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{"title"=>"3D profile-based approach to proteome-wide discovery of novel human chemokines", "type"=>"journal", "authors"=>[{"first_name"=>"Aurelie", "last_name"=>"Tomczak", "scopus_author_id"=>"44361658600"}, {"first_name"=>"Jana", "last_name"=>"Sontheimer", "scopus_author_id"=>"57195121658"}, {"first_name"=>"David", "last_name"=>"Drechsel", "scopus_author_id"=>"7006222773"}, {"first_name"=>"Rainer", "last_name"=>"Hausdorf", "scopus_author_id"=>"55208519000"}, {"first_name"=>"Marc", "last_name"=>"Gentzel", "scopus_author_id"=>"6602158334"}, {"first_name"=>"Andrej", "last_name"=>"Shevchenko", "scopus_author_id"=>"7201467952"}, {"first_name"=>"Stefanie", "last_name"=>"Eichler", "scopus_author_id"=>"55208420100"}, {"first_name"=>"Karim", "last_name"=>"Fahmy", "scopus_author_id"=>"7005554439"}, {"first_name"=>"Frank", "last_name"=>"Buchholz", "scopus_author_id"=>"7004999929"}, {"first_name"=>"M. Teresa", "last_name"=>"Pisabarro", "scopus_author_id"=>"16163569200"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22586462", "doi"=>"10.1371/journal.pone.0036151", "pui"=>"364751088", "issn"=>"19326203", "sgr"=>"84860637588", "scopus"=>"2-s2.0-84860637588"}, "id"=>"90b79b72-c01b-37bd-9bf9-2b386b91b4a8", "abstract"=>"Chemokines are small secreted proteins with important roles in immune responses. They consist of a conserved three-dimensional (3D) structure, so-called IL8-like chemokine fold, which is supported by disulfide bridges characteristic of this protein family. Sequence- and profile-based computational methods have been proficient in discovering novel chemokines by making use of their sequence-conserved cysteine patterns. However, it has been recently shown that some chemokines escaped annotation by these methods due to low sequence similarity to known chemokines and to different arrangement of cysteines in sequence and in 3D. Innovative methods overcoming the limitations of current techniques may allow the discovery of new remote homologs in the still functionally uncharacterized fraction of the human genome. We report a novel computational approach for proteome-wide identification of remote homologs of the chemokine family that uses fold recognition techniques in combination with a scaffold-based automatic mapping of disulfide bonds to define a 3D profile of the chemokine protein family. By applying our methodology to all currently uncharacterized human protein sequences, we have discovered two novel proteins that, without having significant sequence similarity to known chemokines or characteristic cysteine patterns, show strong structural resemblance to known anti-HIV chemokines. Detailed computational analysis and experimental structural investigations based on mass spectrometry and circular dichroism support our structural predictions and highlight several other chemokine-like features. The results obtained support their functional annotation as putative novel chemokines and encourage further experimental characterization. The identification of remote homologs of human chemokines may provide new insights into the molecular mechanisms causing pathologies such as cancer or AIDS, and may contribute to the development of novel treatments. Besides, the genome-wide applicability of our methodology based on 3D protein family profiles may open up new possibilities for improving and accelerating protein function annotation processes.", "link"=>"http://www.mendeley.com/research/3d-profilebased-approach-proteomewide-discovery-novel-human-chemokines", "reader_count"=>15, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Other"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>7, "Chemistry"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "India"=>1}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pone.0094402
• http://doi.org/10.1002/pro.2356
• http://doi.org/10.1002/bip.22771
• http://doi.org/10.1016/j.biotechadv.2017.02.001

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• {"files"=>["https://ndownloader.figshare.com/files/643081"], "description"=>"<p>A) Expression of two B42 isoforms in human tissues (expected size for isoform A: 272 bp). B) Sequencing results of the two different B42 isoforms. Isoform A codes for the full length B42 protein, whereas Isoform B contains a stop codon after 9 residues.</p>", "links"=>[], "tags"=>["b42"], "article_id"=>313568, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_and_gene_structure_of_the_B42_isoforms_/313568", "title"=>"Expression and gene structure of the B42 isoforms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 00:59:28"}
