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Mavadat E, Seyedalipour B, Hosseinkhani S. A double point mutation of SOD1 targeting net charge promotes aggregation under destabilizing conditions: Correlation of charge distribution and ALS-provoking mutation. Biochim Biophys Acta Gen Subj 2023; 1867:130325. [PMID: 36791828 DOI: 10.1016/j.bbagen.2023.130325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/28/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023]
Abstract
A progressive neurodegenerative illness such as amyotrophic lateral sclerosis (ALS) is characterized by the misfolding and aggregation of human CuZn superoxide dismutase (hSOD1) into amyloid aggregates. Thus, designing strategies for the choice of WT-SOD1 and double mutant (G12D/G138E) with an increased net negative charge can be a good idea to elucidate the pathological mechanism of SOD1 in ALS under some destabilizing conditions. Consequently, we show evidence that protein charge, together with other destabilizing conditions, plays an important role in ALS disease. To achieve this purpose, we use methods, such as spectroscopy and transmission electron microscopy (TEM) to monitor the formation of amyloid aggregation. The specific activity of WT-SOD1 was approximately 1.72 times higher than that of the double mutant. Under amyloidogenic circumstances, structural properties such as local, secondary, oligomeric, and fibrillar structures were explored. The double mutant's far-UV CD spectra displayed a broad minimum peak in the region 213 to 218 nm, suggesting the production of β-rich amyloid fibrils. FTIR spectra of the double mutant samples at different incubation times showed a low-frequency peak around 1630-1640 cm-1, attributed to a parallel β-sheet. Moreover, CR-binding assay and TEM analysis revealed and confirmed that mutation with an increased repulsive charge promotes the formation of fibrous aggregates. Consequently, ALS mutations with a higher repulsive charge are the apparent exceptions that validate the rule. This findings revealed that the double mutant increases protein aggregation through a novel mechanism, likely involving destabilization of structure and a change in the net negative charge.
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Affiliation(s)
- Elaheh Mavadat
- 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.
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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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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Chen Q, Wang W, Khanal S, Han J, Zhang M, Chen Y, Li Z, Wang K, Paterson AH, Yu J, Chee PW, Wang B. Transcriptome analysis reveals genes potentially related to high fiber strength in a Gossypium hirsutum line IL9 with Gossypium mustelinum introgression. Genome 2021; 64:985-995. [PMID: 34253086 DOI: 10.1139/gen-2020-0177] [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] [Indexed: 11/22/2022]
Abstract
Cotton (Gossypium L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Wei Wang
- Jiangsu Coastal Area Institute of Agricultural Sciences/Jiangsu Collaborative Innovation Center for Modern Crop Production, Yancheng, Jiangsu 224002, P.R. China
| | - Sameer Khanal
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Jinlei Han
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Mi Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Yan Chen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Zhenjiang Li
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology/Chinese Academy of Agricultural Sciences Cotton Research Institute, Anyang, Henan 455000, P.R. China
| | - Peng W Chee
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
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Sannigrahi A, Chowdhury S, Das B, Banerjee A, Halder A, Kumar A, Saleem M, Naganathan AN, Karmakar S, Chattopadhyay K. The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model. eLife 2021; 10:e61453. [PMID: 33825682 PMCID: PMC8087447 DOI: 10.7554/elife.61453] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
Aggregation of Cu-Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, amyotrophic lateral sclerosis (ALS). Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not correlated with disease pathophysiology. Here, we use multiple mutational variants of SOD1 to show that the absence of Zn, and not Cu, significantly impacts membrane attachment of SOD1 through two loop regions facilitating aggregation driven by lipid-induced conformational changes. These loop regions influence both the primary (through Cu intake) and the gain of function (through aggregation) of SOD1 presumably through a shared conformational landscape. Combining experimental and theoretical frameworks using representative ALS disease mutants, we develop a 'co-factor derived membrane association model' wherein mutational stress closer to the Zn (but not to the Cu) pocket is responsible for membrane association-mediated toxic aggregation and survival time scale after ALS diagnosis.
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Affiliation(s)
- Achinta Sannigrahi
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical BiologyKolkataIndia
| | - Sourav Chowdhury
- Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Bidisha Das
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource development Centre CampusGhaziabadIndia
| | | | | | - Amaresh Kumar
- School of Biological Sciences, National Institute of Science Education and Research (NISER)BhubaneswarIndia
| | - Mohammed Saleem
- School of Biological Sciences, National Institute of Science Education and Research (NISER)BhubaneswarIndia
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology MadrasChennaiIndia
| | | | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource development Centre CampusGhaziabadIndia
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Chowdhury S, Sanyal D, Sen S, Uversky VN, Maulik U, Chattopadhyay K. Evolutionary Analyses of Sequence and Structure Space Unravel the Structural Facets of SOD1. Biomolecules 2019; 9:E826. [PMID: 31817166 PMCID: PMC6995586 DOI: 10.3390/biom9120826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/09/2019] [Accepted: 11/16/2019] [Indexed: 01/08/2023] Open
Abstract
Superoxide dismutase (SOD) is the primary enzyme of the cellular antioxidant defense cascade. Misfolding, concomitant oligomerization, and higher order aggregation of human cytosolic SOD are linked to amyotrophic lateral sclerosis (ALS). Although, with two metal ion cofactors SOD1 is extremely robust, the de-metallated apo form is intrinsically disordered. Since the rise of oxygen-based metabolism and antioxidant defense systems are evolutionary coupled, SOD is an interesting protein with a deep evolutionary history. We deployed statistical analysis of sequence space to decode evolutionarily co-varying residues in this protein. These were validated by applying graph theoretical modelling to understand the impact of the presence of metal ion co-factors in dictating the disordered (apo) to hidden disordered (wild-type SOD1) transition. Contact maps were generated for different variants, and the selected significant residues were mapped on separate structure networks. Sequence space analysis coupled with structure networks helped us to map the evolutionarily coupled co-varying patches in the SOD1 and its metal-depleted variants. In addition, using structure network analysis, the residues with a major impact on the internal dynamics of the protein structure were investigated. Our results reveal that the bulk of these evolutionarily co-varying residues are localized in the loop regions and positioned differentially depending upon the metal residence and concomitant steric restrictions of the loops.
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Affiliation(s)
- Sourav Chowdhury
- Protein Folding and Dynamics Group, Structural Biology and Bio-informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C.Mullick Road, Kolkata 700032, India; (S.C.); (D.S.)
- Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Dwipanjan Sanyal
- Protein Folding and Dynamics Group, Structural Biology and Bio-informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C.Mullick Road, Kolkata 700032, India; (S.C.); (D.S.)
| | - Sagnik Sen
- Department of Computer Science, Jadavpur University, Kolkata 700032, India; (S.S.); (U.M.)
| | - 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 33612, USA;
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Ujjwal Maulik
- Department of Computer Science, Jadavpur University, Kolkata 700032, India; (S.S.); (U.M.)
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Group, Structural Biology and Bio-informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C.Mullick Road, Kolkata 700032, India; (S.C.); (D.S.)
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