Structural and Functional Analysis of Human SOD1 in Amyotrophic Lateral Sclerosis
Publication Date
December 02, 2013
Journal
PLOS ONE
Authors
Lorenna Giannini Alves Moreira, Livia Costa Pereira, Priscila Ramalho Drummond & Joelma Freire De Mesquita
Volume
8
Issue
12
Pages
e81979
DOI
https://dx.plos.org/10.1371/journal.pone.0081979
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0081979
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24312616
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846731
Europe PMC
http://europepmc.org/abstract/MED/24312616
Web of Science
000327944500109
Scopus
84891471650
Mendeley
http://www.mendeley.com/research/structural-functional-analysis-human-sod1-amyotrophic-lateral-sclerosis-3
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1300495"], "description"=>"<p>Blue bar represents the percentage of mutations that, among the seven used algorithms, presented no neutral result and were therefore considered malign by all algorithms. Red bar, the percentage of mutations with neutral results; Green bar, 2 neutral results; Purple bar, 3 neutral results; Yellow bar, 5 neutral results; Orange bar, 6 neutral results; Brown bar, 7 neutral results.</p>", "links"=>[], "tags"=>["mutations", "algorithms"], "article_id"=>866316, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0081979.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_mutations_with_neutral_results_obtained_by_the_algorithms_used_for_analysis_of_SOD1_/866316", "title"=>"Percentage of mutations with neutral results obtained by the algorithms used for analysis of SOD1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1300491"], "description"=>"<p>Blue bars show the total number of mutations classified as responsible for the disease, while the red bars show the total number of mutations considered neutral.</p>", "links"=>[], "tags"=>["designated", "non-neutral"], "article_id"=>866312, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0081979.g001", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mutations_designated_as_neutral_and_non_neutral_by_the_algorithm_/866312", "title"=>"Mutations designated as neutral and non-neutral by the algorithm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1300506", "https://ndownloader.figshare.com/files/1300507"], "description"=>"<div><p>Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with familial inheritance (fALS) in 5% to 10% of cases; 25% of those are caused by mutations in the superoxide dismutase 1 (SOD1) protein. More than 100 mutations in the SOD1 gene have been associated with fALS, altering the geometry of the active site, protein folding and the interaction between monomers. We performed a functional analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in 124 fALS SOD1 mutants. Eleven different algorithms were used to estimate the functional impact of the replacement of one amino acid on protein structure: SNPs&GO, PolyPhen-2, SNAP, PMUT, Sift, PhD-SNP, nsSNPAnalyzer, TANGO, WALTZ, LIMBO and FoldX. For the structural analysis, theoretical models of 124 SNPs of SOD1 were created by comparative modeling using the MHOLline workflow, which includes Modeller and Procheck. Models were aligned with the native protein by the TM-align algorithm. A human-curated database was developed using the server side include in Java, JMOL. The results of this functional analysis indicate that the majority of the 124 natural mutants are harmful to the protein structure and thus corroborate the correlation between the reported mutations and fALS. In the structural analysis, all models showed conformational changes when compared to wild-type SOD1, and the degree of structural alignment varied between them. The SOD1 database converge structural and functional analyses of SOD1; it is a vast resource for the molecular analysis of amyotrophic lateral sclerosis, which allows the user to expand his knowledge on the molecular basis of the disease. The SOD1 database is available at <a href=\"http://bioinfogroup.com/database\" target=\"_blank\"><u>http://bioinfogroup.com/database</u></a>.</p> </div>", "links"=>[], "tags"=>["SOD1", "amyotrophic", "lateral"], "article_id"=>866325, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0081979.s001", "https://dx.doi.org/10.1371/journal.pone.0081979.s002"], "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_and_Functional_Analysis_of_Human_SOD1_in_Amyotrophic_Lateral_Sclerosis_/866325", "title"=>"Structural and Functional Analysis of Human SOD1 in Amyotrophic Lateral Sclerosis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1300505"], "description"=>"<p>Screenshot of the SOD1 Database web interface for structural modelling and comparative analysis.</p>", "links"=>[], "tags"=>["SOD1", "interface", "comparative"], "article_id"=>866324, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0081979.g005", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Screenshot_of_the_SOD1_Database_web_interface_for_structural_modelling_and_comparative_analysis_/866324", "title"=>"Screenshot of the SOD1 Database web interface for structural modelling and comparative analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1300501"], "description"=>"<p>(A) Structural representation of the three-dimensional model of the SOD1 [PDB: 2VOA] in a form of a diagram in cartoon. Different elements of the secondary structure are in various colors: in magenta, the alpha helix; in yellow arrows, beta sheets; and in white lines, coils. (B) Three-dimensional structure of human SOD1, represented in backbone form of, with mutations described on the literature marked in red. (C) Conservation profile of human SOD1 using ConSurf conservation analysis. The protein was visualized using Jmol with color-coded conservations. The conserved and variable residues are presented as space-filled models and colored according to the conservation scores. Each structure is turned 90 degrees to show the different sides of the protein.</p>", "links"=>[], "tags"=>["conformation", "conservational"], "article_id"=>866320, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0081979.g003", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_conformation_and_conservational_analysis_of_the_human_SOD1_/866320", "title"=>"Structural conformation and conservational analysis of the human SOD1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-02 03:31:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1300503"], "description"=>"<p>The ConSurf algorithm was used to provide conservation score for the amino acids of superoxide dismutase 1, starting from the multiple alignment of sequences of SOD1 from 8 different mammalian species that had between 80 and 100% homology with the human SOD1. The color-coding bar shows the coloring scheme: conserved amino acids are colored bordeaux, residues of average conservation are white, and variable amino acids are turquoise. Two columns are basically formed by gaps: at the position of amino acid 26, the gaps are because of sequences of human SOD1, <i>Equus caballus</i> and <i>Morrodelphis domestica</i>; while at amino acid position 28, the gaps are because of the species <i>Mus musculus</i> and <i>Morrodelphis domestica</i>. In addition, it is verified that 61.43% of the amino acids are highly conserved between the analyzed species. The asterisks on the superior region of the alignment delimit the amino acids that have mutations described in the literature.</p>", "links"=>[], "tags"=>["alignment", "color-coded"], "article_id"=>866322, "categories"=>["Biological Sciences"], "users"=>["Lorenna Giannini Alves Moreira", "Livia Costa Pereira", "Priscila Ramalho Drummond", "Joelma Freire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0081979.g004", "stats"=>{"downloads"=>1, "page_views"=>121, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_Sequence_Alignment_Color_Coded_by_Conservation_/866322", "title"=>"Multiple Sequence Alignment Color-Coded by Conservation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-02 03:31:01"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}, {"subject_area"=>"/Medicine and health sciences/Neurology", "average_usage"=>[271, 485, 617, 733, 835, 933, 1026, 1115, 1207, 1294, 1386, 1475, 1543]}]}
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