánchez H, Amanlou M. Phenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation. J Biomol Struct Dyn 2021; 40:7070-7083. [PMID: 33663349 DOI: 10.1080/07391102.2021.1893819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Superoxide dismutases (SODs) are regarded as important antioxidants for protecting cells against damage arising from oxidative stress. Much research is focused on finding new chemicals with an ability to boost human SOD activity. In the research described herein a structure-based approach was used to identify new human Cu-Zn superoxide dismutase (SOD1) modulators based on previously reported plasmodium falciparum iron SOD inhibitors using induced fit docking and molecular dynamic (MD) protocols. The compound with the highest docking binding energy was selected for further structure simplification followed by structural similarity and MD in order to find a new activator/inhibitor scaffold of the SOD1 enzyme. According to the docking survey of the mentioned series, 1,4-bis(3-(1,4,8-trichloro-10Hphenothiazin-10-yl) propyl) piperazine (DS88) was the top scoring compound interacting with the SOD1 active site channel. Following structure simplification and similarity search, the most promising scaffold which is closely related to the phenothiazine antipsychotic class, was identified. Compared with the normal blood SOD1 activity, the percent of O2 production increased with trifluoperazine, while it decreased with the chlorpromazine. The molecular dynamic investigation shows that trifluoperazine exerts its SOD1 activating effect by stabilizing electrostatic loop while chlorpromazine employs SOD1 inhibition activity through repositioning of the electrostatic loop and increasing its distance from the catalytic metal site which diminished substrate specificity and catalytic activity of the SOD1 enzyme. The results identified the preferred region, orientation, and types of interaction for each activator or inhibitor compound.
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Affiliation(s)
- Homa Azizian
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran Iran
| | - Simin Forooghian
- Faculty of Basic Science, Department of Biology, Tehran Payame Noor University, Tehran, Iran
| | - Arash Amanlou
- Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Murcia, Spain
| | - Massoud Amanlou
- Faculty of Pharmacy, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran.,Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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15
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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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16
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George S, Abrahamse H. Redox Potential of Antioxidants in Cancer Progression and Prevention. Antioxidants (Basel) 2020; 9:antiox9111156. [PMID: 33233630 PMCID: PMC7699713 DOI: 10.3390/antiox9111156] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
The benevolent and detrimental effects of antioxidants are much debated in clinical trials and cancer research. Several antioxidant enzymes and molecules are overexpressed in oxidative stress conditions that can damage cellular proteins, lipids, and DNA. Natural antioxidants remove excess free radical intermediates by reducing hydrogen donors or quenching singlet oxygen and delaying oxidative reactions in actively growing cancer cells. These reducing agents have the potential to hinder cancer progression only when administered at the right proportions along with chemo-/radiotherapies. Antioxidants and enzymes affect signal transduction and energy metabolism pathways for the maintenance of cellular redox status. A decline in antioxidant capacity arising from genetic mutations may increase the mitochondrial flux of free radicals resulting in misfiring of cellular signalling pathways. Often, a metabolic reprogramming arising from these mutations in metabolic enzymes leads to the overproduction of so called ’oncometabolites’ in a state of ‘pseudohypoxia’. This can inactivate several of the intracellular molecules involved in epigenetic and redox regulations, thereby increasing oxidative stress giving rise to growth advantages for cancerous cells. Undeniably, these are cell-type and Reactive Oxygen Species (ROS) specific, which is manifested as changes in the enzyme activation, differences in gene expression, cellular functions as well as cell death mechanisms. Photodynamic therapy (PDT) using light-activated photosensitizing molecules that can regulate cellular redox balance in accordance with the changes in endogenous ROS production is a solution for many of these challenges in cancer therapy.
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Affiliation(s)
- Sajan George
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India;
- Laser Research Centre, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
| | - Heidi Abrahamse
- Laser Research Centre, University of Johannesburg, Doornfontein, Johannesburg 2028, South Africa
- Correspondence:
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17
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Molecular analysis and bioinformatic characterization of cooper, zinc-superoxide dismutase (Cu/Zn-sod) gene of Caiman latirostris. Mol Biol Rep 2020; 47:8849-8857. [DOI: 10.1007/s11033-020-05937-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/20/2020] [Indexed: 01/06/2023]
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18
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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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19
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Tompa DR, Muthusamy S, Srikanth S, Kadhirvel S. Molecular dynamics of far positioned surface mutations of Cu/Zn SOD1 promotes altered structural stability and metal-binding site: Structural clues to the pathogenesis of amyotrophic lateral sclerosis. J Mol Graph Model 2020; 100:107678. [PMID: 32768728 DOI: 10.1016/j.jmgm.2020.107678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/18/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022]
Abstract
Cu/Zn superoxide dismutase (SOD1) mutations are associated to the motor neuron disorder, amyotrophic lateral sclerosis (ALS), which is characterized by aggregates of the misfolded proteins. The distribution of mutations all over the three-dimensional structure of SOD1 makes it complex to determine the exact molecular mechanism underlying SOD1 destabilization and the associated ALS pathology. In this study, we have examined structure and dynamics of SOD1 protein upon two ALS associated point mutations at the surface residue Glu100 (E100G and E100K), which is located far from the Cu and Zn sites and dimer interface. The molecular dynamics simulations were performed for these mutants for 50ns using GROMACS package. Our results indicate that the mutations result in structural destabilization by affecting the gate keeping role of Glu100 and loss of electrostatic interactions on the protein surface which stabilizes the β-barrel structure of the native form. Further, these mutations could increase the fluctuations in the zinc-binding loop (loop IV), primarily due to loss of hydrogen bond between Asp101 and Arg79. The relaxed conformation of Arg79 further affects the native conformation of His80 and Asp83, that results in altered zinc site geometry and the structure of the substrate channel. Our results clearly suggest that, similar to the mutations located at metal sites/dimer interface/disulfide regions, the mutations at the far positioned site (Glu100) also induce significant conformational changes that could affect the metallation and structure of SOD1 molecule, resulting in formation of toxic intermediate species that cause ALS.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Sureshan Muthusamy
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Srimari Srikanth
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India.
