Formation of Cystine Slipknots in Dimeric Proteins
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{"title"=>"Formation of Cystine Slipknots in Dimeric Proteins", "type"=>"journal", "authors"=>[{"first_name"=>"Mateusz", "last_name"=>"Sikora", "scopus_author_id"=>"35335335900"}, {"first_name"=>"Marek", "last_name"=>"Cieplak", "scopus_author_id"=>"22960465100"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368490098", "sgr"=>"84874786719", "pmid"=>"23520470", "scopus"=>"2-s2.0-84874786719", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0057443", "issn"=>"19326203"}, "id"=>"3732d393-7509-3746-a714-0dc0a3a4784e", "abstract"=>"We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.", "link"=>"http://www.mendeley.com/research/formation-cystine-slipknots-dimeric-proteins", "reader_count"=>8, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>4, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/982819"], "description"=>"<p>The cysteines involved in the cystine knot motif are shown as yellow circles. Other relevant sites are shown as circles either in blue, green, or magenta. In at least one of the four families shown here, these sites are occupied by cysteines – this happens if the circles are connected by lines, i.e. disulfide bonds. For instance, in 1BMP the green circles do not show cysteines but the sites that would house cysteines in the structure corresponding to 1FZV. The symbols N,C and N′, C′ in the drawings do not indicate locations of the terminal amino acids since the corresponding backbones do not end at these places. Rather, they indicate amino acids which are sequentialy closest to the indicated termini. The intra-monomer disulfide bridges are represented by thick black lines, whereas the inter-monomer bridges are shown as lines in cyan. The monomers in 1BMP and 1M4U<sub>A</sub> are connected through one cystine but in two different ways. In 1M4U<sub>A</sub> the cystine effectively links the rings as it provides connection of Cys230 on the ring through the nearby C termini Cys232 to Cys230′ on the other ring. In 1BMP it links amino acids just next to the ring-piercing cysteins. In 1FZV there are two binding cystines. Each of them links a ring in one monomer with an N-proximal segment in the other monomer. For 1BMP and 1FZV the rings comprise 8 amino acids. In the case of 1M4U<sub>A</sub>–10 amino acids. In the case of 1HRP, The vertical lines between two monomers indicate hydrophobic contacts and hydrogen bonds.</p>", "links"=>[], "tags"=>["representations", "types", "dimer", "architectures", "exemplified", "structures", "1bmp", "tgf", "vegf", "1hrp"], "article_id"=>648864, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g001", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representations_of_four_types_of_dimer_architectures_as_exemplified_by_structures_1BMP_and_1FZV_representing_the_TGF_and_VEGF_families_respectively_and_structures_1M4U_A_and_1HRP_as_indicated_/648864", "title"=>"Schematic representations of four types of dimer architectures as exemplified by structures 1BMP and 1FZV, representing the TGF and VEGF families respectively and structures 1M4U<sub>A</sub> and 1HRP as indicated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:29:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/982821"], "description"=>"<p>The termini are indicated. The unprimed symbols refer to one monomer and the primed symbols to the other. The terminal amino acids are indicated in black. The yellow spheres correspond to the atoms of sulfur belonging to the cystine rings. In the panel corresponding to 1FZV, the green spheres correspond to the cysteines that link the two monomers. In the panel corresponding to 1BMP, the atoms of sulfur in the cystines that link the two monomers are hidden behind the yellow spheres. In the panel corresponding to 1M4U<sub>A</sub>, the inter-monomeric disulfide bond is indicated by two spheres in pink; one of them is in front of the other.</p>", "links"=>[], "tags"=>["molecular", "dimeric", "structures"], "article_id"=>648865, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g002", "stats"=>{"downloads"=>1, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_molecular_representation_of_the_native_dimeric_structures_1FZV_BMP_and_1M4U_A_as_shown_by_the_labels_/648865", "title"=>"The molecular representation of the native dimeric structures 1FZV, BMP, and 1M4U<sub>A</sub> as shown by the labels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:29:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/982822"], "description"=>"<p>The ways of pulling are indicated in the upper left corner of each panel. The line with the symbol 1BMP<sub>M</sub> in the lowest panel indicates the result for a single monomer, if extracted from the dimer. For other curves, the line type for a given protein is the same in each panel.