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{"title"=>"Rapid probing of biological surfaces with a sparse-matrix peptide library", "type"=>"journal", "authors"=>[{"first_name"=>"Daniel K.", "last_name"=>"Yarbrough", "scopus_author_id"=>"12807291400"}, {"first_name"=>"Randal", "last_name"=>"Eckert", "scopus_author_id"=>"12807644600"}, {"first_name"=>"Jian", "last_name"=>"He", "scopus_author_id"=>"56179049500"}, {"first_name"=>"Elizabeth", "last_name"=>"Hagerman", "scopus_author_id"=>"19933307200"}, {"first_name"=>"Fengxia", "last_name"=>"Qi", "scopus_author_id"=>"7101777315"}, {"first_name"=>"Renate", "last_name"=>"Lux", "scopus_author_id"=>"7006319055"}, {"first_name"=>"Ben", "last_name"=>"Wu", "scopus_author_id"=>"7403591573"}, {"first_name"=>"Maxwell H.", "last_name"=>"Anderson", "scopus_author_id"=>"7404765589"}, {"first_name"=>"Wenyuan", "last_name"=>"Shi", "scopus_author_id"=>"7402664618"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "doi"=>"10.1371/journal.pone.0023551", "pui"=>"362343827", "sgr"=>"80051675525", "pmid"=>"21858167", "scopus"=>"2-s2.0-80051675525"}, "id"=>"01e8dbc6-d740-33d4-ad5b-9e7ac924f52c", "abstract"=>"Finding unique peptides to target specific biological surfaces is crucial to basic research and technology development, though methods based on biological arrays or large libraries limit the speed and ease with which these necessary compounds can be found. We reasoned that because biological surfaces, such as cell surfaces, mineralized tissues, and various extracellular matrices have unique molecular compositions, they present unique physicochemical signatures to the surrounding medium which could be probed by peptides with appropriately corresponding physicochemical properties. To test this hypothesis, a naïve pilot library of 36 peptides, varying in their hydrophobicity and charge, was arranged in a two-dimensional matrix and screened against various biological surfaces. While the number of peptides in the matrix library was very small, we obtained \"hits\" against all biological surfaces probed. Sequence refinement of the \"hits\" led to peptides with markedly higher specificity and binding activity against screened biological surfaces. Genetic studies revealed that peptide binding to bacteria was mediated, at least in some cases, by specific cell-surface molecules, while examination of human tooth sections showed that this method can be used to derive peptides with highly specific binding to human tissue.", "link"=>"http://www.mendeley.com/research/rapid-probing-biological-surfaces-sparsematrix-peptide-library", "reader_count"=>6, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Agricultural and Biological Sciences"=>2, "Medicine and Dentistry"=>2, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}}, "group_count"=>0}

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• http://doi.org/10.1111/bph.14680
• http://doi.org/10.1016/j.comche.2011.10.001
• http://doi.org/10.1016/j.comche.2011.10.002
• http://doi.org/10.1016/j.micres.2012.07.004
• http://doi.org/10.1111/bph.14571

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/745698"], "description"=>"<p>Sequences (top) are arranged in a 2D matrix to provide extensive variation in the parameters of charge (bottom left, plot shows formal charge at pH 7.0) and hydrophobicity (bottom right). X and Y axes represent matrix position as defined at top; Z axes show formal charge (amu) and hydrophobicity (arbitrary units), respectively.</p>", "links"=>[], "tags"=>["peptide"], "article_id"=>416067, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Design_of_the_pilot_peptide_matrix_/416067", "title"=>"Design of the pilot peptide matrix.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:41:07"}
• {"files"=>["https://ndownloader.figshare.com/files/746091"], "description"=>"<p>Top panel, sequences of peptides for the refined peptide matrices; bottom panel, fluorescence images showing the binding of refined peptides to immobilized <i>S. aureus</i> cells.</p>", "links"=>[], "tags"=>["refinement", "peptides", "binding"], "article_id"=>416460, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sparse_matrix_refinement_of_peptides_with_binding_to_S_aureus_/416460", "title"=>"Sparse-matrix refinement of peptides with binding to S. aureus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:47:40"}
• {"files"=>["https://ndownloader.figshare.com/files/745831"], "description"=>"<p>Panel A, fluorescence images of bacteria bound with different peptides, collected using identical microscope and camera settings. Peptides are arranged as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023551#pone-0023551-g001\" target=\"_blank\">Figure 1</a>. Panel B, quantitation of fluorescence intensity from images shown in panel A. Binding profile shows the relative intensity of staining for each peptide in the matrix. Z axis shows the ratio of the fluorescence intensity from stained cells to the background fluorescence.</p>", "links"=>[], "tags"=>["peptide", "matrix"], "article_id"=>416202, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_of_the_pilot_peptide_matrix_to_Staphylococcus_aureus_/416202", "title"=>"Binding of the pilot peptide matrix to <i>Staphylococcus aureus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:43:22"}
• {"files"=>["https://ndownloader.figshare.com/files/746315"], "description"=>"<p>Panel A: differential binding of refinement-based <i>S. mutans</i> binding peptide (sma24) to wild type <i>S. mutans</i> (UA140) and EPS mutant <i>gtfB</i>. Panel B: differential binding of peptide B2 (original pilot matrix) to wild type <i>M. xanthus</i> and surface mutant <i>difE</i>. Y axis represents relative levels of peptide binding, as indicated by the intensity of fluorescent staining to different bacterial strains listed along X-axis.</p>", "links"=>[], "tags"=>["binding", "peptides", "mutants", "altered"], "article_id"=>416684, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_binding_of_selected_peptides_to_wild_type_and_mutants_with_altered_surfaces_/416684", "title"=>"Differential binding of selected peptides to wild type and mutants with altered surfaces.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:51:24"}