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20
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Malakooti N, Roberts B, Pritchard MA, Volitakis I, Kim RC, Lott IT, McLean CA, Finkelstein DI, Adlard PA. Characterising the brain metalloproteome in Down syndrome patients with concomitant Alzheimer's pathology. Metallomics 2020; 12:114-132. [PMID: 31764918 DOI: 10.1039/c9mt00196d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Down syndrome (DS) is a common intellectual disability, with an incidence of 1 in 700 and is caused by trisomy 21. People with DS develop Alzheimer's disease (AD)-like neuropathology by the age of 40. As metal ion dyshomeostasis (particularly zinc, iron and copper) is one of the characteristics of AD and is believed to be involved in the pathogenesis of disease, we reasoned that it may also be altered in DS. Thus, we used inductively coupled plasma mass spectrometry to examine metal levels in post-mortem brain tissue from DS individuals with concomitant AD pathology. Size exclusion-ICPMS was also utilised to characterise the metalloproteome in these cases. We report here for the first time that iron levels were higher in a number of regions in the DS brain, including the hippocampus (40%), frontal cortex (100%) and temporal cortex (34%), compared to controls. Zinc and copper were also elevated (both 29%) in the DS frontal cortex, but zinc was decreased (23%) in the DS temporal cortex. Other elements were also examined, a number of which also showed disease-specific changes. The metalloproteomic profile in the DS brain was also different to that in the controls. These data suggest that metals and metal:protein interactions are dysregulated in the DS brain which, given the known role of metals in neurodegeneration and AD, is likely to contribute to the pathogenesis of disease. Interrogation of the underlying cellular mechanisms and consequences of this failure in metal ion homeostasis, and the specific contributions of the individual DS and AD phenotypes to these changes, should be explored.
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Affiliation(s)
- Nakisa Malakooti
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, and The Melbourne Dementia Research Centre, Parkville, 3010, Victoria, Australia.
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21
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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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22
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Chowdhury S, Sen S, Banerjee A, Uversky VN, Maulik U, Chattopadhyay K. Network mapping of the conformational heterogeneity of SOD1 by deploying statistical cluster analysis of FTIR spectra. Cell Mol Life Sci 2019; 76:4145-4154. [PMID: 31011770 PMCID: PMC11105373 DOI: 10.1007/s00018-019-03108-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 02/02/2023]
Abstract
A crucial contribution to the heterogeneity of the conformational landscape of a protein comes from the way an intermediate relates to another intermediate state in its journey from the unfolded to folded or misfolded form. Unfortunately, it is extremely hard to decode this relatedness in a quantifiable manner. Here, we developed an application of statistical cluster analyses to explore the conformational heterogeneity of a metalloenzyme, human cytosolic copper-zinc superoxide dismutase (SOD1), using the inputs from infrared spectroscopy. This study provides a quantifiable picture of how conformational information at one particular site (for example, the copper-binding pocket) is related to the information at the second site (for example, the zinc-binding pocket), and how this relatedness is transferred to the global conformational information of the protein. The distance outputs were used to quantitatively generate a network capturing the folding sub-stages of SOD1.
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Affiliation(s)
- Sourav Chowdhury
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India
- Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Sagnik Sen
- Department of Computer Science, Jadavpur University, Kolkata, 700 032, India
| | - Amrita Banerjee
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India
- Department of Chemistry, Hiralal Mazumdar Memorial College for Women, Dakshineswar, Kolkata, 700035, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290, Moscow Region, Russia
| | - Ujjwal Maulik
- Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700032, India.
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23
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Tompa DR, Kadhirvel S. Far positioned ALS associated mutants of Cu/Zn SOD forms partially metallated, destabilized misfolding intermediates. Biochem Biophys Res Commun 2019; 516:494-499. [PMID: 31230748 DOI: 10.1016/j.bbrc.2019.06.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 11/18/2022]
Abstract
Loss of stability of proteins is associated with their misfolding and aggregation which results in disease. Despite of the higher stability of Cu/Zn superoxide dismutase (SOD1), the point mutations destabilize its structure, results in oligomerization and the aggregation of SOD1 which is closely associated with the motor neuron disorder, amyotrophic lateral sclerosis. In the present study, we analyzed the role of two SOD1 mutants V14G and E100G which are located far away from the metal sites, dimer interface and disulfide region. The SOD1 mutants were recombinantly produced and their activity, structure and stability were investigated using biochemical methods, CD and DSC methods. In comparison with wild-type SOD1, the mutants exhibited reduced activity and the CD data showed comparable secondary structures composition. However, the stability studies using chemical and thermal denaturation methods showed the mutants are destabilized. Interestingly, our DSC data strongly suggested the destabilization of the mutants is due to the partial metalation of Cu/Zn ions. This observation emphasizes that although the mutations V14G and E100G are located away from the metal sites, they could affect the metal binding similar to metal binding region mutants, which are more susceptible to misfold and aggregate.
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Affiliation(s)
- Dharma Rao Tompa
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India
| | - Saraboji Kadhirvel
- Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, 613401, Tamil Nadu, India.
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24
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Ighodaro O, Akinloye O. First line defence antioxidants-superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX): Their fundamental role in the entire antioxidant defence grid. ALEXANDRIA JOURNAL OF MEDICINE 2019. [DOI: 10.1016/j.ajme.2017.09.001] [Citation(s) in RCA: 661] [Impact Index Per Article: 132.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- O.M. Ighodaro
- Department of Biochemistry, Faculty of Sciences, Lead City University, Ibadan, Nigeria
- Department of Biochemistry, College of Biosciences, Federal University of Agriculture, Abeokuta (FUNAAB), Abeokuta, Nigeria
| | - O.A. Akinloye
- Department of Biochemistry, College of Biosciences, Federal University of Agriculture, Abeokuta (FUNAAB), Abeokuta, Nigeria
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25
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Su TA, Shihadih DS, Cao W, Detomasi TC, Heffern MC, Jia S, Stahl A, Chang CJ. A Modular Ionophore Platform for Liver-Directed Copper Supplementation in Cells and Animals. J Am Chem Soc 2018; 140:13764-13774. [PMID: 30351140 PMCID: PMC6465169 DOI: 10.1021/jacs.8b08014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Copper deficiency is implicated in a variety of genetic, neurological, cardiovascular, and metabolic diseases. Current approaches for addressing copper deficiency rely on generic copper supplementation, which can potentially lead to detrimental off-target metal accumulation in unwanted tissues and subsequently trigger oxidative stress and damage cascades. Here we present a new modular platform for delivering metal ions in a tissue-specific manner and demonstrate liver-targeted copper supplementation as a proof of concept of this strategy. Specifically, we designed and synthesized an N-acetylgalactosamine-functionalized ionophore, Gal-Cu(gtsm), to serve as a copper-carrying "Trojan Horse" that targets liver-localized asialoglycoprotein receptors (ASGPRs) and releases copper only after being taken up by cells, where the reducing intracellular environment triggers copper release from the ionophore. We utilized a combination of bioluminescence imaging and inductively coupled plasma mass spectrometry assays to establish ASGPR-dependent copper accumulation with this reagent in both liver cell culture and mouse models with minimal toxicity. The modular nature of our synthetic approach presages that this platform can be expanded to deliver a broader range of metals to specific cells, tissues, and organs in a more directed manner to treat metal deficiency in disease.
