Structural Modeling and In Silico Analysis of Human Superoxide Dismutase 2
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{"title"=>"Structural Modeling and In Silico Analysis of Human Superoxide Dismutase 2", "type"=>"journal", "authors"=>[{"first_name"=>"Mariana Dias Castela", "last_name"=>"de Carvalho", "scopus_author_id"=>"56044611700"}, {"first_name"=>"Joelma Freire", "last_name"=>"De Mesquita", "scopus_author_id"=>"6603659541"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84878986034", "sgr"=>"84878986034", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0065558", "pmid"=>"23785434", "isbn"=>"10.1371/journal.pone.0065558", "pui"=>"369111461"}, "id"=>"2c606cf5-42e0-3f65-a492-4253dc75d17f", "abstract"=>"Aging in the world population has increased every year. Superoxide dismutase 2 (Mn-SOD or SOD2) protects against oxidative stress, a main factor influencing cellular longevity. Polymorphisms in SOD2 have been associated with the development of neurodegenerative diseases, such as Alzheimer's and Parkinson's disease, as well as psychiatric disorders, such as schizophrenia, depression and bipolar disorder. In this study, all of the described natural variants (S10I, A16V, E66V, G76R, I82T and R156W) of SOD2 were subjected to in silico analysis using eight different algorithms: SNPeffect, PolyPhen-2, PhD-SNP, PMUT, SIFT, SNAP, SNPs&GO and nsSNPAnalyzer. This analysis revealed disparate results for a few of the algorithms. The results showed that, from at least one algorithm, each amino acid substitution appears to harmfully affect the protein. Structural theoretical models were created for variants through comparative modelling performed using the MHOLline server (which includes MODELLER and PROCHECK) and ab initio modelling, using the I-Tasser server. The predicted models were evaluated using TM-align, and the results show that the models were constructed with high accuracy. The RMSD values of the modelled mutants indicated likely pathogenicity for all missense mutations. Structural phylogenetic analysis using ConSurf revealed that human SOD2 is highly conserved. As a result, a human-curated database was generated that enables biologists and clinicians to explore SOD2 nsSNPs, including predictions of their effects and visualisation of the alignment of both the wild-type and mutant structures. The database is freely available at http://bioinfogroup.com/database and will be regularly updated.", "link"=>"http://www.mendeley.com/research/structural-modeling-silico-analysis-human-superoxide-dismutase-2-8", "reader_count"=>56, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>8, "Researcher"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>16, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>8, "Researcher"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>16, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>5, "Biochemistry, Genetics and Molecular Biology"=>8, "Medicine and Dentistry"=>6, "Agricultural and Biological Sciences"=>27, "Neuroscience"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>5}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Bangladesh"=>1, "United States"=>1, "Brazil"=>1, "India"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1085064"], "description"=>"<p>The colour-coding bar shows the colouring scheme: conserved amino acids\nare coloured bordeaux, residues of average conservation are white, and variable\namino acids are turquoise. SNP positions are marked by an asterisk.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "alignment", "consurf", "shows", "amino"], "article_id"=>718400, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g005", "stats"=>{"downloads"=>2, "page_views"=>108, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_protein_sequence_alignment_using_ConSurf_shows_evolutionary_conservation_of_amino_acid_residues_/718400", "title"=>"Multiple protein sequence alignment using ConSurf shows evolutionary\nconservation of amino acid residues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:20:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085061"], "description"=>"<p>A) S10I (S-15I) mutation highlighted in red. B) This mutation disrupts\nthe alpha helix, RMSD: 2.02. C) A16V (A-9V) mutation highlighted in red. D)\nThis mutation disrupts the alpha helix, RMSD: 1.94.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "structures", "mutant", "sod2", "produced"], "article_id"=>718398, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Superimposed_native_structures_green_and_mutant_structures_blue_of_the_SOD2_produced_using_ab_initio_modelling_/718398", "title"=>"Superimposed native structures (green) and mutant structures (blue)\nof the SOD2 produced using <i>ab initio</i> modelling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:19:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085069"], "description"=>"<p>Structure alignment comparing mutant models and wild-type SOD2 models.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "alignment", "comparing", "mutant", "wild-type", "sod2"], "article_id"=>718403, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_alignment_comparing_mutant_models_and_wild_type_SOD2_models_/718403", "title"=>"Structure alignment comparing mutant models and wild-type SOD2 models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-13 02:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085068"], "description"=>"<p>Summary of identified SOD2 variants.