• {"files"=>["https://ndownloader.figshare.com/files/643568"], "description"=>"<p><i>ID</i>: Protein name; <i>Conf</i>: confidence level of prediction (TP, true positive; HC, high confidence; LC, low confidence); <i>UniProt</i>: UniProt identifier; <i>Seq</i>: sequence region selected; <i>Cys</i>: number of cysteines remaining after the pre-filtering; <i>Thx</i>: ProHit Threading Index; <i>%ID</i>: percentage of sequence identity between query and template; <i>chemokine template:</i> name of the best chemokine template structure; <i>diS</i>: number of possible disulfide bonds; <i>CK Rank</i>: rank of chemokine fold in the pdb95 control run (only fully covered alignments); <i>Control</i>: agreement of model with control structures; <i>SP</i>: predicted signal peptide; <i>SecP</i>: predicted non-classical secretion; <i>Loc</i>: subcellular location of the query predicted by PSORT (Ex, extracellular; Nu, nuclear), <i>Exon</i>: number of exons in the gene encoding the query protein; <i>Iph</i>: intron phase of the gene encoding the query protein; <i>ChrLoc</i>: chromosomal location of the gene encoding the query protein.</p>", "links"=>[], "tags"=>["properties", "predictions", "chemokine", "cxcl17"], "article_id"=>314050, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_sequence_and_structural_properties_of_the_best_four_predictions_and_chemokine_CXCL17_as_reference_/314050", "title"=>"Summary of sequence and structural properties of the best four predictions and chemokine CXCL17 as reference.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-07 01:07:30"}
• {"files"=>["https://ndownloader.figshare.com/files/642766"], "description"=>"<p>Uncharacterized human proteins are extracted from the UniProt Knowledgebase. Steps 1–4 are fully automated. The number of proteins that remain after each filter step is summarized on the right.</p>", "links"=>[], "tags"=>["genetics and genomics", "immunology", "Computational biology", "Biochemistry"], "article_id"=>313252, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_our_methodology_/313252", "title"=>"Overview of our methodology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 00:54:12"}
• {"files"=>["https://ndownloader.figshare.com/files/643417"], "description"=>"<p>The CD spectrum of chemokine vMIP-II taken from literature <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036151#pone.0036151-Kumar1\" target=\"_blank\">[68]</a> is shown (left) in comparison to the spectrum measured for B42 (right).</p>", "links"=>[], "tags"=>["dichroism", "spectra", "vmip-ii"], "article_id"=>313895, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g007", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_dichroism_CD_spectra_of_vMIP_II_and_B42_/313895", "title"=>"Circular dichroism (CD) spectra of vMIP-II and B42.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 01:04:55"}
• {"files"=>["https://ndownloader.figshare.com/files/642870"], "description"=>"<p>A) Sequence-to-structure alignment of B42 with its best scoring template vMIP-I (PDBId: 1ZXT). The secondary structure of vMIP-I is indicated below (yellow arrows for β-strands, red cylinders for α-helices, and dark grey line for coil regions; the light grey line indicates no atom coordinates for those residues in template). Cysteines are highlighted in boxes coloured (green, red, and blue) according to their pairing in each protein sequence. B) The 3D model of B42 (left) is compared with the X-ray structure of vMIP-I (right) used as template. Disulfide bonds are shown as orange sticks, and corresponding cysteines are labelled according to their pairing with the same colour code as in panel A. C) Sequence alignment of human B42 with its orthologous proteins (Ensembl release 54). Cysteines are highlighted in black boxes. The sequence identity between human and chimpanzee (Chimp_B42: ENSPTRG00000034188) is 98%, and 91% with oranguthan (OranUthan_B42: ENSPPYG00000010339).</p>", "links"=>[], "tags"=>["b42", "il8-like"], "article_id"=>313352, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modelling_of_the_B42_protein_as_an_IL8_like_chemokine_/313352", "title"=>"Modelling of the B42 protein as an IL8-like chemokine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 00:55:52"}
• {"files"=>["https://ndownloader.figshare.com/files/643288"], "description"=>"<p>Upper panel: Deconvolution of experimental spectrum with monoisotopic peak labelled. Inlay: SDS-page gel electrophoresis results to check B42 protein recovery. Lower panel: Theoretical isotopic distribution for [GA-B42] assuming 3 disulfide bonds, with monoisotopic peak labelled.</p>", "links"=>[], "tags"=>["genetics and genomics", "immunology", "Computational biology", "Biochemistry"], "article_id"=>313769, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deconvoluted_mass_spectrum_of_B42_/313769", "title"=>"Deconvoluted mass spectrum of B42.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 01:02:49"}