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Affiliation(s)
- Timothy A. Su
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Diyala S. Shihadih
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA 94720
| | - Wendy Cao
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Tyler C. Detomasi
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Marie C. Heffern
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Shang Jia
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Andreas Stahl
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA 94720
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
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26
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Sirabella R, Valsecchi V, Anzilotti S, Cuomo O, Vinciguerra A, Cepparulo P, Brancaccio P, Guida N, Blondeau N, Canzoniero LMT, Franco C, Amoroso S, Annunziato L, Pignataro G. Ionic Homeostasis Maintenance in ALS: Focus on New Therapeutic Targets. Front Neurosci 2018; 12:510. [PMID: 30131665 PMCID: PMC6090999 DOI: 10.3389/fnins.2018.00510] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/05/2018] [Indexed: 01/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is one of the most threatening neurodegenerative disease since it causes muscular paralysis for the loss of Motor Neurons in the spinal cord, brainstem and motor cortex. Up until now, no effective pharmacological treatment is available. Two forms of ALS have been described so far: 90% of the cases presents the sporadic form (sALS) whereas the remaining 10% of the cases displays the familiar form (fALS). Approximately 20% of fALS is associated with inherited mutations in the Cu, Zn-superoxide dismutase 1 (SOD1) gene. In the last decade, ionic homeostasis dysregulation has been proposed as the main trigger of the pathological cascade that brings to motor-neurons loss. In the light of these premises, the present review will analyze the involvement in ALS pathophysiology of the most well studied metal ions, i.e., calcium, sodium, iron, copper and zinc, with particular focus to the role of ionic channels and transporters able to contribute in the regulation of ionic homeostasis, in order to propose new putative molecular targets for future therapeutic strategies to ameliorate the progression of this devastating neurodegenerative disease.
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Affiliation(s)
- Rossana Sirabella
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy.,Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Valbonne, France
| | - Valeria Valsecchi
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
| | | | - Ornella Cuomo
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Antonio Vinciguerra
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Pasquale Cepparulo
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Paola Brancaccio
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
| | | | - Nicolas Blondeau
- Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Valbonne, France
| | - Lorella M T Canzoniero
- Division of Pharmacology, Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Cristina Franco
- Division of Pharmacology, Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Salvatore Amoroso
- Department of Neuroscience, Università Politecnica delle Marche, Ancona, Italy
| | | | - Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Naples, Italy
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27
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Robinett NG, Peterson RL, Culotta VC. Eukaryotic copper-only superoxide dismutases (SODs): A new class of SOD enzymes and SOD-like protein domains. J Biol Chem 2017; 293:4636-4643. [PMID: 29259135 DOI: 10.1074/jbc.tm117.000182] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The copper-containing superoxide dismutases (SODs) represent a large family of enzymes that participate in the metabolism of reactive oxygen species by disproportionating superoxide anion radical to oxygen and hydrogen peroxide. Catalysis is driven by the redox-active copper ion, and in most cases, SODs also harbor a zinc at the active site that enhances copper catalysis and stabilizes the protein. Such bimetallic Cu,Zn-SODs are widespread, from the periplasm of bacteria to virtually every organelle in the human cell. However, a new class of copper-containing SODs has recently emerged that function without zinc. These copper-only enzymes serve as extracellular SODs in specific bacteria (i.e. Mycobacteria), throughout the fungal kingdom, and in the fungus-like oomycetes. The eukaryotic copper-only SODs are particularly unique in that they lack an electrostatic loop for substrate guidance and have an unusual open-access copper site, yet they can still react with superoxide at rates limited only by diffusion. Copper-only SOD sequences similar to those seen in fungi and oomycetes are also found in the animal kingdom, but rather than single-domain enzymes, they appear as tandem repeats in large polypeptides we refer to as CSRPs (copper-only SOD-repeat proteins). Here, we compare and contrast the Cu,Zn versus copper-only SODs and discuss the evolution of copper-only SOD protein domains in animals and fungi.
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Affiliation(s)
- Natalie G Robinett
- Department of Biochemistry and Molecular Biology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Ryan L Peterson
- Department of Biochemistry and Molecular Biology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Valeria C Culotta
- Department of Biochemistry and Molecular Biology, The Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205.
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28
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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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29
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Zinc Signal in Brain Diseases. Int J Mol Sci 2017; 18:ijms18122506. [PMID: 29168792 PMCID: PMC5751109 DOI: 10.3390/ijms18122506] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
The divalent cation zinc is an integral requirement for optimal cellular processes, whereby it contributes to the function of over 300 enzymes, regulates intracellular signal transduction, and contributes to efficient synaptic transmission in the central nervous system. Given the critical role of zinc in a breadth of cellular processes, its cellular distribution and local tissue level concentrations remain tightly regulated via a series of proteins, primarily including zinc transporter and zinc import proteins. A loss of function of these regulatory pathways, or dietary alterations that result in a change in zinc homeostasis in the brain, can all lead to a myriad of pathological conditions with both acute and chronic effects on function. This review aims to highlight the role of zinc signaling in the central nervous system, where it may precipitate or potentiate diverse issues such as age-related cognitive decline, depression, Alzheimer's disease or negative outcomes following brain injury.
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30
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Riera‐Romo M. COMMD1: A Multifunctional Regulatory Protein. J Cell Biochem 2017; 119:34-51. [DOI: 10.1002/jcb.26151] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Mario Riera‐Romo
- Department of PharmacologyInstitute of Marine SciencesHavanaCuba
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31
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Cu II(atsm) improves the neurological phenotype and survival of SOD1 G93A mice and selectively increases enzymatically active SOD1 in the spinal cord. Sci Rep 2017; 7:42292. [PMID: 28205575 PMCID: PMC5304223 DOI: 10.1038/srep42292] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/09/2017] [Indexed: 11/23/2022] Open
Abstract
Ubiquitous expression of mutant Cu/Zn-superoxide dismutase (SOD1) selectively affects motor neurons in the central nervous system (CNS), causing the adult-onset degenerative disease amyotrophic lateral sclerosis (ALS). The CNS-specific impact of ubiquitous mutant SOD1 expression is recapitulated in transgenic mouse models of the disease. Here we present outcomes for the metallo-complex CuII(atsm) tested for therapeutic efficacy in mice expressing SOD1G93A on a mixed genetic background. Oral administration of CuII(atsm) delayed the onset of neurological symptoms, improved locomotive capacity and extended overall survival. Although the ALS-like phenotype of SOD1G93A mice is instigated by expression of the mutant SOD1, we show the improved phenotype of the CuII(atsm)-treated animals involves an increase in mature mutant SOD1 protein in the disease-affected spinal cord, where concomitant increases in copper and SOD1 activity are also evident. In contrast to these effects in the spinal cord, treating with CuII(atsm) had no effect in liver on either mutant SOD1 protein levels or its activity, indicating a CNS-selective SOD1 response to the drug. These data provide support for CuII(atsm) as a treatment option for ALS as well as insight to the CNS-selective effects of mutant SOD1.