</p>", "links"=>[], "tags"=>["curves", "proteins", "tgf", "listed"], "article_id"=>648866, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g003", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_curves_for_the_proteins_of_the_TGF_family_that_are_listed_in_Table_1_/648866", "title"=>"The curves for the proteins of the TGF family that are listed in Table 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:29:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/982823"], "description"=>"<p>Similar to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-g002\" target=\"_blank\">figure 2</a> but for the VEGF proteins listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["vegf", "proteins", "listed"], "article_id"=>648867, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similar_to_figure_2_but_for_the_VEGF_proteins_listed_in_Table_1_/648867", "title"=>"Similar to figure 2 but for the VEGF proteins listed in Table 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:29:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/982824"], "description"=>"<p>peaks arise through manipulations of these kinds. The color coding is similar to that used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-g001\" target=\"_blank\">Figure 1</a>. In the top panel, the N terminus pulls on the blue loop of the first monomer. The resulting force is transferred to the second monomer through the inter-molecular cystine bridge that is shown in cyan. The second monomer is too big to cross the cystine ring and, therefore, the tension grows indefinitely, exceeding values needed to break covalent bonds. In the bottom panel, stretching results in an immediate allignment of the three cystine bridges: within the cystine knots (in yellow) and the intermolecular one, and in an indefinite growth of the tension.</p>", "links"=>[], "tags"=>["stretched", "conformations", "1bmp", "nc", "pulling"], "article_id"=>648868, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g005", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_stretched_conformations_of_1BMP_for_the_NC_top_panel_and_NN_bottom_panel_pulling_at_d_250_/648868", "title"=>"Examples of stretched conformations of 1BMP for the NC (top panel) and NN′ (bottom panel) pulling at <i>d</i> = 250 Å.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/982825"], "description"=>"<p>The corresponding values of <i>d</i> are indicated. The figure shows only the region in which the cystine slipknot forms. The first of the frames shows the knot near it’s native state. In the middle left panel the knot loop (shown in black) approaches the inside of the ring. In the next snapshot, it squeezes halfway through the ring. This is the stage corresponding to the highest tension reached during unfolding. In the next frame (top right), the loop has already slipped past the ring. At this point, the system is unable to return to the native state rapidly if the pulling spring is removed. Two subsequent frames show further extension of the protein. In the bottom right panel, the whole length of the slip-loop has crossed the ring: the slipknot is released. The second force peak is due to the formation of the cystine slipknot in the second monomer (not shown).</p>", "links"=>[], "tags"=>["snapshots", "1bmp"], "article_id"=>648869, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g006", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subsequent_snapshots_of_the_model_1BMP_during_the_C_C_8242_stretching_/648869", "title"=>"Subsequent snapshots of the model 1BMP during the C-C′ stretching.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/982826"], "description"=>"<p>Similar to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-g003\" target=\"_blank\">figures 3</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-g004\" target=\"_blank\">4</a> but for and the remaining proteins with cystine knots listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["proteins", "cystine", "knots", "listed"], "article_id"=>648870, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g007", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similar_to_figures_3_and_4_but_for_and_the_remaining_proteins_with_cystine_knots_listed_in_Table_1_/648870", "title"=>"Similar to figures 3 and 4 but for and the remaining proteins with cystine knots listed in Table 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/982828"], "description"=>"<p>The stretching is accomplished by the termini.</p>", "links"=>[], "tags"=>["curves", "monomeric", "proteins", "cystine", "knot", "listed"], "article_id"=>648872, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g008", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_curves_for_the_monomeric_proteins_with_a_cystine_knot_that_are_listed_in_Table_1_/648872", "title"=>"The curves for the monomeric proteins with a cystine knot that are listed in Table 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/982830"], "description"=>"<p>Below each panel, there is a corresponding plot obtained for 1BMP.</p>", "links"=>[], "tags"=>["stretching", "tgf", "choices", "attachment"], "article_id"=>648873, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g009", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanisms_involved_in_stretching_of_a_protein_from_the_TGF_family_for_the_four_choices_of_attachment_points_/648873", "title"=>"Mechanisms involved in stretching of a protein from the TGF family for the four choices of attachment points.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/982831"], "description"=>"<p>Below each panel, there is a corresponding plot.</p>", "links"=>[], "tags"=>["stretching", "noggin", "choices", "attachment"], "article_id"=>648874, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g010", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mechanisms_involved_in_stretching_of_noggin_for_the_four_choices_of_attachment_points_/648874", "title"=>"Mechanisms involved in stretching of noggin () for the four choices of attachment points.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/982834"], "description"=>"<p>The plots are for 1FZV.</p>", "links"=>[], "tags"=>["vegf"], "article_id"=>648876, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g011", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similar_to_figures_9_and_10_but_for_a_protein_from_the_VEGF_family_/648876", "title"=>"Similar to figures 9 and 10 but for a protein from the VEGF family.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/982835"], "description"=>"<p>Bottom row of panels: stretching of the monomeric 2GH0. The thick force line is for the N-Cys187 pulling and the thin force line is for a similar situation, in which, however, the contacts between the knot-loop (strands and in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057443#pone-0057443-g002\" target=\"_blank\">figure 2</a>) and the rest of the protein is removed. These contacts affect the angle at which the ring piercing cystine is dragged across the ring: they make the pulling at a small angle between the plane of the ring and the plane of the slipknot. In the absence of these contacts, the approach is more vertical which results in the observed reduction of the force.</p>", "links"=>[], "tags"=>["rows", "pulling", "monomeric", "1bmp", "points", "attachment"], "article_id"=>648877, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g012", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_two_rows_of_panels_Comparison_of_pulling_of_the_monomeric_1BMP_at_different_points_of_attachment_of_the_pulling_force_/648877", "title"=>"Top two rows of panels: Comparison of pulling of the monomeric 1BMP at different points of attachment of the pulling force.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/982836"], "description"=>"<p>The top panel shows the conventional stretching of a monomer by N and C termini. This kind of manipulation is inaccessible when the protein is in its active, dimeric state. Stretching in the dimeric N-C case, however, results in effectively shifting the location of the pulling force from the C-proximal cysteine on the ring to another cystine, Cys69, on this ring. The deformation of the ring is different and, in addition, the slip-loop crosses the ring more vertically. Both of these factors result in an overall reduction in the force in the dimeric N-C stretching.</p>", "links"=>[], "tags"=>["monomer", "1fzv", "points"], "article_id"=>648878, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.g013", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Stretching_of_the_monomer_of_1FZV_at_different_points_of_force_attachment_/648878", "title"=>"Stretching of the monomer of 1FZV at different points of force attachment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-09 12:30:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1006595"], "description"=>"<p> denotes in the monomeric case – when only one chain of the dimer is considered in the N-C mode. The four penultimate columns are for the the dimeric situation. The subscripts of indicate the mode of pulling. denotes the number of amino acids in the cystine ring. The last column shows a difference between melting temperature of a dimer and two separated monomers, in units of .</p>", "links"=>[], "tags"=>["proteins", "studied", "units", "pulling"], "article_id"=>667223, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057443.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Values_of_of_the_proteins_studied_here_in_units_of_and_for_different_pulling_schemes_/667223", "title"=>"Values of of the proteins studied here in units of /Å and for different pulling schemes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-08 02:00:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/982848", "https://ndownloader.figshare.com/files/982849"], "description"=>"<div><p>We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.</p> </div>", "links"=>[], "tags"=>["cystine", "slipknots", "dimeric", "proteins"], "article_id"=>648890, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Physics", "Biochemistry", "Biophysics"], "users"=>["Mateusz Sikora", "Marek Cieplak"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057443.s001", "https://dx.doi.org/10.1371/journal.pone.0057443.s002"], "stats"=>{"downloads"=>2, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Formation_of_Cystine_Slipknots_in_Dimeric_Proteins__/648890", "title"=>"Formation of Cystine Slipknots in Dimeric Proteins", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-09 12:35:32"}

PMC Usage Stats | Further Information

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Relative Metric

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