Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
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{"title"=>"Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding", "type"=>"journal", "authors"=>[{"first_name"=>"Suhani", "last_name"=>"Nagpal", "scopus_author_id"=>"56895781500"}, {"first_name"=>"Satyam", "last_name"=>"Tiwari", "scopus_author_id"=>"55319308700"}, {"first_name"=>"Koyeli", "last_name"=>"Mapa", "scopus_author_id"=>"24332393700"}, {"first_name"=>"Lipi", "last_name"=>"Thukral", "scopus_author_id"=>"16064985200"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "scopus"=>"2-s2.0-84943574390", "pui"=>"606367093", "doi"=>"10.1371/journal.pcbi.1004496", "sgr"=>"84943574390", "pmid"=>"26394388"}, "id"=>"1d68b2c7-0400-35e8-a3a0-cd0817337944", "abstract"=>"Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central \"hubs\". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.", "link"=>"http://www.mendeley.com/research/decoding-structural-properties-partially-unfolded-protein-substrate-en-route-chaperone-binding", "reader_count"=>13, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>6, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>5, "Chemical Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "India"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2284294", "https://ndownloader.figshare.com/files/2284295", "https://ndownloader.figshare.com/files/2284296", "https://ndownloader.figshare.com/files/2284297", "https://ndownloader.figshare.com/files/2284298", "https://ndownloader.figshare.com/files/2284299", "https://ndownloader.figshare.com/files/2284300", "https://ndownloader.figshare.com/files/2284301"], "description"=>"<div><p>Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The <i>E.coli</i> chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native <i>β</i>-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.</p></div>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552928, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004496.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s004", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s005", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s006", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s007", "https://dx.doi.org/10.1371/journal.pcbi.1004496.s008"], "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Decoding_Structural_Properties_of_a_Partially_Unfolded_Protein_Substrate_En_Route_to_Chaperone_Binding_/1552928", "title"=>"Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284292"], "description"=>"<p>A) Protein structures of DapA and TIM, highlighting their similar TIM barrel topology. B) Free energy contour map of TIM as a function of RMSD and <i>ρ</i> at 400 K as a control is depicted. The color bar denotes the Gibbs free energy in kJ/mol. The inset within the map shows distribution of fraction of native contacts, Q.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552926, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g009", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Energetics_of_GroEL_independent_protein_/1552926", "title"=>"Energetics of GroEL-independent protein.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284289"], "description"=>"<p>A) Emission spectra of free 1–8 ANS (final 10 <i>μ</i>M) in buffer solution and bound to DapA incubated at 308 K and 333 K are plotted. The spectra was recorded after incubation with DapA (final 2 <i>μ</i>M) subjected to thermal denaturation by gradual increase in temperature. B) “Exposed Hydrophobic Surface Contribution” (EHSC) as a function of major conformational transition events in I<sub>1</sub> and I<sub>2</sub> are plotted. Four primary events contribute to conformational transitions in DapA, namely, i) <i>α</i>-helix to random coil ii) <i>β</i>-sheet to random coil iii) random coil to <i>β</i>-sheet, and iv) <i>α</i>-helix to <i>β</i>-sheet. The contribution of each event is attributed to the surface exposed hydrophobic patches i.e., how much percentage of <i>α</i>-helix to random coil event is giving rise to the total hydrophobicity in intermediate structures. C-E) Representative snapshots of N, I<sub>1</sub> and I<sub>2</sub> showing a clear increase in exposed hydrophobic patches in intermediates with respect to native, where exposed non-polar atoms of the contributing residues are highlighted in red color.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552923, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g006", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Surface_exposed_hydrophobic_patches_/1552923", "title"=>"Surface exposed hydrophobic patches.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284288"], "description"=>"<p>A) Probability of each <i>α</i> and <i>β</i> secondary structural element normalized to the native protein structure as a function of amino acid residues is calculated. Comparison of I<sub>1</sub> and I<sub>2</sub> with N (native) reveals multiple conformational changes of <i>β</i>-sheets and <i>α</i>-helices as marked above in blue and green respectively. The secondary structures were assigned with DSSP. Error bars denote the standard deviation calculated from three simulations. B) The top panel shows the time occurrence of <i>α</i>-helix (magenta) to <i>β</i>-sheet (green) transition observed in <i>α</i>4 helix in one of the representative trajectory. In addition, <i>α</i>4 hydrogen bonds (in blue) and dihedral angle of His118 belonging to <i>α</i>4 (below) as a function of time are displayed, to indicate rearrangement of local bonding patterns.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552922, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g005", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_characteristics_of_intermediates_/1552922", "title"=>"Structural characteristics of intermediates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284291"], "description"=>"<p>A-C) Distribution of C-<i>α</i> distances of three crucial non-native interactions in I<sub>2</sub>: Val191-Leu151, His53-Tyr107, and His118-Leu114, as shown in blue, red, and magenta, respectively. The native protein distance distribution is shown in gray, where these non-native contacts are largely absent. D-E) Representative snapshots of the native and I<sub>2</sub> displaying the corresponding residues in colored stick representation.