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32
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Arundhoti Mandal AM, Maity A, Bag S, Bhattacharya P, Das AK, Basak A. Design and synthesis of dual probes for detection of metal ions by LALDI MS and fluorescence: application in Zn(ii) imaging in cells. RSC Adv 2017. [DOI: 10.1039/c6ra27302e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A Label-Assisted Laser Desorption/Ionization (LALDI) technique has recently been applied to the detection of metal ions through a time of flight (TOF) mass spectrometric measurement.
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Affiliation(s)
| | - Asim Maity
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Swarnendu Bag
- Centre for Healthcare Science and Technology
- Indian Institute of Engineering Science and Technology
- Shibpur-711103
- India
| | | | - Amit K. Das
- Department of Biotechnology
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Amit Basak
- Department of Chemistry
- Indian Institute of Technology
- Kharagpur 721302
- India
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33
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Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P. The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PLoS Comput Biol 2016; 12:e1005091. [PMID: 27564311 PMCID: PMC5001644 DOI: 10.1371/journal.pcbi.1005091] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/02/2016] [Indexed: 01/12/2023] Open
Abstract
Elucidating the precise molecular events altered by disease-causing genetic variants represents a major challenge in translational bioinformatics. To this end, many studies have investigated the structural and functional impact of amino acid substitutions. Most of these studies were however limited in scope to either individual molecular functions or were concerned with functional effects (e.g. deleterious vs. neutral) without specifically considering possible molecular alterations. The recent growth of structural, molecular and genetic data presents an opportunity for more comprehensive studies to consider the structural environment of a residue of interest, to hypothesize specific molecular effects of sequence variants and to statistically associate these effects with genetic disease. In this study, we analyzed data sets of disease-causing and putatively neutral human variants mapped to protein 3D structures as part of a systematic study of the loss and gain of various types of functional attribute potentially underlying pathogenic molecular alterations. We first propose a formal model to assess probabilistically function-impacting variants. We then develop an array of structure-based functional residue predictors, evaluate their performance, and use them to quantify the impact of disease-causing amino acid substitutions on catalytic activity, metal binding, macromolecular binding, ligand binding, allosteric regulation and post-translational modifications. We show that our methodology generates actionable biological hypotheses for up to 41% of disease-causing genetic variants mapped to protein structures suggesting that it can be reliably used to guide experimental validation. Our results suggest that a significant fraction of disease-causing human variants mapping to protein structures are function-altering both in the presence and absence of stability disruption. Identifying the molecular changes caused by mutations is a major challenge in understanding and treating human genetic disease. To address this problem, we have developed a wide range of profiling tools designed to predict specific types of functional site from protein 3D structures. We then apply these tools to data sets of inherited disease-associated and putatively neutral amino acid substitutions and estimate the relative contribution of the loss and gain of functional residues in disease. Our results suggest that alterations of molecular function are involved in a significant number of cases of human genetic disease and are over-represented as compared to putatively neutral variants. Additionally, we use experimental data to show that it is possible to computationally identify the loss of specific functional events in disease pathogenesis. Finally, our methodology can be used to reliably identify the potential molecular consequences of disease-causing genetic variants and hence prioritize experimental validation.
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Affiliation(s)
- Jose Lugo-Martinez
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Kymberleigh A. Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Shantanu Jain
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SDM); (PR)
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
- * E-mail: (SDM); (PR)
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34
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Eftekharzadeh B, Hyman BT, Wegmann S. Structural studies on the mechanism of protein aggregation in age related neurodegenerative diseases. Mech Ageing Dev 2016; 156:1-13. [PMID: 27005270 DOI: 10.1016/j.mad.2016.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/12/2016] [Accepted: 03/03/2016] [Indexed: 01/09/2023]
Abstract
The progression of many neurodegenerative diseases is assumed to be caused by misfolding of specific characteristic diseases related proteins, resulting in aggregation and fibril formation of these proteins. Protein misfolding associated age related diseases, although different in disease manifestations, share striking similarities. In all cases, one disease protein aggregates and loses its function or additionally shows a toxic gain of function. However, the clear link between these individual amyloid-like protein aggregates and cellular toxicity is often still uncertain. The similar features of protein misfolding and aggregation in this group of proteins, all involved in age related neurodegenerative diseases, results in high interest in characterization of their structural properties. We review here recent findings on structural properties of some age related disease proteins, in the context of their biological importance in disease.
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Affiliation(s)
- Bahareh Eftekharzadeh
- Department of Neurology, Massachusetts General Hospital and Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA.
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital and Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Susanne Wegmann
- Department of Neurology, Massachusetts General Hospital and Mass General Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
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35
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De Luka SR, Ilić AŽ, Janković S, Djordjevich DM, Ćirković S, Milovanovich ID, Stefanović S, Vesković-Moračanin S, Ristić-Djurović JL, Trbovich AM. Subchronic exposure to static magnetic field differently affects zinc and copper content in murine organs. Int J Radiat Biol 2016; 92:140-7. [PMID: 26850041 DOI: 10.3109/09553002.2016.1135266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PURPOSE Static magnetic fields (SMF) have been widely used in research, medicine and industry. Since zinc and copper play an important role in biological systems, we studied the effects of the subchronic continuous SMF exposure on their distribution in murine tissues. MATERIALS AND METHODS For 30 days, mice were exposed to inhomogeneous, vertical, downward or upward oriented SMF of 1 mT averaged intensity with spatial gradient in vertical direction. RESULTS SMF decreased the amount of copper and zinc in liver. In brain, zinc levels were increased and copper levels were decreased. In spleen, zinc content was reduced, while copper amount remained unchanged. CONCLUSIONS Subchronic exposure to SMF differently affected copper and zinc content in examined organs, and the changes were more pronounced for the downward oriented field. The outcome could be attributed to the protective, rather than the harmful effect of SMF.