• {"files"=>["https://ndownloader.figshare.com/files/375976", "https://ndownloader.figshare.com/files/376007"], "description"=>"<div><p>Finding unique peptides to target specific biological surfaces is crucial to basic research and technology development, though methods based on biological arrays or large libraries limit the speed and ease with which these necessary compounds can be found. We reasoned that because biological surfaces, such as cell surfaces, mineralized tissues, and various extracellular matrices have unique molecular compositions, they present unique physicochemical signatures to the surrounding medium which could be probed by peptides with appropriately corresponding physicochemical properties. To test this hypothesis, a naïve pilot library of 36 peptides, varying in their hydrophobicity and charge, was arranged in a two-dimensional matrix and screened against various biological surfaces. While the number of peptides in the matrix library was very small, we obtained “hits” against all biological surfaces probed. Sequence refinement of the “hits” led to peptides with markedly higher specificity and binding activity against screened biological surfaces. Genetic studies revealed that peptide binding to bacteria was mediated, at least in some cases, by specific cell-surface molecules, while examination of human tooth sections showed that this method can be used to derive peptides with highly specific binding to human tissue.</p> </div>", "links"=>[], "tags"=>["probing", "surfaces", "sparse-matrix", "peptide"], "article_id"=>134267, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0023551.s001", "https://dx.doi.org/10.1371/journal.pone.0023551.s002"], "stats"=>{"downloads"=>9, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rapid_Probing_of_Biological_Surfaces_with_a_Sparse_Matrix_Peptide_Library/134267", "title"=>"Rapid Probing of Biological Surfaces with a Sparse-Matrix Peptide Library", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-08-15 01:11:07"}
• {"files"=>["https://ndownloader.figshare.com/files/746624"], "description"=>"<p>Selected peptides are those that showed Langmuir-type behavior (See supplemental <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023551#pone.0023551.s001\" target=\"_blank\">Figure S1</a> for representative data plots).</p>", "links"=>[], "tags"=>["binding", "affinity", "monolayer", "concentrations", "peptides"], "article_id"=>416987, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Surface_binding_affinity_and_monolayer_concentrations_for_selected_peptides_against_S_aureus_/416987", "title"=>"Surface binding affinity and monolayer concentrations for selected peptides against <i>S. aureus</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-08-15 01:56:27"}
• {"files"=>["https://ndownloader.figshare.com/files/746494"], "description"=>"<p>Panel A, binding of pilot peptide matrix to human tooth enamel; panel B, binding of pilot matrix to human tooth dentin. Z axes show fluorescence intensity from stained cells (arbitrary units). Panel C, fluorescence image showing the binding of peptides E4 to human tooth enamel; panel D, fluorescence image showing the binding of peptide E6 to human tooth dentin. E, enamel; DEJ, dentin-enamel junction; D; dentin.</p>", "links"=>[], "tags"=>["matrix", "peptide", "e4", "e6", "enamel", "denin"], "article_id"=>416855, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g007", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_of_matrix_peptide_E4_and_E6_to_human_tooth_enamel_and_denin_respectively_/416855", "title"=>"Binding of matrix peptide E4 and E6 to human tooth enamel and denin respectively.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:54:15"}
• {"files"=>["https://ndownloader.figshare.com/files/746199"], "description"=>"<p>Fluorescence images were recorded and quantitated for peptide bound to various bacterial species. Panel A, peptide C3 from the original pilot matrix; Panel B, peptide A3 from the In-Plane refined matrix. Y axis represents relative levels of peptide binding, as indicated by the ratio of the intensity of fluorescent staining vs. background staining for the different bacteria listed along X-axis.</p>", "links"=>[], "tags"=>["binding"], "article_id"=>416569, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Specificities_of_representative_binding_peptides_/416569", "title"=>"Specificities of representative binding peptides.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:49:29"}
• {"files"=>["https://ndownloader.figshare.com/files/745940"], "description"=>"<p>Different bacterial and eukaryotic cells were immobilized, exposed to the peptides from the pilot peptide matrix, imaged and analyzed with image quantitation as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0023551#s2\" target=\"_blank\"><i>Methods</i></a>. Relative levels of peptide binding (as indicated by the ratio of the intensity of fluorescent staining vs background fluorescence) are shown on the Z axes.</p>", "links"=>[], "tags"=>["profiles", "peptide", "matrix"], "article_id"=>416315, "categories"=>["Biotechnology", "Biochemistry", "Microbiology"], "users"=>["Daniel K. Yarbrough", "Randal Eckert", "Jian He", "Elizabeth Hagerman", "Fengxia Qi", "Renate Lux", "Ben Wu", "Maxwell H. Anderson", "Wenyuan Shi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0023551.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_profiles_of_the_pilot_peptide_matrix_to_different_biological_surfaces_/416315", "title"=>"Binding profiles of the pilot peptide matrix to different biological surfaces.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-08-15 01:45:15"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime