Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Publication Date
April 17, 2009
Journal
PLoS Computational Biology
Authors
Zheng Yang, Peter Májek & Ivet Bahar
Volume
5
Issue
4
Pages
e1000360
DOI
https://dx.plos.org/10.1371/journal.pcbi.1000360
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000360
Web of Science
000266214200025
Scopus
66249135330
Mendeley
http://www.mendeley.com/research/allosteric-transitions-supramolecular-systems-explored-network-models-application-chaperonin-groel
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL", "type"=>"journal", "authors"=>[{"first_name"=>"Zheng", "last_name"=>"Yang", "scopus_author_id"=>"57198698622"}, {"first_name"=>"Peter", "last_name"=>"Májek", "scopus_author_id"=>"26639616800"}, {"first_name"=>"Ivet", "last_name"=>"Bahar", "scopus_author_id"=>"7006697439"}], "year"=>2009, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-66249135330", "sgr"=>"66249135330", "issn"=>"1553734X", "doi"=>"10.1371/journal.pcbi.1000360", "pmid"=>"19381265", "isbn"=>"1553-734X", "pui"=>"354658169"}, "id"=>"da9c7e42-e0b0-3add-a292-92b27457a27e", "abstract"=>"Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensional energy landscape. This task becomes even more challenging in exploring molecular systems on the order of megadaltons. Coarse-grained models that lend themselves to analytical solutions appear to be the only possible means of approaching such cases. Motivated by the utility of elastic network models for describing the collective dynamics of biomolecular systems and by the growing theoretical and experimental evidence in support of the intrinsic accessibility of functional substates, we introduce a new method, adaptive anisotropic network model (aANM), for exploring functional transitions. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimization algorithm, and previous simulations support the utility of aANM as a computationally efficient, yet physically plausible, tool for unraveling potential transition pathways sampled by large complexes/assemblies. An important outcome is the assessment of the critical inter-residue interactions formed/broken near the transition state(s), most of which involve conserved residues.", "link"=>"http://www.mendeley.com/research/allosteric-transitions-supramolecular-systems-explored-network-models-application-chaperonin-groel", "reader_count"=>75, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>31, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>31, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Physics and Astronomy"=>8, "Chemical Engineering"=>1, "Chemistry"=>17, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>17}, "Physics and Astronomy"=>{"Physics and Astronomy"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Korea (South)"=>1, "Turkey"=>2, "Hong Kong"=>1, "Norway"=>1, "United States"=>5, "China"=>1, "United Kingdom"=>3, "Italy"=>1, "Estonia"=>1}, "group_count"=>3}

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Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/445892", "https://ndownloader.figshare.com/files/445934", "https://ndownloader.figshare.com/files/445979", "https://ndownloader.figshare.com/files/446005", "https://ndownloader.figshare.com/files/446040", "https://ndownloader.figshare.com/files/446088", "https://ndownloader.figshare.com/files/446130", "https://ndownloader.figshare.com/files/446176"], "description"=>"<div><p>Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensional energy landscape. This task becomes even more challenging in exploring molecular systems on the order of megadaltons. Coarse-grained models that lend themselves to analytical solutions appear to be the only possible means of approaching such cases. Motivated by the utility of elastic network models for describing the collective dynamics of biomolecular systems and by the growing theoretical and experimental evidence in support of the intrinsic accessibility of functional substates, we introduce a new method, <em>adaptive anisotropic network model</em> (<em>a</em>ANM), for exploring functional transitions. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimization algorithm, and previous simulations support the utility of <em>a</em>ANM as a computationally efficient, yet physically plausible, tool for unraveling potential transition pathways sampled by large complexes/assemblies. An important outcome is the assessment of the critical inter-residue interactions formed/broken near the transition state(s), most of which involve conserved residues.