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Affiliation(s)
- Silvio R De Luka
- a Department of Pathological Physiology, School of Medicine , University of Belgrade , Belgrade , Serbia
| | - Andjelija Ž Ilić
- b Institute of Physics , University of Belgrade , Zemun-Belgrade , Serbia
| | - Saša Janković
- c Institute of Meat Hygiene and Technology , Belgrade , Serbia
| | - Drago M Djordjevich
- a Department of Pathological Physiology, School of Medicine , University of Belgrade , Belgrade , Serbia
| | - Saša Ćirković
- b Institute of Physics , University of Belgrade , Zemun-Belgrade , Serbia
| | - Ivan D Milovanovich
- a Department of Pathological Physiology, School of Medicine , University of Belgrade , Belgrade , Serbia
| | | | | | | | - Alexander M Trbovich
- a Department of Pathological Physiology, School of Medicine , University of Belgrade , Belgrade , Serbia
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36
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Portbury SD, Yévenes LF, Adlard PA. Novel zinc-targeted therapeutic options for cognitive decline. FUTURE NEUROLOGY 2015. [DOI: 10.2217/fnl.15.40] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Zinc (Zn2+) is an essential metal in the brain, having critical roles in many proteins and cellular pathways, including synaptic plasticity and the normal functioning of long-term potentiation, the in vitro correlate of learning and memory. Importantly, several neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease, show alterations in Zn2+ metabolism that may be involved in the pathogenesis of these disorders. Therefore, the modulation of Zn2+ levels and/or distribution may prove an important target for the treatment of neurodegenerative diseases. This review aims to evaluate the current efforts directed at therapeutic Zn2+ modulation as it relates to disease-associated cognitive decline.
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Affiliation(s)
- Stuart D Portbury
- The Florey Institute of Neuroscience & Mental Health, Kenneth Myer Building, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Luz Fernanda Yévenes
- The Florey Institute of Neuroscience & Mental Health, Kenneth Myer Building, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
| | - Paul A Adlard
- The Florey Institute of Neuroscience & Mental Health, Kenneth Myer Building, The University of Melbourne, 30 Royal Parade, Parkville, Victoria 3052, Australia
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37
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McAllum EJ, Roberts BR, Hickey JL, Dang TN, Grubman A, Donnelly PS, Liddell JR, White AR, Crouch PJ. ZnII(atsm) is protective in amyotrophic lateral sclerosis model mice via a copper delivery mechanism. Neurobiol Dis 2015; 81:20-4. [DOI: 10.1016/j.nbd.2015.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 10/23/2022] Open
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38
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Montero-Morán GM, Sampedro JG, Saab-Rincón G, Cervantes-González MA, Huerta-Ocampo JÁ, De León-Rodríguez A, Barba de la Rosa AP. Biochemical and Molecular Characterization of a Novel Cu/Zn Superoxide Dismutase from Amaranthus hypochondriacus L.: an Intrinsically Disordered Protein. Appl Biochem Biotechnol 2015; 176:2328-45. [PMID: 26129702 DOI: 10.1007/s12010-015-1721-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
Abstract
A novel Cu/ZnSOD from Amaranthus hypochondriacus was cloned, expressed, and characterized. Nucleotide sequence analysis showed an open reading frame (ORF) of 456 bp, which was predicted to encode a 15.6-kDa molecular weight protein with a pI of 5.4. Structural analysis showed highly conserved amino acid residues involved in Cu/Zn binding. Recombinant amaranth superoxide dismutase (rAhSOD) displayed more than 50 % of catalytic activity after incubation at 100 °C for 30 min. In silico analysis of Amaranthus hypochondriacus SOD (AhSOD) amino acid sequence for globularity and disorder suggested that this protein is mainly disordered; this was confirmed by circular dichroism, which showed the lack of secondary structure. Intrinsic fluorescence studies showed that rAhSOD undergoes conformational changes in two steps by the presence of Cu/Zn, which indicates the presence of two binding sites displaying different affinities for metals ions. Our results show that AhSOD could be classified as an intrinsically disordered protein (IDP) that is folded when metals are bound and with high thermal stability.
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Affiliation(s)
- Gabriela M Montero-Morán
- División Biología Molecular, IPICyT, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Col. Lomas 4a. Sección, 78216, San Luis Potosí, SLP, Mexico
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39
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Squadrone S, Brizio P, Mancini C, Pozzi E, Cavalieri S, Abete MC, Brusco A. Blood metal levels and related antioxidant enzyme activities in patients with ataxia telangiectasia. Neurobiol Dis 2015; 81:162-7. [PMID: 25882094 DOI: 10.1016/j.nbd.2015.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 04/04/2015] [Accepted: 04/07/2015] [Indexed: 10/23/2022] Open
Abstract
Transition metals are cofactors for a wide range of vital enzymes and are directly or indirectly involved in the response against reactive oxygen species (ROS), which can damage cellular components. Their altered homeostasis has been studied in neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS), but no data are available on rarer conditions. We aimed at studying the role of essential trace elements in ataxia telangiectasia (A-T), a rare form of pediatric autosomal recessive cerebellar ataxia with altered antioxidant response. We found an increased level of copper (Cu, p=0.0002) and a reduced level of zinc (Zn, p=0.0002) in the blood of patients (n. 16) compared to controls, using inductively coupled plasma mass spectrometry (ICP-MS). Other trace elements involved in the oxidative stress response, such as manganese (Mn) and selenium (Se), were unaltered. Cu/Zn-dependent superoxide dismutase (SOD1) was shown to have a 30% reduction in gene expression and 40% reduction in enzyme activity upon analysis of lymphoblastoid cell lines of patients (Student's t-test, p=0.0075). We also found a 30% reduction of Mn-SOD (SOD2; Student's t-test, p=0.02), probably due to a feedback regulatory loop between the two enzymes. The expression of antioxidant enzymes, such as erythrocyte glutathione peroxidase (GPX1), and SOD2 was unaltered, whereas catalase (CAT) was increased in A-T cells, both at the mRNA level and in terms of enzyme activity (~25%). Enhanced CAT expression can be attributed to the high ROS status, which induces CAT transcription. These results suggest that alterations in essential trace elements and their related enzymes may play a role in the pathogenesis of A-T, although we cannot conclude if altered homeostasis is a direct effect of A-T mutated genes (ATM). Altered homeostasis of trace elements may be more prevalent in neurodegenerative diseases than previously thought, and it may represent both a biomarker and a generic therapeutic target for different disorders with the common theme of altered antioxidant enzyme responses associated with an unbalance of metals.