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "sod2"], "article_id"=>718402, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_identified_SOD2_variants_/718402", "title"=>"Summary of identified SOD2 variants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-13 02:20:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085059"], "description"=>"<p>Two subunits are represented as a backbone in green and blue. Four mutation\nsites are shown in a sphere representation: E66V, G76R, I82T and R156. The\nmanganese binding site is shown in ball-stick form.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "sod2", "missense", "mutation"], "article_id"=>718397, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3D_structure_of_human_SOD2_with_four_missense_mutation_sites_/718397", "title"=>"3D structure of human SOD2 with four missense mutation sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:19:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085057"], "description"=>"<p>A) mutation E66V (E42V), RMSD: 0.21; B) mutation G76R (G52R), RMSD: 0.38;\nC) mutation I82T (I58T), RMSD: 0.45; D) mutation R156W (R132W), RMSD: 0.16.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "structures", "mutant", "sod2", "produced", "comparative"], "article_id"=>718396, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Superimposed_native_structures_green_and_mutant_structures_blue_of_the_SOD2_produced_using_comparative_modelling_/718396", "title"=>"Superimposed native structures (green) and mutant structures (blue)\nof the SOD2 produced using comparative modelling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:19:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085071"], "description"=>"<p>Structure alignment of <i>ab initio</i> SOD2 mutant models\nwith the <i>ab initio</i> wild-type model.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "alignment", "sod2", "mutant", "wild-type"], "article_id"=>718405, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.t004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_alignment_of_ab_initio_SOD2_mutant_models_with_the_ab_initio_wild_type_model_/718405", "title"=>"Structure alignment of <i>ab initio</i> SOD2 mutant models\nwith the <i>ab initio</i> wild-type model.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-13 02:20:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085070"], "description"=>"<p>Predictions of the effect of the missense variations on SOD2 protein\nfunction.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "missense", "variations", "sod2"], "article_id"=>718404, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predictions_of_the_effect_of_the_missense_variations_on_SOD2_protein_function_/718404", "title"=>"Predictions of the effect of the missense variations on SOD2 protein\nfunction.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-06-13 02:20:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085066"], "description"=>"<p>Screenshot of the SOD2 Database web interface for structural modelling\nand comparative analysis.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "sod2", "interface", "comparative"], "article_id"=>718401, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Screenshot_of_the_SOD2_Database_web_interface_for_structural_modelling_and_comparative_analysis_/718401", "title"=>"Screenshot of the SOD2 Database web interface for structural modelling\nand comparative analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:20:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1085062"], "description"=>"<p>Mn-SOD is represented as a spacefill model, where the residue conservation\nscored is colour-coded onto the surface. The backbone model represents the\nother chain of a Mn-SOD dimer, chain B. The colour-coding bar shows the colouring\nscheme: conserved amino acids are coloured bordeaux, residues with average\nconservation are white, and variable amino acids are turquoise.</p>", "links"=>[], "tags"=>["Biochemistry", "proteins", "protein structure", "Biochemistry simulations", "biophysics", "Biophysics simulations", "Computational biology", "Macromolecular\nstructure analysis", "Biochemical simulations", "Biophysic al simulations", "genetics", "Human genetics", "genomics", "Genome\ndatabases", "Mutation databases", "algorithms", "Computer modeling", "mn-sod", "consurf"], "article_id"=>718399, "categories"=>["Information And Computing Sciences", "Physics", "Biological Sciences"], "users"=>["Mariana\nDias Castela de Carvalho", "Joelma\nFreire De Mesquita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0065558.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conservation_profile_of_the_Mn_SOD_PDB_ID_1LUV_using_ConSurf_conservational_analysis_/718399", "title"=>"Conservation profile of the Mn-SOD (PDB ID: 1LUV) using ConSurf conservational\nanalysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-13 02:19:59"}

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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"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}]}
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