</p> </div>", "links"=>[], "tags"=>["allosteric", "transitions", "supramolecular", "systems", "explored", "network", "chaperonin", "groel"], "article_id"=>147880, "categories"=>["Biological Sciences", "Medicine", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s005", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s006", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s007", "https://dx.doi.org/10.1371/journal.pcbi.1000360.s008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Allosteric_Transitions_of_Supramolecular_Systems_Explored_by_Network___Models_Application_to_Chaperonin_GroEL/147880", "title"=>"Allosteric Transitions of Supramolecular Systems Explored by Network\n Models: Application to Chaperonin GroEL", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-04-17 02:11:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/901008"], "description"=>"<p>GroEL consists of two rings, <i>cis</i> and <i>trans</i>,\n which assume the states: T: ATP-free; R: ATP-bound prior to substrate\n (peptide) and co-chaperonin (GroES) binding; R′: ATP-, substrate-\n and GroES-bound; R″: ADP-, substrate- and GroES-bound. Subunits in\n the T state are shown in red, R in cyan; R′ in green, R″\n in blue, and the cap in purple. ATP and ADP are shown by blue and orange\n boxes. Successive events/reactions along the cycle are (A) binding of seven\n ATPs to induce the binding of the unfolded substrate (orange), (B)\n co-chaperonin binding, (C) ATP hydrolysis, (D) ATP binding to\n <i>trans</i> ring subunits, (E) release of ADPs, substrate (folded\n or partially folded) and GroES from the <i>cis</i> ring, (F)\n initiation of a new cycle where the roles of the <i>cis</i> and\n <i>trans</i> rings are inverted. Top-middle and bottom-left\n structures are related by rigid body rotation. Diagrams were generated using\n the data from the PDB in PyMOL (<a href=\"http://www.pymol.org\" target=\"_blank\">http://www.pymol.org</a>),\n except for the schematic views of the substrate and ligands included to\n provide a clearer description. The PDB ids for the structures T/T, R/T,\n R″/R, R′/T and R″/T are 1GR5, 2C7E and 1GRU\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Ranson2\" target=\"_blank\">[68]</a>, 2C7C <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Ranson1\" target=\"_blank\">[15]</a> and 1AON <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Xu1\" target=\"_blank\">[20]</a>,\n respectively.</p>", "links"=>[], "tags"=>["allosteric"], "article_id"=>571465, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GroEL_GroES_allosteric_cycle_/571465", "title"=>"GroEL/GroES allosteric cycle.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:24:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/901125"], "description"=>"<p>Two sets of intermediate conformations are generated, and \n (1≤<i>k</i>≤<i>k<sub>tot</sub></i>),\n starting from the known substates and , illustrated here for\n <i>k</i> = 1 and 2. The\n distance vector between the instantaneous endpoints at the\n <i>k<sup>th</sup></i> step is denoted as , and the deformation at each step is or . Dashed ellipses indicate isoenergetic\n contours.</p>", "links"=>[], "tags"=>["biophysics/theory and simulation", "Computational biology", "computational biology/macromolecular structure analysis", "computational biology/molecular dynamics"], "article_id"=>571587, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_description_of_a_ANM_method_/571587", "title"=>"Schematic description of <i>a</i>ANM method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:26:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/901213"], "description"=>"<p>Results are illustrated for <i>a</i>ANM steps\n <i>k</i> = 1, 7 and 13\n along the transition R″→T of a single subunit\n (subunit A in the respective PDB structures 1GRU and 1GR5). The left\n ordinate displays the correlation cosine between the distance vector\n <i>d</i><sup>(<i>k−1</i>)</sup>\n and the eigenvectors for 1≤<i>i</i>≤30 (black\n bars), and the right ordinate shows the corresponding cumulative\n squared cosine (Eq. (5)) (blue curve). The threshold\n <i>F<sub>min</sub></i> = 0.5\n for the cumulative square cosine implies the selection of\n <i>m<sub>A</sub></i><sup>(1)</sup> = 1,\n <i>m<sub>A</sub></i><sup>(7)</sup> = 3,\n and\n <i>m<sub>A</sub></i><sup>(13)</sup> = 23\n in evaluating <i>v</i><i><sub>A</sub></i><sup>(<i>k</i>)</sup> as indicated by the red\n lines and filled bars. See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-t001\" target=\"_blank\">Table 1</a> for the complete list of and values and associated RMSDs between intermediate\n conformations.</p>", "links"=>[], "tags"=>["cosine", "instantaneous", "vector", "and"], "article_id"=>571669, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_cosine_between_instantaneous_distance_vector_and_____eigenmodes_/571669", "title"=>"Correlation cosine between instantaneous distance vector and\n eigenmodes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:27:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/901436"], "description"=>"<p>(A) RMSD values, |<i>d</i><sup>(<i>k</i>)</sup>|\n /N, between instantaneous endpoints plotted as a function of\n iteration number <i>k</i>. The end states refer to subunit\n A in the PDB structures 1GRU and 1GR5. Results are shown for\n <i>F<sub>min</sub></i> = 0.4,\n 0.5, 0.6 and 0.7, corresponding to the allowable angular deviations\n of up to 50.8°, 45.0°, 39.2° and\n 33.2°, respectively, between and <i>v</i><i><sub>A</sub></i><sup>(<i>k</i>)</sup> (or <i>v</i><i><sub>B</sub></i><sup>(<i>k</i>)</sup>). (B) The energy profile\n for alternative pathways in arbitrary units. Note the significantly\n lower energy barrier compared to the interpolation (orange curve)\n between the endpoints. The black curve refers to the SDP trajectory.