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Affiliation(s)
- Stefania Squadrone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, via Bologna 148, Torino 10154, Italy.
| | - Paola Brizio
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, via Bologna 148, Torino 10154, Italy
| | - Cecilia Mancini
- Department of Medical Sciences, University of Torino, Torino 10126, Italy
| | - Elisa Pozzi
- Department of Medical Sciences, University of Torino, Torino 10126, Italy
| | - Simona Cavalieri
- Department of Medical Sciences, University of Torino, Torino 10126, Italy; Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Torino 10126, Italy
| | - Maria Cesarina Abete
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, via Bologna 148, Torino 10154, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino 10126, Italy; Città della Salute e della Scienza University Hospital, Medical Genetics Unit, Torino 10126, Italy
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40
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Salehi M, Nikkhah M, Ghasemi A, Arab SS. Mitochondrial membrane disruption by aggregation products of ALS-causing superoxide dismutase-1 mutants. Int J Biol Macromol 2015; 75:290-7. [DOI: 10.1016/j.ijbiomac.2015.01.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/09/2015] [Accepted: 01/10/2015] [Indexed: 11/24/2022]
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Cotruvo JA, Aron AT, Ramos-Torres KM, Chang CJ. Synthetic fluorescent probes for studying copper in biological systems. Chem Soc Rev 2015; 44:4400-14. [PMID: 25692243 DOI: 10.1039/c4cs00346b] [Citation(s) in RCA: 367] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The potent redox activity of copper is required for sustaining life. Mismanagement of its cellular pools, however, can result in oxidative stress and damage connected to aging, neurodegenerative diseases, and metabolic disorders. Therefore, copper homeostasis is tightly regulated by cells and tissues. Whereas copper and other transition metal ions are commonly thought of as static cofactors buried within protein active sites, emerging data points to the presence of additional loosely bound, labile pools that can participate in dynamic signalling pathways. Against this backdrop, we review advances in sensing labile copper pools and understanding their functions using synthetic fluorescent indicators. Following brief introductions to cellular copper homeostasis and considerations in sensor design, we survey available fluorescent copper probes and evaluate their properties in the context of their utility as effective biological screening tools. We emphasize the need for combined chemical and biological evaluation of these reagents, as well as the value of complementing probe data with other techniques for characterizing the different pools of metal ions in biological systems. This holistic approach will maximize the exciting opportunities for these and related chemical technologies in the study and discovery of novel biology of metals.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
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42
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Hennig J, Andrésen C, Museth AK, Lundström P, Tibell LAE, Jonsson BH. Local Destabilization of the Metal-Binding Region in Human Copper–Zinc Superoxide Dismutase by Remote Mutations Is a Possible Determinant for Progression of ALS. Biochemistry 2015; 54:323-33. [DOI: 10.1021/bi500606j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Janosch Hennig
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
- Institute
of Structural Biology, Helmholtz Zentrum München GmbH, DE-85764 Neuherberg, Germany
- Chair
of Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, DE-85748 Garching, Germany
| | - Cecilia Andrésen
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - A. Katrine Museth
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Patrik Lundström
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
| | - Lena A. E. Tibell
- Department
of Science and Technology, Linköping University, SE-601 74, Norrköping, Sweden
| | - Bengt-Harald Jonsson
- Division
of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Linköping, Sweden
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Szpryngiel S, Oliveberg M, Mäler L. Diffuse binding of Zn(2+) to the denatured ensemble of Cu/Zn superoxide dismutase 1. FEBS Open Bio 2015; 5:56-63. [PMID: 25685664 PMCID: PMC4309841 DOI: 10.1016/j.fob.2014.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/30/2014] [Accepted: 12/30/2014] [Indexed: 11/24/2022] Open
Abstract
Nearly complete backbone assignments for monomeric SOD1 were obtained. Monomeric SOD1 is unstructured in 9 M urea. Zn2+-binding to monomeric SOD1 occurs through diffuse coordination to most His residues. The binding geometry of Zn2+ is different than in the native, folded SOD1.
The stability and structural properties of the metalloprotein superoxide dismutase 1 (SOD1) are found to depend critically on metal ions. Native SOD1 monomers coordinate one structural Zn2+ and one redox-active Cu2+/1+ to the active site. To do this, the Zn2+ ions need to interact with the SOD1 protein on the denatured side of the folding barrier, prior to the formation of the folding nucleus. In this study, we have examined at residue level the nature of this early Zn2+ binding by NMR studies on the urea denatured-state of SOD1. Nearly complete backbone chemical shift assignments were obtained in 9 M urea at physiological pH, conditions at which NMR studies are scarce. Our results demonstrate that SOD1 is predominantly unstructured under these conditions. Chemical-shift changes upon Zn2+ titration show that denatured SOD1 retains a significant affinity to Zn2+ ions, even in 9 M urea. However, the Zn2+ interactions are not limited to the native metal-binding ligands in the two binding sites, but are seen for all His residues. Moreover, the native Cu2+/1+ ligand H46 seems not to bind as well as the other His residues, while the nearby non-native H43 does bind, indicating that the binding geometry is relaxed. The result suggests that the Zn2+-binding observed to catalyze folding of SOD1 in physiological buffer is initiated by diffuse, non-specific coordination to the coil, which subsequently funnels by ligand exchange into the native coordination geometry of the folded monomer. Altogether, this diffuse binding is a result with fundamental implications for folding of metalloproteins in general.
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Affiliation(s)
- Scarlett Szpryngiel
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, The Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes. Proc Natl Acad Sci U S A 2014; 111:E4568-76. [PMID: 25316790 DOI: 10.1073/pnas.1308531111] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Protein framework alterations in heritable Cu, Zn superoxide dismutase (SOD) mutants cause misassembly and aggregation in cells affected by the motor neuron disease ALS. However, the mechanistic relationship between superoxide dismutase 1 (SOD1) mutations and human disease is controversial, with many hypotheses postulated for the propensity of specific SOD mutants to cause ALS. Here, we experimentally identify distinguishing attributes of ALS mutant SOD proteins that correlate with clinical severity by applying solution biophysical techniques to six ALS mutants at human SOD hotspot glycine 93. A small-angle X-ray scattering (SAXS) assay and other structural methods assessed aggregation propensity by defining the size and shape of fibrillar SOD aggregates after mild biochemical perturbations. Inductively coupled plasma MS quantified metal ion binding stoichiometry, and pulsed dipolar ESR spectroscopy evaluated the Cu(2+) binding site and defined cross-dimer copper-copper distance distributions. Importantly, we find that copper deficiency in these mutants promotes aggregation in a manner strikingly consistent with their clinical severities. G93 mutants seem to properly incorporate metal ions under physiological conditions when assisted by the copper chaperone but release copper under destabilizing conditions more readily than the WT enzyme. Altered intradimer flexibility in ALS mutants may cause differential metal retention and promote distinct aggregation trends observed for mutant proteins in vitro and in ALS patients. Combined biophysical and structural results test and link copper retention to the framework destabilization hypothesis as a unifying general mechanism for both SOD aggregation and ALS disease progression, with implications for disease severity and therapeutic intervention strategies.
