Imperfect Duplicate Insertions Type of Mutations in Plasmepsin V Modulates Binding Properties of PEXEL Motifs of Export Proteins in Indian Plasmodium vivax
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{"title"=>"Imperfect Duplicate Insertions Type of Mutations in Plasmepsin V Modulates Binding Properties of PEXEL Motifs of Export Proteins in Indian Plasmodium vivax", "type"=>"journal", "authors"=>[{"first_name"=>"Manmeet", "last_name"=>"Rawat", "scopus_author_id"=>"37050209300"}, {"first_name"=>"Sonam", "last_name"=>"Vijay", "scopus_author_id"=>"37050400000"}, {"first_name"=>"Yash", "last_name"=>"Gupta", "scopus_author_id"=>"56264689600"}, {"first_name"=>"Pramod Kumar", "last_name"=>"Tiwari", "scopus_author_id"=>"8673676200"}, {"first_name"=>"Arun", "last_name"=>"Sharma", "scopus_author_id"=>"7404971328"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23555891", "sgr"=>"84875492431", "doi"=>"10.1371/journal.pone.0060077", "scopus"=>"2-s2.0-84875492431", "pui"=>"368612384", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"3d556ac2-cbad-3e22-9003-c447c2cd20fe", "abstract"=>"INTRODUCTION: Plasmepsin V (PM-V) have functionally conserved orthologues across the Plasmodium genus who's binding and antigenic processing at the PEXEL motifs for export about 200-300 essential proteins is important for the virulence and viability of the causative Plasmodium species. This study was undertaken to determine P. vivax plasmepsin V Ind (PvPM-V-Ind) PEXEL motif export pathway for pathogenicity-related proteins/antigens export thereby altering plasmodium exportome during erythrocytic stages.\\n\\nMETHOD: We identify and characterize Plasmodium vivax plasmepsin-V-Ind (mutant) gene by cloning, sequence analysis, in silico bioinformatic protocols and structural modeling predictions based on docking studies on binding capacity with PEXEL motifs processing in terms of binding and accessibility of export proteins.\\n\\nRESULTS: Cloning and sequence analysis for genetic diversity demonstrates PvPM-V-Ind (mutant) gene is highly conserved among all isolates from different geographical regions of India. Imperfect duplicate insertion types of mutations (SVSE from 246-249 AA and SLSE from 266-269 AA) were identified among all Indian isolates in comparison to P.vivax Sal-1 (PvPM-V-Sal 1) isolate. In silico bioinformatics interaction studies of PEXEL peptide and active enzyme reveal that PvPM-V-Ind (mutant) is only active in endoplasmic reticulum lumen and membrane embedding is essential for activation of plasmepsin V. Structural modeling predictions based on docking studies with PEXEL motif show significant variation in substrate protein binding of these imperfect mutations with data mined PEXEL sequences. The predicted variation in the docking score and interacting amino acids of PvPM-V-Ind (mutant) proteins with PEXEL and lopinavir suggests a modulation in the activity of PvPM-V in terms of binding and accessibility at these sites.\\n\\nCONCLUSION/SIGNIFICANCE: Our functional modeled validation of PvPM-V-Ind (mutant) imperfect duplicate insertions with data mined PEXEL sequences leading to altered binding and substrate accessibility of the enzyme makes it a plausible target to investigate export mechanisms for in silico virtual screening and novel pharmacophore designing.", "link"=>"http://www.mendeley.com/research/imperfect-duplicate-insertions-type-mutations-plasmepsin-v-modulates-binding-properties-pexel-motifs", "reader_count"=>23, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>11, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"India"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1002377"], "description"=>"<p>(<b>A</b>) <i>Pv</i>PM-V Sal-1 (Wild Type) (<b>B</b>) <i>Pv</i>PM-V-Ind (mutant). Displaying docked PEXEL motif (sky blue helix) with the active site showing different pockets of interaction with different PEXEL amino acid side chains. Deepest pockets for are for first (green) and last (blue) AA. Low number of interacting AA (white) suggests more ambiguity allowed at the PEXEL member. Active aspartyl residues (red) clearly interact with the backbone of docked peptide at the point of cleavage.