\n The reaction coordinate refers to the normalized projection of the\n instantaneous displacement on the original distance vector. (C)\n Series of conformations sampled along the reaction coordinate. The\n diagrams are colored by domains (equatorial, blue; intermediate,\n green; apical, red). (D) Movements of helices H, K and M sampled\n along the transition pathway. Three conformations are shown at\n decreasing transparency levels, starting from R″ (lightest\n color), to T (darkest).</p>", "links"=>[], "tags"=>["subunit"], "article_id"=>571901, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_R_8243_8594_T_transition_for_a_single_subunit_of_GroEL_/571901", "title"=>"R″→T transition for a single subunit of GroEL.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:31:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/901568"], "description"=>"<p>(A) Fragmentation of the SDP pathway for the transition\n 1GRU←→1GR5 of a subunit into nine macrosteps,\n consisting each of five frames. Same color scheme is adopted in\n panels B and C. (B) Correlation between SDP macrosteps and ANM modes\n accessible to the original conformation . (C) Same as panel B, for the right portion of the\n trajectory, i.e. the reconfiguration from 1GR5_A to 1GRU_A using the\n eigenvectors generated for 1GRU_A. Note that the early\n macrosteps from both directions are accounted for by a few slowest\n ANM modes, while increasingly higher modes are being recruited as\n the molecule proceeds away from its original conformation,\n consistent with the results found by <i>a</i>ANM (see\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-t001\" target=\"_blank\">Table 1</a>).\n (D) RMSD values between the intermediate conformations sampled by\n the <i>a</i>ANM and SDP methods. The <i>a</i>ANM\n results refer to the trajectory\n <i>F<sub>min</sub></i> = 0.5.\n The RMSDs between pairs of intermediates remain lower than 2.0\n Å at all steps (see the color-coded scale on the\n right).</p>", "links"=>[], "tags"=>["steepest", "descent", "pathway"], "article_id"=>572027, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_with_the_results_from_steepest_descent_pathway_SDP_____based_on_action_minimization_/572027", "title"=>"Comparison with the results from steepest descent pathway (SDP)\n based on action minimization.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:33:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/901709"], "description"=>"<p>(A) Energy profiles of the intact GroEL complex\n (R/T→R″/R) along the reaction coordinate computed\n by <i>a</i>ANM (blue) and Cartesian interpolation (orange)\n using the double-well potential given by Eq. (7). (B) Contribution\n of different modes at various steps (1, 6, 11 and 15) along the\n transition R/T→R″/R. Broader numbers of higher\n frequency modes are recruited as the structure approaches the energy\n barrier (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-t005\" target=\"_blank\">Table\n 5</a>). (C) Top view of structures sampled along the transition.\n Snapshots corresponding to conformations , , , and are shown. (D) Side view of the same structures.\n (E) Close-up views of pairs of adjacent subunits. The diagrams in\n panels C–E are color-coded according to the mobilities of\n residues (red: most mobile; blue: almost fixed). Note that the\n equatorial domains of <i>cis</i> ring subunits are almost\n fixed, while the largest motions occur at the apical domains of the\n same subunits.</p>", "links"=>[], "tags"=>["forms", "groel"], "article_id"=>572176, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transition_among_T_T_8594_R_T_8594_R_8243_R_forms_____of_the_intact_GroEL_complex_/572176", "title"=>"Transition among T/T→R/T→R″/R forms\n of the intact GroEL complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:36:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/901862"], "description"=>"<p>(A) Intersubunit interface near the intermediate domains (green) of\n two adjacent subunits in the <i>cis</i> ring. The\n backbones are shown in cartoon view and colored by domains: A\n (orange), I (green), and E (blue). Backbone atoms of three charged\n residues are shown by spheres. Positively and negatively charged\n residues are colored blue and red, respectively. (B) The\n inter-subunit hydrogen bond, E386-R197, in the T state of the\n <i>cis</i> ring (1GR5). (C) During the transition to\n state R″/R, residue E386 in the I domain moves towards K80\n (blue sphere) in the E domain of the adjacent subunit, while R197 on\n the A domain moves away from E386. (D) The final configuration in\n the R″ state of the <i>cis</i> ring, represented\n by 1GRU. Residue E386 now forms a new hydrogen bond with K80.