Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
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{"title"=>"Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Shuo", "last_name"=>"Gu", "scopus_author_id"=>"55203941800"}, {"first_name"=>"Daniel Adriano", "last_name"=>"Silva", "scopus_author_id"=>"57188924698"}, {"first_name"=>"Luming", "last_name"=>"Meng", "scopus_author_id"=>"55267364700"}, {"first_name"=>"Alexander", "last_name"=>"Yue", "scopus_author_id"=>"56226780600"}, {"first_name"=>"Xuhui", "last_name"=>"Huang", "scopus_author_id"=>"55500171200"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"607916989", "sgr"=>"84928697282", "pmid"=>"25101697", "scopus"=>"2-s2.0-84928697282", "doi"=>"10.1371/journal.pcbi.1003767", "issn"=>"15537358"}, "id"=>"0c5f2f66-119e-3b55-b3ef-f1d1b2762894", "abstract"=>"Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.", "link"=>"http://www.mendeley.com/research/quantitatively-characterizing-ligand-binding-mechanisms-choline-binding-protein-using-markov-state-m", "reader_count"=>6, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>5}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>5}, "reader_count_by_subject_area"=>{"Physics and Astronomy"=>2, "Chemistry"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Computer Science"=>{"Computer Science"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1625671"], "description"=>"<p>(a) The X-ray bound conformation (red, PDB ID: 2REG) is superimposed with a conformation selected from MD simulations in the presence of ligands and with smallest RMSD to the bound state (blue). Four critical residues in the binding sites that are in direct contact with the ligand are highlighted in stick representation. (b) Distances (Å) between the center of mass of ligand and four centers of mass of critical residues in the binding site obtained from the holo structure (red bars) and five MD trajectories in which only those conformations after the ligand binding have been included in the analysis (blue bars).</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "selectively", "conformation", "s1", "holo"], "article_id"=>1131040, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Choline_can_selectively_bind_to_the_closed_protein_conformation_S1_to_reach_the_holo_state_/1131040", "title"=>"Choline can selectively bind to the closed protein conformation S1 to reach the holo state.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625669"], "description"=>"<p>(b) Representative conformations from these five states. The two domains of the protein are colored in cyan and green respectively, and two viewpoints, front and side views, are shown. (c) Projections of free energy landscape on the protein opening and twisting angle for each metastable conformational state. The interval between two adjacent contour levels is 1 kT.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "equilibrium", "populations", "metastable", "states", "MSM", "apo"], "article_id"=>1131038, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_a_The_equilibrium_populations_of_five_metastable_states_obtained_from_the_MSM_for_apo_ChoX_/1131038", "title"=>"(a) The equilibrium populations of five metastable states obtained from the MSM for apo ChoX.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625674"], "description"=>"<p>Conformational selection is dominant for most of the ligand concentration range for ChoX.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "conformational", "ligand"], "article_id"=>1131043, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_percentage_of_conformational_selection_mechanism_as_a_function_of_ligand_concentration_/1131043", "title"=>"The percentage of conformational selection mechanism as a function of ligand concentration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625673"], "description"=>"<p>(a) A representative conformation of S3L (blue) is overlaid with the X-ray bound state (red, PDB ID: 2REG). (b) The same as <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003767#pcbi-1003767-g004\" target=\"_blank\">Fig. 4b</a> except that the distances computed from 7 50-ns ligand binding MD simulations that the ligand binds state S3.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "simulations", "initiated", "s3", "spontaneous", "ligand"], "article_id"=>1131042, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g005", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MD_simulations_initiated_from_the_state_S3_that_exhibit_spontaneous_ligand_binding_/1131042", "title"=>"MD simulations initiated from the state S3 that exhibit spontaneous ligand binding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625694", "https://ndownloader.figshare.com/files/1625695", "https://ndownloader.figshare.com/files/1625696", "https://ndownloader.figshare.com/files/1625697", "https://ndownloader.figshare.com/files/1625698", "https://ndownloader.figshare.com/files/1625699", "https://ndownloader.figshare.com/files/1625700", "https://ndownloader.figshare.com/files/1625701", "https://ndownloader.figshare.com/files/1625702", "https://ndownloader.figshare.com/files/1625703", "https://ndownloader.figshare.com/files/1625704", "https://ndownloader.figshare.com/files/1625706", "https://ndownloader.figshare.com/files/1625707", "https://ndownloader.figshare.com/files/1625708", "https://ndownloader.figshare.com/files/1625709", "https://ndownloader.figshare.com/files/1625710", "https://ndownloader.figshare.com/files/1625711"], "description"=>"<div><p>Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.</p></div>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "characterizing", "ligand", "binding", "mechanisms", "choline", "markov"], "article_id"=>1131051, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003767.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s004", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s005", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s006", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s007", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s008", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s009", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s010", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s011", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s012", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s013", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s014", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s015", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s016", "https://dx.doi.org/10.1371/journal.pcbi.1003767.s017"], "stats"=>{"downloads"=>8, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitatively_Characterizing_the_Ligand_Binding_Mechanisms_of_Choline_Binding_Protein_Using_Markov_State_Model_Analysis_/1131051", "title"=>"Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625664"], "description"=>"<p>The free energy profiles were obtained by averaging over contributions from five different metastable states of MSMs weighted by their equilibrium populations. The unit of the color bar is kT. See SI Fig. S9 and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003767#s3\" target=\"_blank\">Methods</a> for the definition of opening and twisting angles.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "twisting", "angles", "apo"], "article_id"=>1131033, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Projections_of_the_free_energy_landscape_onto_the_opening_and_twisting_angles_for_the_apo_ChoX_/1131033", "title"=>"Projections of the free energy landscape onto the opening and twisting angles for the apo ChoX.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625663"], "description"=>"<p>The ligand choline is shown in red spheres.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "choline-binding", "chox", "apo-closed", "holo-closed"], "article_id"=>1131032, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.g001", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_cartoon_representation_of_the_choline_binding_protein_ChoX_in_a_apo_closed_PDB_ID_2RF1_and_b_holo_closed_PDB_ID_2REG_states_/1131032", "title"=>"A cartoon representation of the choline-binding protein ChoX in (a) apo-closed (PDB ID: 2RF1) and (b) holo-closed (PDB ID: 2REG) states.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-07 02:45:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/1625675"], "description"=>"<p>Parameters for the flux analysis.</p>", "links"=>[], "tags"=>["biophysics", "Biophysical simulations", "Computational biology", "flux"], "article_id"=>1131045, "categories"=>["Biological Sciences"], "users"=>["Shuo Gu", "Daniel-Adriano Silva", "Luming Meng", "Alexander Yue", "Xuhui Huang"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003767.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_for_the_flux_analysis_/1131045", "title"=>"Parameters for the flux analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-07 02:45:46"}

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Relative Metric

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