</p>", "links"=>[], "tags"=>["representations"], "article_id"=>663552, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g006", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_representations_of_model_Pv_PM_V_/663552", "title"=>"Structural representations of model <i>Pv</i>PM-V.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:48:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1013802"], "description"=>"*<p>The five true PEXEL used for the docking studies displaying the gene number and position of PEXEL motif on the gene. The true PEXEL used in this study tightly follows the true PEXEL formula i.e. [KR][GAVLIMFWPSTCYNQ][LI][GAVLIMFWPSTCYNQ] [DEQ]--.</p>", "links"=>[], "tags"=>["comparative", "docking", "pexel", "sal-1", "v-", "ind"], "article_id"=>674210, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.t002", "stats"=>{"downloads"=>5, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_comparative_docking_score_of_true_PEXEL_with_Pv_PM_V_Sal_1_wild_and_Pv_PM_V_Ind_mutant_/674210", "title"=>"The comparative docking score of true PEXEL with <i>Pv</i>PM-V Sal-1 (wild) and <i>Pv</i>PM V- Ind (mutant).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-29 01:10:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1013780"], "description"=>"<p>Variations in the interacting amino acids speculates that a modulation in the activity of plasmepsin-V might have resulted from imperfect duplicate mutations.</p>", "links"=>[], "tags"=>["variations", "interacting", "amino", "residues", "chains", "sal-1", "pexel", "inhibitor"], "article_id"=>674185, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_predicted_variations_in_the_interacting_amino_acid_residues_side_chains_of_Pv_PM_V_Sal_1_wild_and_Pv_PM_V_Ind_mutant_with_PEXEL_and_only_known_inhibitor_Lopinavir_/674185", "title"=>"The predicted variations in the interacting amino acid residues side chains of <i>Pv</i>PM-V Sal-1 (wild) and <i>Pv</i>PM-V-Ind (mutant) with PEXEL and only known inhibitor Lopinavir.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-29 01:09:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002381"], "description"=>"<p>(<b>A</b>) Displaying active site of the <i>Pv</i>PM-V Sal-1 (wild type) and its interaction with only known inhibitor lopinavir (red) (<b>B</b>) Displaying active site of the <i>Pv</i>PM-V-Ind (mutant) and its interaction with known inhibitor lopinavir (red). The docked lopinavir (red) showing interaction with hydrophobic amino acid residue (white) of the active site, while hydrophilic residues: acidic (red), Basic (blue) and neutral (green) comprise of the docking site. There are clear overall changes in structure as well as in interacting amino acids with the ligand.</p>", "links"=>[], "tags"=>["representations", "lopinavir"], "article_id"=>663554, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g007", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_representations_with_Lopinavir_interactions_/663554", "title"=>"Structural representations with Lopinavir interactions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:49:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1013824"], "description"=>"*<p>The loose PEXEL used in this study follows the PEXEL formula i.e. {[KR].[LI].[DEQ]}, where capital letters denote individual amino acids, multiple amino acids in brackets[XZ] represent ambiguity in pattern and full stop (.) means any amino acid.</p>", "links"=>[], "tags"=>["comparative", "docking", "pexel", "sal-1", "ind"], "article_id"=>674232, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.t003", "stats"=>{"downloads"=>4, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_comparative_docking_score_of_loose_PEXEL_with_Pv_PM_V_Sal_1_wild_and_Pv_PM_V_Ind_mutant_/674232", "title"=>"The comparative docking score of loose PEXEL with <i>Pv</i>PM-V Sal-1 (wild) and <i>Pv</i>PM-V- Ind (mutant).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-29 01:10:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002371"], "description"=>"<p><i>P. vivax</i>_Ind showing first imperfect duplication insertion type of mutation from 246 AA to 249 AA positions and second duplication insertion from 262 AA to 264 AA position.