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552925, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g008", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_native_interactions_/1552925", "title"=>"Non-native interactions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284290"], "description"=>"<p>Representative snapshot of the native (A) and the I<sub>2</sub> structure (B), displaying IVL residues constituting a part of GroES-like binding motifs. In comparison to the native structure, these clusters are mostly solvent-exposed.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552924, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g007", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Surface_exposed_IVL_clusters_/1552924", "title"=>"Surface exposed IVL clusters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284287"], "description"=>"<p>A) Representative snapshots showing disruption of TIM barrel topology with <i>α</i> and <i>β</i>-region shown in blue and red color, respectively. B) Time evolution of distance between <i>α</i> and <i>β</i>-core for all three 400 K simulation shown in three shades of orange. For comparison, native 300 K is also shown in black. C) Time occurrence of representative <i>β</i>-core residues. The brown color represents the existence of beta-sheet secondary structure based on the dihedral angles.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552921, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g004", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conformational_heterogeneity_/1552921", "title"=>"Conformational heterogeneity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284285"], "description"=>"<p>A-C) Free energy contour maps of DapA as a function of RMSD and <i>ρ</i> for three different temperatures, namely; 310 K, 360 K and 400 K, respectively. The color bar denotes the Gibbs free energy in kJ/mol. The inset within the maps show distribution of fraction of native contacts, Q. Q is defined by the total number of native contacts for each trajectory frame divided by the total number of contacts in the native structure. D) Thermal melting curve of DapA derived from CD (in black) and REMD simulations (in green), is depicted (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004496#sec002\" target=\"_blank\">Methods</a> for details). The molar ellipticity values obtained at 222 nm were normalized between 0 to 1 as a function of temperature. E-F) displays RMSD distributions of <i>ρ</i>-RMSD, Q-RMSD SASA-RMSD maps for I<sub>1</sub> and I<sub>2</sub> configurations, respectively. The RMSD was calculated with respect to the native structure.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552919, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g002", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Thermodynamics_of_DapA_unfolding_/1552919", "title"=>"Thermodynamics of DapA unfolding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284286"], "description"=>"<p>A) Red and blue colored regions represents experimental characterization [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004496#pcbi.1004496.ref051\" target=\"_blank\">51</a>], displaying high- and less-protected amide groups, respectively. B) For all the peptide segments, number of hydrogen bonds with solvent molecules is shown. Dotted line indicates mean value of high-protected amide groups. The error bars denote the values computed from three 400 K trajectories populating I<sub>2</sub> conformers.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552920, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g003", "stats"=>{"downloads"=>3, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_Validation_of_intermediate_structures_with_HDX_MS_data_/1552920", "title"=>"Experimental Validation of intermediate structures with HDX-MS data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284284"], "description"=>"<p>A) The protein is composed of eleven <i>α</i>-helices surrounding the <i>β</i>-barrel superstructure composed of eight parallel <i>β</i>-strands shown in red and blue, respectively. B) Schematic representation of DapA topology displaying (<i>α/β</i>)<sub>8</sub> TIM barrel fold along with C-terminal <i>α</i>-helices (<i>α</i>9–11). The terminal residues of each secondary structural elements are labeled.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552918, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DapA_structure_/1552918", "title"=>"DapA structure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/2284293"], "description"=>"<p>Network graphs of N, I<sub>1</sub>, and I<sub>2</sub> are shown in panel A-C, respectively. The nodes represents the amino-acid residues, communication pathways are depicted in bold lines and two connected residues by thin lines. Residues are colored from dark to light violet according to their communication efficiency, calculated by the number of residues to which they are connected. High communication between interacting residues describe pathways of well-defined interactions and such chains of residues constitute the communication pathway through which signals are transmitted efficiently. D-F) Snapshots of native and intermediates, highlighting the stable cluster within each structure. The 2D and 3D graphs are drawn with GEPHI and CHIMERA. The communication pathways are calculated using the MONETA tool.</p>", "links"=>[], "tags"=>["binding measurements", "Partially Unfolded Protein Substrate", "En Route", "Decoding Structural Properties", "Chaperone Binding", "protein structures", "topologie", "mass spectrometry", "genomic variations", "topological signatures", "region", "obligate GroEL folder", "ans", "network graphs", "Thermodynamics analyses", "dynamics simulations", "E.coli chaperone"], "article_id"=>1552927, "categories"=>["Uncategorised"], "users"=>["Suhani Nagpal", "Satyam Tiwari", "Koyeli Mapa", "Lipi Thukral"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004496.g010", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intra_protein_network_representation_of_native_and_intermediate_structures_/1552927", "title"=>"Intra-protein network representation of native and intermediate structures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-09-22 04:18:28"}

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