• {"files"=>["https://ndownloader.figshare.com/files/643608"], "description"=>"<p>Secondary structure fractions (in percentage and number of amino acids) calculated for the 3D model of B42 and compared with the experimentally determined fractions obtained by Circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopy.</p>", "links"=>[], "tags"=>["experimentally"], "article_id"=>314095, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.t004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_and_experimentally_determined_secondary_structure_content_of_B42_/314095", "title"=>"Predicted and experimentally determined secondary structure content of B42.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-07 01:08:15"}
• {"files"=>["https://ndownloader.figshare.com/files/331419", "https://ndownloader.figshare.com/files/331480", "https://ndownloader.figshare.com/files/331549", "https://ndownloader.figshare.com/files/331596", "https://ndownloader.figshare.com/files/331651", "https://ndownloader.figshare.com/files/331700", "https://ndownloader.figshare.com/files/331749", "https://ndownloader.figshare.com/files/331800", "https://ndownloader.figshare.com/files/331854", "https://ndownloader.figshare.com/files/331914", "https://ndownloader.figshare.com/files/331958", "https://ndownloader.figshare.com/files/332011"], "description"=>"<div><p>Chemokines are small secreted proteins with important roles in immune responses. They consist of a conserved three-dimensional (3D) structure, so-called IL8-like chemokine fold, which is supported by disulfide bridges characteristic of this protein family. Sequence- and profile-based computational methods have been proficient in discovering novel chemokines by making use of their sequence-conserved cysteine patterns. However, it has been recently shown that some chemokines escaped annotation by these methods due to low sequence similarity to known chemokines and to different arrangement of cysteines in sequence and in 3D. Innovative methods overcoming the limitations of current techniques may allow the discovery of new remote homologs in the still functionally uncharacterized fraction of the human genome. We report a novel computational approach for proteome-wide identification of remote homologs of the chemokine family that uses fold recognition techniques in combination with a scaffold-based automatic mapping of disulfide bonds to define a 3D profile of the chemokine protein family. By applying our methodology to all currently uncharacterized human protein sequences, we have discovered two novel proteins that, without having significant sequence similarity to known chemokines or characteristic cysteine patterns, show strong structural resemblance to known anti-HIV chemokines. Detailed computational analysis and experimental structural investigations based on mass spectrometry and circular dichroism support our structural predictions and highlight several other chemokine-like features. The results obtained support their functional annotation as putative novel chemokines and encourage further experimental characterization. The identification of remote homologs of human chemokines may provide new insights into the molecular mechanisms causing pathologies such as cancer or AIDS, and may contribute to the development of novel treatments. Besides, the genome-wide applicability of our methodology based on 3D protein family profiles may open up new possibilities for improving and accelerating protein function annotation processes.</p> </div>", "links"=>[], "tags"=>["3d", "profile-based", "proteome-wide", "chemokines"], "article_id"=>125428, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036151.s001", "https://dx.doi.org/10.1371/journal.pone.0036151.s002", "https://dx.doi.org/10.1371/journal.pone.0036151.s003", "https://dx.doi.org/10.1371/journal.pone.0036151.s004", "https://dx.doi.org/10.1371/journal.pone.0036151.s005", "https://dx.doi.org/10.1371/journal.pone.0036151.s006", "https://dx.doi.org/10.1371/journal.pone.0036151.s007", "https://dx.doi.org/10.1371/journal.pone.0036151.s008", "https://dx.doi.org/10.1371/journal.pone.0036151.s009", "https://dx.doi.org/10.1371/journal.pone.0036151.s010", "https://dx.doi.org/10.1371/journal.pone.0036151.s011", "https://dx.doi.org/10.1371/journal.pone.0036151.s012"], "stats"=>{"downloads"=>72, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/3D_Profile_Based_Approach_to_Proteome_Wide_Discovery_of_Novel_Human_Chemokines/125428", "title"=>"3D Profile-Based Approach to Proteome-Wide Discovery of Novel Human Chemokines", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-07 01:30:28"}
• {"files"=>["https://ndownloader.figshare.com/files/643487"], "description"=>"<p><i>Rank</i>: rank of hit within all chemokine structures in the fold library; <i>Thx</i>: threading index; <i>%ID</i>: percentage of sequence identity between query and template; <i>CK Template</i>: PDB template; <i>PDB</i>: template identifier in the Protein Data Bank; <i>chain:</i> template chain; <i>pl</i>: alignment path length; <i>fl</i>: template fold length; <i>UniProt</i>: UniProt identifier; <i>Ragonist</i>: Chemokine receptors for which the template protein is an agonist; <i>Rantagonist</i>: Chemokine receptors for which the template protein is an antagonist.</p>", "links"=>[], "tags"=>["hits", "b42"], "article_id"=>313976, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fold_recognition_results_for_the_top_five_hits_obtained_for_B42_with_the_Chemokine_fold_library_/313976", "title"=>"Fold recognition results for the top five hits obtained for B42 with the <i>Chemokine fold library</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-07 01:06:16"}