</p>", "links"=>[], "tags"=>["domains", "sal-1"], "article_id"=>663547, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g001", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_various_protein_signatures_domains_and_other_features_of_both_P_vivax_Sal_1_wild_type_and_P_vivax_Ind_mutant_plasmepsin_V_/663547", "title"=>"Schematic representation of various protein signatures, domains and other features of both <i>P. vivax</i> Sal-1 (wild type) and <i>P. vivax</i>_Ind (mutant) plasmepsin-V.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:46:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002373"], "description"=>"<p><i>Plasmodium vivax Pv</i>PM-V-Ind is the mutant sequence from the Indian isolates.</p>", "links"=>[], "tags"=>["alignment", "plasmepsin-v", "orthologues", "plasmodium"], "article_id"=>663548, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g002", "stats"=>{"downloads"=>2, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustal_W_multiple_sequence_alignment_of_plasmepsin_V_orthologues_within_plasmodium_genera_/663548", "title"=>"<i>Clustal W</i> multiple sequence alignment of plasmepsin-V orthologues within plasmodium genera.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:46:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002374"], "description"=>"<p>(<b>A</b>) Different orthologue sequences of plasmepsin-V from different pathogenic protozoan. <i>Plasmodium vivax</i>_Ind (<i>Pv</i>PM-V-Ind) is the mutant sequence from the Indian isolates. (<b>B</b>) Cropped and zoomed in phylogenetic tree from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060077#pone-0060077-g003\" target=\"_blank\">Figure 3A</a> showing Indian isolates to be a more evolved gene.</p>", "links"=>[], "tags"=>["plasmepsin", "-v", "joining"], "article_id"=>663549, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g003", "stats"=>{"downloads"=>2, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_bootstrap_of_plasmepsin_V_using_neighbor_joining_method_/663549", "title"=>"Phylogenetic analysis (bootstrap) <i>of</i> plasmepsin -V using neighbor joining method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:47:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002375"], "description"=>"<p>(<b>A</b>) Complete model with C-terminal trans-membrane domain (purple), the n-terminal pro-domain (lime) inhibiting the complete active site cleft with aspartic acid residue (red) and side chains. (<b>B</b>) Displaying structural changes after the cleavage of c-terminal trans-membrane domain (purple). The N-terminal prodomain peptide (lime) frees complete active site cleft after folding at hinge and competitively interacts with same amino acid residue side chains of the model as that of C-terminal in the native structure.</p>", "links"=>[], "tags"=>["representations", "plasmepsin-v"], "article_id"=>663550, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g004", "stats"=>{"downloads"=>1, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_cartoon_representations_of_model_of_plasmepsin_V_of_P_vivax_/663550", "title"=>"Structural cartoon representations of model of plasmepsin-V of <i>P. vivax</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:47:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/1002376"], "description"=>"<p>Showing high structural consensus in the side chain topology in even dissimilar sequences. Brown PVX10368 (tsekdfsvdkikeeyKFIEDsnfykiynelnwdcn) PEXEL sequence and Purple PVX092305 (ksedlpskvpdkllnKSLIDilnynfnvndvmgif) PEXEL sequence.</p>", "links"=>[], "tags"=>["alignment", "pexel"], "article_id"=>663551, "categories"=>["Biotechnology", "Biochemistry", "Infectious Diseases", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Manmeet Rawat", "Sonam Vijay", "Yash Gupta", "Pramod Kumar Tiwari", "Arun Sharma"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0060077.g005", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_alignment_of_PEXEL_domains_/663551", "title"=>"Structural alignment of PEXEL domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-30 07:48:02"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Parasitology", "average_usage"=>[354, 586, 723, 820, 941, 1045, 1176, 1283, 1391, 1469, 1526, 1639, 1730]}]}
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