Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof
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{"title"=>"Physical properties of intact proteins may predict allergenicity or lack thereof", "type"=>"journal", "authors"=>[{"first_name"=>"Suchita", "last_name"=>"Singh", "scopus_author_id"=>"35216172600"}, {"first_name"=>"Bhupesh", "last_name"=>"Taneja", "scopus_author_id"=>"6603217660"}, {"first_name"=>"Sundeep Santosh", "last_name"=>"Salvi", "scopus_author_id"=>"7005258777"}, {"first_name"=>"Anurag", "last_name"=>"Agrawal", "scopus_author_id"=>"35214460700"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pmid"=>"19609445", "pui"=>"354947406", "scopus"=>"2-s2.0-67650914562", "doi"=>"10.1371/journal.pone.0006273", "isbn"=>"1932-6203 (Electronic)", "sgr"=>"67650914562"}, "id"=>"430f34fe-91f1-3f05-b0a4-5c23ac05dfb0", "abstract"=>"BACKGROUND: Predicting the allergenicity of proteins is challenging. We considered the possibility that the properties of the intact protein that may alter the likelihood of being taken up by antigen presenting cells, may be useful adjuncts in predicting allergens and non-allergens in silico. It has been shown that negatively charged acidic proteins are preferentially processed by dendritic cells.\\n\\nMETHODOLOGY: Datasets (aeroallergen, food-allergen and non-allergen) for in-silico study were obtained from public databases. Isoelectric point (pI), net charge, and electrostatic potential (EP) were calculated from the protein sequence (for pI and net charge) or predicted structure (for EP).\\n\\nRESULT: Allergens and non allergens differed significantly in pI, net charge, and EP (p<0.0001). Cluster analysis based on these parameters resulted in well defined clusters. Non-allergens were characterized by neutral to basic pI (mean+/-SE, 7.6+/-0.16) and positive charge. In contrast allergens were acidic (5.7+/-0.15) and negatively charged. Surface electrostatic potentials calculated from predicted structures were mostly negative for allergens and mostly positive for non-allergens. The classification accuracy for non-allergens was superior to that for allergens. Thus neutral to basic pI, positive charge, and positive electrostatic potentials characterize non-allergens, and seem rare in allergens (p<0.0001). It may be possible to predict reduced likelihood of allergenicity in such proteins, but this needs to be prospectively validated.", "link"=>"http://www.mendeley.com/research/physical-properties-intact-proteins-predict-allergenicity-lack-thereof", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>2, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>2, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/441370"], "description"=>"<div><h3>Background</h3><p>Predicting the allergenicity of proteins is challenging. We considered the possibility that the properties of the intact protein that may alter the likelihood of being taken up by antigen presenting cells, may be useful adjuncts in predicting allergens and non-allergens <em>in silico</em>. It has been shown that negatively charged acidic proteins are preferentially processed by dendritic cells.</p><h3>Methodology</h3><p>Datasets (aeroallergen, food-allergen and non-allergen) for <em>in-silico</em> study were obtained from public databases. Isoelectric point (pI), net charge, and electrostatic potential (EP) were calculated from the protein sequence (for pI and net charge) or predicted structure (for EP).</p><h3>Result</h3><p>Allergens and non allergens differed significantly in pI, net charge, and EP (p<0.0001). Cluster analysis based on these parameters resulted in well defined clusters. Non-allergens were characterized by neutral to basic pI (mean±SE, 7.6±0.16) and positive charge. In contrast allergens were acidic (5.7±0.15) and negatively charged. Surface electrostatic potentials calculated from predicted structures were mostly negative for allergens and mostly positive for non-allergens. The classification accuracy for non-allergens was superior to that for allergens. Thus neutral to basic pI, positive charge, and positive electrostatic potentials characterize non-allergens, and seem rare in allergens (p<0.0001). It may be possible to predict reduced likelihood of allergenicity in such proteins, but this needs to be prospectively validated.</p></div>", "links"=>[], "tags"=>["properties", "proteins", "allergenicity", "thereof"], "article_id"=>146992, "categories"=>["Immunology", "Biological Sciences", "Medicine", "Cancer"], "users"=>["Suchita Singh", "Bhupesh Taneja", "Sundeep Santosh Salvi", "Anurag Agrawal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006273", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Physical_Properties_of_Intact_Proteins_May_Predict_Allergenicity_or_Lack_Thereof/146992", "title"=>"Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-07-17 01:56:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/890802"], "description"=>"<p>Square symbols denote aeroallergens, plus denotes food allergens, and inverted triangles denote non-allergens. pI is used as the X dimension in both analysis. The Y dimension is the (A) electrostatic potential score calculated from protein structure; and (B) net charge per amino acid calculated from peptide sequence.</p>", "links"=>[], "tags"=>["dimensional", "allergens", "non-allergens"], "article_id"=>561257, "categories"=>["Immunology", "Biological Sciences", "Medicine", "Infectious Diseases"], "users"=>["Suchita Singh", "Bhupesh Taneja", "Sundeep Santosh Salvi", "Anurag Agrawal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006273.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_dimensional_cluster_analysis_of_allergens_and_non_allergens_based_on_charge_and_pI_/561257", "title"=>"Two dimensional cluster analysis of allergens and non-allergens based on charge and pI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-17 00:20:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/891100"], "description"=>"<p>Asterix (*) denotes significant differences when compared to non-allergens. (§) denotes significant difference from random proteins. There were no significant differences between aeroallergens or dietary allergens.</p>", "links"=>[], "tags"=>["calculated", "peptide", "amino", "semiquantitative", "electrostatic", "shown"], "article_id"=>561551, "categories"=>["Immunology", "Biological Sciences", "Medicine", "Infectious Diseases"], "users"=>["Suchita Singh", "Bhupesh Taneja", "Sundeep Santosh Salvi", "Anurag Agrawal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006273.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculated_pI_net_charge_calculated_from_peptide_sequence_net_charge_per_amino_acid_and_a_semiquantitative_electrostatic_potential_score_EP_calculated_from_protein_structure_are_shown_as_mean_177_standard_error_mean_SEM_or_median_177_interquartile_range_/561551", "title"=>"Calculated pI, net charge calculated from peptide sequence, net charge per amino acid, and a semiquantitative electrostatic potential score (EP) calculated from protein structure, are shown as mean±standard error mean (SEM) or median±interquartile range (IQR).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-07-17 00:25:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/890903"], "description"=>"<p>The proportion of non-allergens is shown as a linear function of surface electrostatic potential (A) and isoelectric point (B)</p>", "links"=>[], "tags"=>["shows", "proportions", "non-allergens", "ep"], "article_id"=>561360, "categories"=>["Immunology", "Biological Sciences", "Medicine", "Infectious Diseases"], "users"=>["Suchita Singh", "Bhupesh Taneja", "Sundeep Santosh Salvi", "Anurag Agrawal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006273.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linear_trend_analysis_shows_increasing_proportions_of_non_allergens_with_increasing_EP_Score_and_pI_/561360", "title"=>"Linear trend analysis shows increasing proportions of non-allergens with increasing EP Score and pI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-17 00:22:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/891010"], "description"=>"<p>Probability of allergenicity is a cumulative function of probability of uptake (X axis) and probability of IgE induction by the processed protein (Y axis). It is conjectured that physical properties of the intact protein influence the probability of uptake.</p>", "links"=>[], "tags"=>["properties", "determining"], "article_id"=>561473, "categories"=>["Immunology", "Biological Sciences", "Medicine", "Infectious Diseases"], "users"=>["Suchita Singh", "Bhupesh Taneja", "Sundeep Santosh Salvi", "Anurag Agrawal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006273.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_theoretical_influence_of_physical_properties_of_intact_protein_determining_allergenicity_/561473", "title"=>"Schematic representation of the theoretical influence of physical properties of intact protein determining allergenicity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-07-17 00:24:33"}

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