</p>", "links"=>[], "tags"=>["inter-subunit", "interactions", "during", "groel"], "article_id"=>572316, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_cis_ring_inter_subunit_interactions_during_____the_transition_T_R_based_on_the_intact_GroEL_____structure_calculation_/572316", "title"=>"The <i>cis</i> ring inter-subunit interactions during\n the transition T→R″, based on the intact GroEL\n structure calculation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:38:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/901958"], "description"=>"<p>Results are shown for (A) T→R and (B)\n R→R″ transitions. See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360.s004\" target=\"_blank\">Figure\n S4</a> for the corresponding time dependences, and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-t006\" target=\"_blank\">Table 6</a> for the\n kinetic expressions and the comparison with the results from BD\n simulations by Hyeon <i>et al.</i><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Hyeon1\" target=\"_blank\">[18]</a>.</p>", "links"=>[], "tags"=>["distances", "salt-bridge", "forming", "pairs", "along"], "article_id"=>572419, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changes_in_the_distances_between_salt_bridge_forming_pairs_along_____the_a_ANM_reaction_coordinate_/572419", "title"=>"Changes in the distances between salt-bridge forming pairs along\n the <i>a</i>ANM reaction coordinate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:40:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/902071"], "description"=>"<p>The number of intra-subunit (panel A) and inter-subunit (panel B)\n native contacts that are disrupted (upper panel) and formed (lower\n panel) <i>vs.</i> the reaction coordinate. The results\n refer to\n <i>F<sub>min</sub></i> = 0.5\n for <i>cis</i> ring subunits along the transition from\n 2C7E (R/T) to 1GRU (R″/R). Each bar represents the number\n of native contacts formed/broken at a given <i>a</i>ANM\n iteration. Note the sharp increase near the energy barrier. See\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-g010\" target=\"_blank\">Figure 10</a>\n for the corresponding critical contacts.</p>", "links"=>[], "tags"=>["contacts", "r"], "article_id"=>572531, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_native_contacts_along_the_structural_transition_from_R_____to_R_8243_states_/572531", "title"=>"Evolution native contacts along the structural transition from R\n to R″ states.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:42:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/902234"], "description"=>"<p>Panel (A) shows the inter-residue contacts between adjacent subunits\n of the <i>cis</i> ring, which break up during the\n transition. The two subunits are colored in light pink and blue.\n Contact pairs are represented by spheres at the\n C<sup>α</sup> position, and by distinctive colors.\n Similarly, panel (B) shows the contacts newly formed during the\n transition. See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-t007\" target=\"_blank\">Table\n 7</a> for the complete list of residue pairs shown here. The\n contacts involving a pair of conserved residues are labeled using\n the same colors as the corresponding residues.</p>", "links"=>[], "tags"=>["inter-residue", "contacts", "r"], "article_id"=>572696, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Redistribution_of_inter_residue_contacts_at_the_transition_from_R_____to_R_8243_state_/572696", "title"=>"Redistribution of inter-residue contacts at the transition from R\n to R″ state.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-17 00:44:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/902313"], "description"=>"(*)<p><i>m<sub>T</sub></i><sup>(<i>k</i>)</sup> and\n <i>m<sub>R″</sub></i><sup>(<i>k</i>)</sup>\n are the number of modes recruited at step <i>k</i>,\n starting from the respective states\n <i>R″</i> and <i>T</i>;\n <i>RMSD</i> values are calculated using Eq. (3). A\n and B designate the respective states T and R″. The\n first row indicates the original RMSD of 12.33 Å\n between the two end points.</p>", "links"=>[], "tags"=>["groel", "subunit"], "article_id"=>572773, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_a_ANM_data_for_the_transition_of_a_GroEL_subunit_____between_R_and_T_forms__/572773", "title"=>"<i>a</i>ANM data for the transition of a GroEL subunit\n between R″ and T forms<sup>(*)</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:46:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/902332"], "description"=>"(*)<p>based on α-carbons. The states refer to <i>cis</i>\n ring subunit A (indicated by suffix _A).