• {"files"=>["https://ndownloader.figshare.com/files/643523"], "description"=>"<p>Only best template per SCOP fold is shown. <i>Rank</i>: rank of hit within all structures in the fold library <i>Conf:</i> confidence level of prediction (HC, high confidence; FP, false positive); <i>sse</i>: all secondary structure elements present in alignment; <i>gap</i>: gaps shorter than 10 amino acids; <i>fcov</i>: fold coverage based on ratio of fold length/path length (fl/pl); <i>Thx</i>: threading index; <i>%ID</i>: percentage of sequence identity between query and template; <i>SCOP</i>: SCOP family identifier; <i>%Cov</i>: percentage of domain coverage; <i>Template</i>: PDB template; <i>PDB</i>: template identifier in the Protein Data Bank, <i>Chain</i>: template chain; <i>pl</i>: alignment path length; <i>fl</i>: template fold length; <i>UniProt</i>: template UniProt identifier; <i>Pfam</i>: Pfam description.</p>", "links"=>[], "tags"=>["hits", "b42"], "article_id"=>314010, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fold_recognition_results_for_the_five_top_fold_hits_obtained_for_B42_with_the_pdb95_fold_library_/314010", "title"=>"Fold recognition results for the five top fold hits obtained for B42 with the <i>pdb95 fold library</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-07 01:06:50"}
• {"files"=>["https://ndownloader.figshare.com/files/643173"], "description"=>"<p>A) Westernblot analysis of the C-terminal GFP-tagged B42 transgenic cell pool using an antibody to GFP. A weak band of the expected size 39.8 kDa (GFP-tag: 31 kDa+B42 8.8 kDa) was detected (marked with *). B) Immunoflourescent staining of the transgenic cell line. Two positive and two negative cells of the cell pool are shown. Localization of the C-terminal GFP-tagged B42 protein is mainly in the cytoplasm of HeLa cells: GFP - green, alpha-tubulin - red, DNA (DAPI) – blue. C) Only GFP-signal of B is shown in grey scale.</p>", "links"=>[], "tags"=>["localization"], "article_id"=>313661, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_localization_results_of_B42_/313661", "title"=>"Protein localization results of B42.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 01:01:01"}
• {"files"=>["https://ndownloader.figshare.com/files/642985"], "description"=>"<p>A) Sequence-to-structure alignment of the mature N73 (without signal peptide) with its best scoring template vMIP-II (PDBId: 2FJ2). The secondary structure of vMIP-II is indicated below (yellow arrows for β-strands, red cylinders for α-helices, and dark grey line for coil regions; the light grey line indicates no atom coordinates for those residues in template). Cysteines are highlighted in boxes coloured (green, red, and blue) according to their pairing in each protein sequence. B) The 3D model of N73 (left) is compared with the X-ray structure of vMIP-II (right) used as template. Disulfide bonds are shown as orange sticks, and corresponding cysteines are labelled according to their pairing with the same colour code as in panel A. C) Sequence alignment of the human N73 precursor with its orthologous proteins. Cysteines are highlighted in black boxes. Predicted N-glycosylation sites are shown in pink boxes, and the RGD motif in orange boxes. Under the alignment, ‘s’ indicates location of signal peptide (SP), ‘*’ indicates location of low complexity region (LCR), ‘c’ indicates location of predicted chemokine domain, ‘g’ indicates motif for glycosaminoglycan attachment at a serine residue, and ‘∼’ indicates location of disordered region predicted by GlobPlot. The sequence identity between human and gorilla (pre_N73_Gorilla: ENSGGOP00000010336) is 96%, and 45% with bushbaby (pre_N73_Bushb: ENSOGAP00000012479).</p>", "links"=>[], "tags"=>["n73", "il8-like"], "article_id"=>313471, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Immunology"], "users"=>["Aurelie Tomczak", "Jana Sontheimer", "David Drechsel", "Rainer Hausdorf", "Marc Gentzel", "Andrej Shevchenko", "Stefanie Eichler", "Karim Fahmy", "Frank Buchholz", "M. Teresa Pisabarro"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036151.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modelling_of_the_N73_protein_as_an_IL8_like_chemokine_/313471", "title"=>"Modelling of the N73 protein as an IL8-like chemokine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-07 00:57:51"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime