The Structure of Plasmodium falciparum Blood-Stage 6-Cys Protein Pf41 Reveals an Unexpected Intra-Domain Insertion Required for Pf12 Coordination
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{"title"=>"The structure of plasmodium falciparum blood-stage 6-cys protein Pf41 reveals an unexpected intra-domain insertion required for Pf12 coordination", "type"=>"journal", "authors"=>[{"first_name"=>"Michelle L.", "last_name"=>"Parker", "scopus_author_id"=>"56957606400"}, {"first_name"=>"Fangni", "last_name"=>"Peng", "scopus_author_id"=>"55270083200"}, {"first_name"=>"Martin J.", "last_name"=>"Boulanger", "scopus_author_id"=>"7004573128"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84946924606", "sgr"=>"84946924606", "pui"=>"606828478", "isbn"=>"1932-6203 (Electronic) 1932-6203 (Linking)", "pmid"=>"26414347", "doi"=>"10.1371/journal.pone.0139407"}, "id"=>"43684868-3367-3b8c-979f-977915df63b2", "abstract"=>"Plasmodium falciparum is an apicomplexan parasite and the etiological agent of severe human malaria. The complex P. falciparum life cycle is supported by a diverse repertoire of surface proteins including the family of 6-Cys s48/45 antigens. Of these, Pf41 is localized to the surface of the blood-stage merozoite through its interaction with the glycophosphatidylinositol-anchored Pf12. Our recent structural characterization of Pf12 revealed two juxtaposed 6-Cys domains (D1 and D2). Pf41, however, contains an additional segment of 120 residues predicted to form a large spacer separating its two 6-Cys domains. To gain insight into the assembly mechanism and overall architecture of the Pf12-Pf41 complex, we first determined the 2.45 Å resolution crystal structure of Pf41 using zinc single-wavelength anomalous dispersion. Structural analysis revealed an unexpected domain organization where the Pf41 6-Cys domains are, in fact, intimately associated and the additional residues instead map predominately to an inserted domain-like region (ID) located between two β-strands in D1. Notably, the ID is largely proteolyzed in the final structure suggesting inherent flexibility. To assess the contribution of the ID to complex formation, we engineered a form of Pf41 where the ID was replaced by a short glycine-serine linker and showed by isothermal titration calorimetry that binding to Pf12 was abrogated. Finally, protease protection assays showed that the proteolytic susceptibility of the ID was significantly reduced in the complex, consistent with the Pf41 ID directly engaging Pf12. Collectively, these data establish the architectural organization of Pf41 and define an essential role for the Pf41 ID in promoting assembly of the Pf12-Pf41 heterodimeric complex.", "link"=>"http://www.mendeley.com/research/structure-plasmodium-falciparum-bloodstage-6cys-protein-pf41-reveals-unexpected-intradomain-insertio", "reader_count"=>13, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>3, "Student > Master"=>4, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>3, "Student > Master"=>4, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>7, "Medicine and Dentistry"=>1, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2291658"], "description"=>"<p><b>(A)</b> Schematic of the refined model of <i>Pf</i>41 domain organization. SP, signal peptide; D1, domain 1; D2, domain 2; ID, inserted domain-like region. Two constructs, <i>Pf</i>41 full length (FL, Lys21 to Ser378) and <i>Pf</i>41ΔID (Lys21 to Asp116–GSGGSG–Ser226 to Ser378), were used for ITC studies. <b>(B)</b> SEC column elution profiles of <i>Pf</i>41 FL (top) and <i>Pf</i>41ΔID (bottom). Solid lines represent the trace of <i>Pf</i>41 constructs (expected molecular mass: <i>Pf</i>41 FL, 41 kDa; <i>Pf</i>41ΔID, 29 kDa); the gray dashed lines represent SEC globular molecular mass standards, labelled in kDa. Note that the small peak at approximately 80 kDa for the <i>Pf</i>41 FL trace represents contaminating MBP-tagged protein due to incomplete cleavage with TEV protease. Monomeric peak fractions were pooled for ITC studies. <b>(C)</b> ITC profile of <i>Pf</i>41 constructs (FL and ΔID) titrated against <i>Pf</i>12 at 25°C.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558733, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.g003", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ITC_analysis_of_Pf_12_Pf_41_coordination_reveals_a_critical_role_for_the_Pf_41_ID_/1558733", "title"=>"ITC analysis of <i>Pf</i>12-<i>Pf</i>41 coordination reveals a critical role for the <i>Pf</i>41 ID.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-28 03:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2291651"], "description"=>"<p><b>(A)</b> Schematic comparison of predicted <i>Pf</i>41 domain organization with established <i>Pf</i>12 tandem 6-Cys domains. SP, signal peptide; D1, domain 1; D2, domain 2; arrow indicates GPI anchor attachment site. Black bars indicate disulfide connectivity. <b>(B)</b> Anomalous difference electron density map of <i>Pf</i>41 calculated at 8 sigma (orange mesh) around one of two high confidence zinc sites (grey sphere) used for phasing. Two Glu residues (Glu 132 and 134) were found to coordinate the zinc ion (along with His23 and Glu369 of two neighboring chains, not shown) and are shown in green ball-and-stick colored by element. <b>(C)</b> Left/middle<b>–</b>Orthogonal views of the <i>Pf</i>41 structure, shown as a cartoon backbone colored as in (A). Disulfides are shown in the left panel as ball-and-stick colored by element. A four residue un-modeled region in D1 is indicated by a dotted green connecting loop. Grey dotted lines extending out of α1” (inserted domain-like region, ID) and into β9 (D1) indicate the un-modeled region of the ID (~85 residues). Right–green surface of <i>Pf</i>41 in same orientation as (C, middle) colored as in (A), with the previously undefined region shown with a semi-transparent grey surface with underlying cartoon. <b>(D)</b> Left–Lys349 shown as green sticks colored by element with the positive Fo-Fc map shown as an orange mesh contoured at 2.5σ. Right–final σ-A weighted 2Fo-Fc electron density map shown as a purple mesh contoured at 1σ around the dimethylated lysines (MLY347 and 349). The symmetry mate against which the methylated lysines pack is shown as a semi-transparent grey surface. <b>(E)</b> Sequence of the ID and flanking secondary structure elements colored as in (A). Regions observed in the structure have a solid underline; un-modelled sequence and predicted secondary structure elements are indicated by dashed lines.