</p>", "links"=>[], "tags"=>["forms", "subunit", "states"], "article_id"=>572796, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RMSD_values_in_197_between_A_different_forms_of_a_subunit____and_B_different_states_of_the_intact_GroEL_/572796", "title"=>"RMSD values (in Å) between (A) different forms of a subunit\n and (B) different states of the intact GroEL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:46:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/902380"], "description"=>"(a)<p>The <i>RMSD</i>s refer to those between the\n intermediates generated by moving along the 1<sup>st</sup> ANM\n mode (columns 5–7), two modes (8–10) and\n three modes (11–13) in iteration\n <i>k</i> = 1 (see Eq.\n (3)). For each step (1<sup>st</sup> column), the results are\n separately given for the reconfiguration of the forward (first\n row), backward (2<sup>nd</sup> row) and simultaneous\n (3<sup>rd</sup> row) passages between the two endpoints.</p>(b)<p>Lowest frequency modes that exhibit a correlation cosine of\n >0.1 with <b><i>d</i></b><sup>(0)</sup> are selected. Note that these are all\n confined to the lowest frequency six ANM modes (see listed mode\n numbers).</p>", "links"=>[], "tags"=>["lowest", "modes", "cycle"], "article_id"=>572839, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contributions_of_the_lowest_frequency_modes_to_the_cycle_____T_R_R_T_a_/572839", "title"=>"Contributions of the lowest frequency modes to the cycle\n T→R→R″→T <sup>(a)</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:47:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/902413"], "description"=>"(a)<p>Major steps are those involving an RMSD larger than 3.2\n Å (∼resolution of some structures) between the\n end points.</p>(b)<p>2C7E′ is same as the PDB structure 2C7E, except for the\n inversion shown in step F of the allosteric cycle in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi-1000360-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["lowest", "modes", "major", "steps", "chaperonin", "allosteric"], "article_id"=>572867, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_contribution_of_lowest_frequency_modes_to_the_three_major_____steps_of_the_chaperonin_allosteric_cycle_a_/572867", "title"=>"The contribution of lowest frequency modes to the three major\n steps of the chaperonin allosteric cycle<sup>(a)</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:47:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/902441"], "description"=>"(*)<p><i>k</i> = 0 refers to\n the original RMSD between the end points. Results are obtained\n with\n <i>F<sub>min</sub></i> = 0.5.</p>", "links"=>[], "tags"=>["groel"], "article_id"=>572902, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_a_ANM_data_for_the_transition_of_Intact_GroEL_____complex__/572902", "title"=>"<i>a</i>ANM data for the transition of Intact GroEL\n complex<sup>(*)</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:48:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/902478"], "description"=>"(a)<p>BD simulations results were reported by Hyeon <i>et\n al.</i> (2006) <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Hyeon1\" target=\"_blank\">[18]</a>;\n time (t) in microseconds.</p>(b)<p><i>a</i>ANM results are reported for all salt-bridges\n that exhibited a monotonic time dependence (single or double\n exponential) with R<sup>2</sup>>0.85.</p>(c)<p>between the two sets of data (<i>a</i>ANM and BD) for\n each salt bridge.</p>", "links"=>[], "tags"=>["kinetics", "salt-bridge", "forming", "residues", "bd"], "article_id"=>572933, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_kinetics_of_salt_bridge_forming_residues_____obtained_by_a_ANM_and_BD_simulations_a_/572933", "title"=>"Comparison of the kinetics of salt-bridge forming residues\n obtained by <i>a</i>ANM and BD simulations<sup>(a)</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:48:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/902504"], "description"=>"(a)<p>Conserved residues are highlighted in boldface. The domains are\n shown in parentheses. The equatorial domain residues are\n Met1-Pro137 (E1) and Val411-Pro525 (E2); intermediate domain\n residues are Cys138-Gly192 (I1) and Val376-Gly419(I2); and the\n apical domain (A) consists of a contiguous segment\n Met193-Gly375.</p>(b)<p>The scores are based ConSurf Server <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Glaser1\" target=\"_blank\">[72]</a>,<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000360#pcbi.1000360-Landau1\" target=\"_blank\">[73]</a>\n calculation for GroEL sequence.</p>", "links"=>[], "tags"=>["inter-subunit", "contacts", "during"], "article_id"=>572969, "categories"=>["Biological Sciences", "Medicine", "Computational Biology", "Biophysics"], "users"=>["Zheng Yang", "Peter Májek", "Ivet Bahar"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000360.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Critical_inter_subunit_contacts_broken_formed_during_____R_8594_R_8243_/572969", "title"=>"Critical inter-subunit contacts broken/formed during\n R→R″.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-17 00:49:29"}

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