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Anchordoquy JM, Anchordoquy JP, Sirini MA, Picco SJ, Peral-García P, Furnus CC. The importance of having zinc during in vitro maturation of cattle cumulus-oocyte complex: role of cumulus cells. Reprod Domest Anim 2014; 49:865-74. [PMID: 25131826 DOI: 10.1111/rda.12385] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/22/2014] [Indexed: 12/17/2022]
Abstract
The aim of this study was to investigate the influence of zinc (Zn) on the health of cumulus-oocyte complex (COC) during in vitro maturation (IVM). Experiments were designed to evaluate the effect of Zn added to IVM medium on: DNA integrity, apoptosis, cumulus expansion and superoxide dismutase (SOD) activity of cumulus cells (CC). Also, role of CC on Zn transport during IVM was evaluated on oocyte developmental capacity. DNA damage and early apoptosis were higher in CC matured with 0 μg/ml Zn compared with 0.7, 1.1 and 1.5 μg/ml Zn (p < 0.05). Cumulus expansion did not show differences in COC matured with or without Zn supplementation (p > 0.05). Superoxide dismutase activity was higher in COC matured with 1.5 μg/ml Zn than with 0 μg/ml Zn (p < 0.05). Cleavage and blastocyst rates were recorded after IVM in three maturation systems: intact COCs, denuded oocytes with cumulus cells monolayer (DO + CC) and denuded oocytes (DO). Cleavage rates were similar when COC, DO + CC or DO were matured with 1.5 μg/ml Zn compared with control group (p > 0.05). Blastocyst rates were significantly higher in COC than in DO + CC and DO with the addition of 1.5 μg/ml Zn during IVM (p < 0.01). Blastocyst quality was enhanced in COC and DO + CC compared with DO when Zn was added to IVM medium (p < 0.001). The results of this study indicate that Zn supplementation to IVM medium (i) decreased DNA damage and apoptosis in CC; (ii) increased SOD activity in CC; (iii) did not modify cumulus expansion and cleavage rates after in vitro fertilization; (iv) improved subsequent embryo development up to blastocyst stage; and (v) enhanced blastocyst quality when CC were present either in intact COC or in coculture during IVM.
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Affiliation(s)
- J M Anchordoquy
- Instituto de Genética Veterinaria Prof. Fernando N. Dulout (IGEVET), Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, CONICET, La Plata, Buenos Aires, Argentina; Cátedra de Fisiología, Laboratorio de Nutrición Mineral, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive. J Mol Biol 2014; 426:4112-4124. [PMID: 25083917 DOI: 10.1016/j.jmb.2014.07.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/05/2014] [Accepted: 07/20/2014] [Indexed: 02/04/2023]
Abstract
Amyotrophic lateral sclerosis has been linked to the gain of aberrant function of superoxide dismutase, Cu,Zn-SOD1 upon protein misfolding. The mechanism of SOD1 misfolding is thought to involve mutations leading to the loss of Zn, followed by protein unfolding and aggregation. We show that the removal of Zn from SOD1 may not lead to an immediate unfolding but immediately deactivates the enzyme through a combination of subtle structural and electronic effects. Using quantum mechanics/discrete molecular dynamics, we showed that both Zn-less wild-type (WT)-SOD1 and its D124N mutant that does not bind Zn have at least metastable folded states. In those states, the reduction potential of Cu increases, leading to the presence of detectable amounts of Cu(I) instead of Cu(II) in the active site, as confirmed experimentally. The Cu(I) protein cannot participate in the catalytic Cu(I)-Cu(II) cycle. However, even without the full reduction to Cu(I), the Cu site in the Zn-less variants of SOD1 is shown to be catalytically incompetent: unable to bind superoxide in a way comparable to the WT-SOD1. The changes are more radical and different in the D124N Zn-less mutant than in the Zn-less WT-SOD1, suggesting D124N being perhaps not the most adequate model for Zn-less SOD1. Overall, Zn in SOD1 appears to be influencing the Cu site directly by adjusting its reduction potential and geometry. Thus, the role of Zn in SOD1 is not just structural, as was previously thought; it is a vital part of the catalytic machinery.
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Oral treatment with Cu(II)(atsm) increases mutant SOD1 in vivo but protects motor neurons and improves the phenotype of a transgenic mouse model of amyotrophic lateral sclerosis. J Neurosci 2014; 34:8021-31. [PMID: 24899723 DOI: 10.1523/jneurosci.4196-13.2014] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutations in the metallo-protein Cu/Zn-superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS) in humans and an expression level-dependent phenotype in transgenic rodents. We show that oral treatment with the therapeutic agent diacetyl-bis(4-methylthiosemicarbazonato)copper(II) [Cu(II)(atsm)] increased the concentration of mutant SOD1 (SOD1G37R) in ALS model mice, but paradoxically improved locomotor function and survival of the mice. To determine why the mice with increased levels of mutant SOD1 had an improved phenotype, we analyzed tissues by mass spectrometry. These analyses revealed most SOD1 in the spinal cord tissue of the SOD1G37R mice was Cu deficient. Treating with Cu(II)(atsm) decreased the pool of Cu-deficient SOD1 and increased the pool of fully metallated (holo) SOD1. Tracking isotopically enriched (65)Cu(II)(atsm) confirmed the increase in holo-SOD1 involved transfer of Cu from Cu(II)(atsm) to SOD1, suggesting the improved locomotor function and survival of the Cu(II)(atsm)-treated SOD1G37R mice involved, at least in part, the ability of the compound to improve the Cu content of the mutant SOD1. This was supported by improved survival of SOD1G37R mice that expressed the human gene for the Cu uptake protein CTR1. Improving the metal content of mutant SOD1 in vivo with Cu(II)(atsm) did not decrease levels of misfolded SOD1. These outcomes indicate the metal content of SOD1 may be a greater determinant of the toxicity of the protein in mutant SOD1-associated forms of ALS than the mutations themselves. Improving the metal content of SOD1 therefore represents a valid therapeutic strategy for treating ALS caused by SOD1.
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Gleason JE, Galaleldeen A, Peterson RL, Taylor AB, Holloway SP, Waninger-Saroni J, Cormack BP, Cabelli DE, Hart PJ, Culotta VC. Candida albicans SOD5 represents the prototype of an unprecedented class of Cu-only superoxide dismutases required for pathogen defense. Proc Natl Acad Sci U S A 2014; 111:5866-71. [PMID: 24711423 PMCID: PMC4000858 DOI: 10.1073/pnas.1400137111] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human fungal pathogens Candida albicans and Histoplasma capsulatum have been reported to protect against the oxidative burst of host innate immune cells using a family of extracellular proteins with similarity to Cu/Zn superoxide dismutase 1 (SOD1). We report here that these molecules are widespread throughout fungi and deviate from canonical SOD1 at the primary, tertiary, and quaternary levels. The structure of C. albicans SOD5 reveals that although the β-barrel of Cu/Zn SODs is largely preserved, SOD5 is a monomeric copper protein that lacks a zinc-binding site and is missing the electrostatic loop element proposed to promote catalysis through superoxide guidance. Without an electrostatic loop, the copper site of SOD5 is not recessed and is readily accessible to bulk solvent. Despite these structural deviations, SOD5 has the capacity to disproportionate superoxide with kinetics that approach diffusion limits, similar to those of canonical SOD1. In cultures of C. albicans, SOD5 is secreted in a disulfide-oxidized form and apo-pools of secreted SOD5 can readily capture extracellular copper for rapid induction of enzyme activity. We suggest that the unusual attributes of SOD5-like fungal proteins, including the absence of zinc and an open active site that readily captures extracellular copper, make these SODs well suited to meet challenges in zinc and copper availability at the host-pathogen interface.