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558726, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_of_Pf_41_reveals_that_a_large_sequence_insertion_predominately_maps_between_two_strands_in_D1_/1558726", "title"=>"The structure of <i>Pf</i>41 reveals that a large sequence insertion predominately maps between two β-strands in D1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-28 03:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2291661"], "description"=>"<p>SDS-PAGE analysis under reducing conditions of trypsin cleavage over time of <i>Pf</i>41 (top), <i>Pf</i>12 (middle) and <i>Pf</i>12-<i>Pf</i>41 mixture (bottom). FL, full length. Expected molecular weights: <i>Pf</i>41 FL, 41 kDa; D1, 25 kDa; D1 with the ID clipped in predicted coil region, 18 to 23 kDa; D2, 16 kDa. <i>Pf</i>12 FL, 34 kDa (C-term clipped: 32 kDa); D1, 18 kDa; D2, 16 kDa; N-term/C-term fragments from disordered loop cleavage: 10/24 kDa. <i>Pf</i>41 D1 doublet (+/- ID) and D2 were confirmed by mass spectrometry. Magenta arrows indicate clear <i>Pf</i>12 cleavage products.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558736, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.g004", "stats"=>{"downloads"=>0, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trypsin_protection_assay_reveals_complex_dependent_proteolytic_resistance_/1558736", "title"=>"Trypsin protection assay reveals complex-dependent proteolytic resistance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-28 03:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2291655"], "description"=>"<p><b>(A)</b> Orthogonal views of an overlay of <i>Pf</i>41 D1 (green cartoon with dark grey loops) on <i>Pf</i>12 D1 (PDB ID 2YMO; magenta cartoon and light grey loops). Disulfides are labeled, shown as ball-and-stick, and colored by element. <b>(B)</b> Orthogonal views of an overlay of <i>Pf</i>41 D2 on <i>Pf</i>12 D2, colored as in (A). <b>(C)</b> Overlay of <i>Pf</i>41 on <i>Pf</i>12, with the alignment anchored on D2, showing the different rotation of D1 relative to D2 (yellow curved arrow) in the two structures. The <i>Pf</i>41 linker sequence is indicated in the black box.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558730, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_of_Pf_41_refines_the_description_of_the_6_Cys_domain_and_shows_strong_similarity_to_Pf_12_/1558730", "title"=>"The structure of <i>Pf</i>41 refines the description of the 6-Cys domain and shows strong similarity to <i>Pf</i>12.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-28 03:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2291668"], "description"=>"<p><sup>a</sup> Values in parentheses are for the highest resolution shell</p><p><sup>b</sup> FOM is Figure of Merit from Phenix AutoSol [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139407#pone.0139407.ref025\" target=\"_blank\">25</a>]</p><p>DATA COLLECTION AND REFINEMENT STATISTICS.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558743, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.t001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DATA_COLLECTION_AND_REFINEMENT_STATISTICS_/1558743", "title"=>"DATA COLLECTION AND REFINEMENT STATISTICS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-09-28 03:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2291667"], "description"=>"<p><b>(A)</b> Cross-linking designations revised from [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139407#pone.0139407.ref015\" target=\"_blank\">15</a>]; <i>Pf</i>41 ID specific interactions are bolded and shaded light grey. <b>(B)</b> Refined model of <i>Pf</i>12-<i>Pf</i>41 complex generated by manual docking and guided by cross-linking data. <i>Pf</i>12 is shown as a magenta surface, and <i>Pf</i>41 as a green surface except a model of the ID generated in iTASSER [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139407#pone.0139407.ref042\" target=\"_blank\">42</a>] displayed as a grey semi-transparent surface. The <i>Pf</i>41 ID model represents the relative size of this region compared to D1 and D2 and approximates how the ID could contact both <i>Pf</i>12 D1 and D2, but further studies probing the detailed structure and flexibility of this region are still needed. A previously identified <i>Pf</i>41 ID phosphorylation site [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139407#pone.0139407.ref043\" target=\"_blank\">43</a>] is shown in yellow and indicated by a yellow arrow. The black dotted line indicates uncertainty in the exact interface between the tandem 6-Cys domains of <i>Pf</i>12 and <i>Pf</i>41.</p>", "links"=>[], "tags"=>["Pf 41", "protease protection assays", "2.45 Å resolution crystal structure", "Pf 12 Coordination Plasmodium falciparum", "falciparum life cycle", "Pf 12", "Pf 41 ID"], "article_id"=>1558742, "categories"=>["Uncategorised"], "users"=>["Michelle L. Parker", "Fangni Peng", "Martin J. Boulanger"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139407.g005", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_refined_Pf_12_Pf_41_heterodimeric_assembly_model_/1558742", "title"=>"A refined <i>Pf</i>12-<i>Pf</i>41 heterodimeric assembly model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-28 03:02:53"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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