Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions
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{"title"=>"Structure and function in homodimeric enzymes: Simulations of cooperative and independent functional motions", "type"=>"journal", "authors"=>[{"first_name"=>"Stephen A.", "last_name"=>"Wells", "scopus_author_id"=>"9237874800"}, {"first_name"=>"Marc W.", "last_name"=>"Van Der Kamp", "scopus_author_id"=>"22136534400"}, {"first_name"=>"John D.", "last_name"=>"McGeagh", "scopus_author_id"=>"37081583400"}, {"first_name"=>"Adrian J.", "last_name"=>"Mulholland", "scopus_author_id"=>"7004313834"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84941975748", "pui"=>"606057463", "doi"=>"10.1371/journal.pone.0133372", "sgr"=>"84941975748", "pmid"=>"26241964"}, "id"=>"76593d38-4f4e-3054-b64c-e0ccc74d5a8e", "abstract"=>"Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.", "link"=>"http://www.mendeley.com/research/structure-function-homodimeric-enzymes-simulations-cooperative-independent-functional-motions", "reader_count"=>30, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>9, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Researcher"=>9, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>4, "Chemistry"=>9}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>9}, "Physics and Astronomy"=>{"Physics and Astronomy"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "China"=>1, "Poland"=>1, "United Kingdom"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2200218"], "description"=>"<p>Chain A is depicted in dark blue, chain B in dark green, with the small domains transparent. A) open structure, PDB ID: 3ENJ.[<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.ref023\" target=\"_blank\">23</a>] B) closed structure, PDB ID: 2CTS.[<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.ref007\" target=\"_blank\">7</a>]</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501937, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g004", "stats"=>{"downloads"=>13, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pig_heart_citrate_synthase_CS_crystal_structures_with_the_angle_and_dihedral_measurements_labelled_/1501937", "title"=>"Pig heart citrate synthase (CS) crystal structures with the angle and dihedral measurements labelled.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200221"], "description"=>"<p>Plots of the ABC and BCD angles (panels A,B) and ABCD dihedral (panels C,D) that define the active sites opening as observed in the flexible motion trajectories biased along modes 7, 8 and 9 (small closed symbols) and in the MD trajectories (plus signs for every 100 ps) obtained starting from the open structure (A,C) and the closed structure (B,D). Trajectories are also shown for motion biased along constructed modes “9+7” (open triangles) and “9–7” (open diamonds). Measurements for the open (PDB ID: 3ENJ) and closed (PDB ID: 2CTS) structures are also indicated. (For definitions of ABC and BCD angles and ABCD dihedral, see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.g004\" target=\"_blank\">Fig 4</a>.)</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501940, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_geometric_simulation_and_molecular_dynamics_trajectories_of_citrate_synthase_/1501940", "title"=>"Comparison of geometric simulation and molecular dynamics trajectories of citrate synthase.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200222"], "description"=>"<p>Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501941, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g006", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Symmetric_A_and_asymmetric_B_forms_of_citrate_synthase_as_generated_by_the_geometric_simulations_red_blue_biased_along_normal_modes_9_A_and_7_B_started_from_the_open_structure_PDB_ID_3ENJ_compared_to_the_closed_structure_PDB_ID_2CTS_light_gray_/1501941", "title"=>"Symmetric (A) and asymmetric (B) forms of citrate synthase as generated by the geometric simulations (red, blue) biased along normal modes 9 (A) and 7 (B), started from the open structure (PDB ID: 3ENJ), compared to the closed structure (PDB ID: 2CTS, light gray).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200213"], "description"=>"<p>Chain A is depicted in dark purple, chain B in dark green, with C-terminal domains transparent. A) symmetric structure, PDB ID: 1XML.[<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.ref001\" target=\"_blank\">1</a>] B) asymmetric structure, PDB ID: 1XMM (complexed with m7GDP; not shown here).[<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.ref001\" target=\"_blank\">1</a>]</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501932, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g001", "stats"=>{"downloads"=>4, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DcpS_crystal_structures_with_the_cleft_distance_and_the_8216_hinge_angle_8217_measurements_labelled_/1501932", "title"=>"DcpS crystal structures with the cleft-distance and the ‘hinge-angle’ measurements labelled.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200214"], "description"=>"<p>1XML refers to the (approximately) symmetric structure (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.g001\" target=\"_blank\">Fig 1A</a>), 1XMM to the assymetric structure (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0133372#pone.0133372.g001\" target=\"_blank\">Fig 1B</a>) and 1XMM swapped to the asymmetric structure with swapped chain IDs. Plots of the Cα distance between Trp175 and Asp111’ for both actives sites (“AB” and “BA”) as observed in the flexible motion trajectories biased along modes 7, 8 and the linear combination of 7+8 (small closed symbols) and in the individual MD trajectories (crosses for every 100 ps); A) run 1, B) run 2, C) run 3, D) run 4.</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501933, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_geometric_simulation_and_molecular_dynamics_trajectories_of_DcpS_/1501933", "title"=>"Comparison of geometric simulation and molecular dynamics trajectories of DcpS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200232", "https://ndownloader.figshare.com/files/2200233", "https://ndownloader.figshare.com/files/2200234", "https://ndownloader.figshare.com/files/2200235", "https://ndownloader.figshare.com/files/2200236", "https://ndownloader.figshare.com/files/2200237", "https://ndownloader.figshare.com/files/2200238", "https://ndownloader.figshare.com/files/2200239", "https://ndownloader.figshare.com/files/2200240"], "description"=>"<div><p>Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) <i>and</i> asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.</p></div>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501950, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0133372.s001", "https://dx.doi.org/10.1371/journal.pone.0133372.s002", "https://dx.doi.org/10.1371/journal.pone.0133372.s003", "https://dx.doi.org/10.1371/journal.pone.0133372.s004", "https://dx.doi.org/10.1371/journal.pone.0133372.s005", "https://dx.doi.org/10.1371/journal.pone.0133372.s006", "https://dx.doi.org/10.1371/journal.pone.0133372.s007", "https://dx.doi.org/10.1371/journal.pone.0133372.s008", "https://dx.doi.org/10.1371/journal.pone.0133372.s009"], "stats"=>{"downloads"=>22, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_and_Function_in_Homodimeric_Enzymes_Simulations_of_Cooperative_and_Independent_Functional_Motions_/1501950", "title"=>"Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-04 03:18:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/2200216"], "description"=>"<p>C) Cα RMSDs to the symmetric (1XML) and asymmetric (1XMM) crystal structures for every 100<sup>th</sup> frame of the flexible motion simulations along mode 8 (blue) and mode 8+7 (red).</p>", "links"=>[], "tags"=>["DcpS scavenger decapping enzyme", "protein structure", "cs", "Many enzymes function", "dynamics simulations"], "article_id"=>1501935, "categories"=>["Biological Sciences"], "users"=>["Stephen A. Wells", "Marc W. van der Kamp", "John D. McGeagh", "Adrian J. Mulholland"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0133372.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structures_obtained_from_geometric_simulations_of_flexible_motion_biased_along_different_normal_mode_directions_mode_7_8_in_red_8211_see_text_mode_8_in_blue_and_MD_simulations_light_green_that_are_most_similar_to_A_the_asymmetric_structure_gray_PDB_ID_1X/1501935", "title"=>"Structures obtained from geometric simulations of flexible motion biased along different normal mode directions (mode 7+8 in red–see text, mode 8 in blue) and MD simulations (light green) that are most similar to (A) the asymmetric structure (gray; PDB ID: 1XMM) and (B) the chain-swapped asymmetric structure (gray).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-04 03:18:58"}

PMC Usage Stats | Further Information

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