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Affiliation(s)
- Julie E. Gleason
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Ahmad Galaleldeen
- Department of Biological Sciences, St. Mary’s University, San Antonio, TX 78228
| | - Ryan L. Peterson
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
| | - Alexander B. Taylor
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | - Stephen P. Holloway
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
| | | | - Brendan P. Cormack
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Diane E. Cabelli
- Chemistry Department, Brookhaven National Laboratories, Upton, NY 11973-5000; and
| | - P. John Hart
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229
- Department of Veterans Affairs, Geriatric Research, Education, and Clinical Center, South Texas Veterans Health Care System, San Antonio, TX 78229
| | - Valeria Cizewski Culotta
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205
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SOD1 oxidation and formation of soluble aggregates in yeast: relevance to sporadic ALS development. Redox Biol 2014; 2:632-9. [PMID: 24936435 PMCID: PMC4052529 DOI: 10.1016/j.redox.2014.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 03/24/2014] [Indexed: 11/22/2022] Open
Abstract
Misfolding and aggregation of copper–zinc superoxide dismutase (Sod1) are observed in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Mutations in Sod1 lead to familial ALS (FALS), which is a late-onset disease. Since oxidative damage to proteins increases with age, it had been proposed that oxidation of Sod1 mutants may trigger their misfolding and aggregation in FALS. However, over 90% of ALS cases are sporadic (SALS) with no obvious genetic component. We hypothesized that oxidation could also trigger the misfolding and aggregation of wild-type Sod1 and sought to confirm this in a cellular environment. Using quiescent, stationary-phase yeast cells as a model for non-dividing motor neurons, we probed for post-translational modification (PTM) and aggregation of wild-type Sod1 extracted from these cells. By size-exclusion chromatography (SEC), we isolated two populations of Sod1 from yeast: a low-molecular weight (LMW) fraction that is catalytically active and a catalytically inactive, high-molecular weight (HMW) fraction. High-resolution mass spectrometric analysis revealed that LMW Sod1 displays no PTMs but HMW Sod1 is oxidized at Cys146 and His71, two critical residues for the stability and folding of the enzyme. HMW Sod1 is also oxidized at His120, a copper ligand, which will promote loss of this catalytic metal cofactor essential for SOD activity. Monitoring the fluorescence of a Sod1-green-fluorescent-protein fusion (Sod1-GFP) extracted from yeast chromosomally expressing this fusion, we find that HMW Sod1-GFP levels increase up to 40-fold in old cells. Thus, we speculate that increased misfolding and inclusion into soluble aggregates is a consequence of elevated oxidative modifications of wild-type Sod1 as cells age. Our observations argue that oxidative damage to wild-type Sod1 initiates the protein misfolding mechanisms that give rise to SALS. Key Sod1 catalytic and structure-stabilizing residues (Cys146, His120, His71) are oxidized in stationary-phase yeast. Oxidized Sod1 is isolated in an inactive, high-molecular-weight, soluble aggregate. Sod1 with native mass isolated from the same samples is not oxidized and is catalytically active. Our results argue that oxidation triggers the formation of soluble Sod1-containing aggregates that may contribute to sporadic ALS development.
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Dang TNT, Lim NKH, Grubman A, Li QX, Volitakis I, White AR, Crouch PJ. Increased metal content in the TDP-43(A315T) transgenic mouse model of frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Front Aging Neurosci 2014; 6:15. [PMID: 24575040 PMCID: PMC3920072 DOI: 10.3389/fnagi.2014.00015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/24/2014] [Indexed: 12/13/2022] Open
Abstract
Disrupted metal homeostasis is a consistent feature of neurodegenerative disease in humans and is recapitulated in mouse models of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) and neuronal ceriod lipofuscinosis. While the definitive pathogenesis of neurodegenerative disease in humans remains to be fully elucidated, disease-like symptoms in the mouse models are all driven by the presence or over-expression of a putative pathogenic protein, indicating an in vivo relationship between expression of these proteins, disrupted metal homeostasis and the symptoms of neuronal failure. Recently it was established that mutant TAR DNA binding protein-43 (TDP-43) is associated with the development of frontotemporal lobar degeneration and ALS. Subsequent development of transgenic mice that express human TDP-43 carrying the disease-causing A315T mutation has provided new opportunity to study the underlying mechanisms of TDP-43-related neurodegenerative disease. We assessed the cognitive and locomotive phenotype of TDP-43 (A315T) mice and their wild-type littermates and also assessed bulk metal content of brain and spinal cord tissues. Metal levels in the brain were not affected by the expression of mutant TDP-43, but zinc, copper, and manganese levels were all increased in the spinal cords of TDP-43 (A315T) mice when compared to wild-type littermates. Performance of the TDP-43 (A315T) mice in the Y-maze test for cognitive function was not significantly different to wild-type mice. By contrast, performance of the TDP-43 (A315T) in the rotarod test for locomotive function was consistently worse than wild-type mice. These preliminary in vivo data are the first to show that expression of a disease-causing form of TDP-43 is sufficient to disrupt metal ion homeostasis in the central nervous system. Disrupted metal ion homeostasis in the spinal cord but not the brain may explain why the TDP-43 (A315T) mice show symptoms of locomotive decline and not cognitive decline.
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Affiliation(s)
- Theresa N T Dang
- Department of Pathology, The University of Melbourne VIC, Australia
| | - Nastasia K H Lim
- Department of Pathology, The University of Melbourne VIC, Australia
| | | | - Qiao-Xin Li
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne VIC, Australia
| | - Irene Volitakis
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne VIC, Australia
| | - Anthony R White
- Department of Pathology, The University of Melbourne VIC, Australia ; Florey Institute of Neuroscience and Mental Health, The University of Melbourne VIC, Australia
| | - Peter J Crouch
- Department of Pathology, The University of Melbourne VIC, Australia ; Florey Institute of Neuroscience and Mental Health, The University of Melbourne VIC, Australia
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