Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors
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{"title"=>"Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors", "type"=>"journal", "authors"=>[{"first_name"=>"Tino", "last_name"=>"Wolter", "scopus_author_id"=>"55633154600"}, {"first_name"=>"Thomas", "last_name"=>"Steinbrecher", "scopus_author_id"=>"6506854425"}, {"first_name"=>"Marcus", "last_name"=>"Elstner", "scopus_author_id"=>"7004554960"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84875433653", "doi"=>"10.1371/journal.pone.0058774", "pui"=>"368601581", "pmid"=>"23536824", "scopus"=>"2-s2.0-84875433653", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"7e8762d6-4f48-3989-80c9-5fef58738f3f", "abstract"=>"Neurological glutamate receptors are among the most important and intensely studied protein ligand binding systems in humans. They are crucial for the functioning of the central nervous system and involved in a variety of pathologies. Apart from the neurotransmitter glutamate, several artificial, agonistic and antagonistic ligands are known. Of particular interest here are novel photoswitchable agonists that would open the field of optogenetics to glutamate receptors. The receptor proteins are complex, membrane-bound multidomain oligomers that undergo large scale functional conformational changes, making detailed studies of their atomic structure challenging. Therefore, a thorough understanding of the microscopic details of ligand binding and receptor activation remains elusive in many cases. This topic has been successfully addressed by theoretical studies in the past and in this paper, we present extensive molecular dynamics simulation and free energy calculation results on the binding of AMPA and an AMPA derivative, which is the basis for designing light-sensitive ligands. We provide a two-step model for ligand binding domain activation and predict binding free energies for novel compounds in good agreement to experimental observations.", "link"=>"http://www.mendeley.com/research/computational-study-synthetic-agonist-ligands-ionotropic-glutamate-receptors", "reader_count"=>29, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>3}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>6, "Student > Postgraduate"=>3, "Student > Master"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>3, "Agricultural and Biological Sciences"=>13, "Neuroscience"=>1, "Physics and Astronomy"=>3, "Chemistry"=>5}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "reader_count_by_country"=>{"United States"=>1, "Japan"=>1, "Portugal"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/996459"], "description"=>"<p>Left: view from the front; middle: from the side. A wider opening of the LBD in MD compared to the crystal structure is observed. The two amino acid residues used to defined the opening reaction coordinate are shown in green. Right: Interdomain angle for the three simulations. Complex angles remain at ca 112 degrees compared to 140 degrees for the apo structure. To compute the interdomain angle, the domains have been defined as residues 394–495 and 732–771 for domain 1 and residues 500–728 for domain 2, connected by a flexible hinge comprising residues 496–499 and 729–731.</p>", "links"=>[], "tags"=>["apo-protein", "x-ray", "pdb", "interdomain", "300", "ns", "md", "simulation"], "article_id"=>659020, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g003", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_apo_protein_X_ray_crystal_structure_red_pdb_code_1FTO_and_the_structure_of_maximum_interdomain_angle_from_the_end_of_a_300_ns_MD_simulation_blue_/659020", "title"=>"Comparison of apo-protein X-ray crystal structure (red, pdb code 1FTO) and the structure of maximum interdomain angle from the end of a 300 ns MD simulation (blue).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/996461"], "description"=>"<p>At the start of the MD simulations, the AMPA-Thr655 hydrogen bond is water mediated (left), but after water dissociates out of the binding site it is replaced by a direct hydrogen bond (right). This is accompanied by a change of the AMPA-Ser654 backbone hydrogen bond into an AMPA-Ser654 sidechain one. The main ligand-LBD interaction between the AMPA-carboxylate and Arg485 is maintained. Shown is the part of the protein structure comprising the binding site (cyan cartoon representation), the ligand colored by element type in stick representation and crucial receptor amino acid sidechains interacting with the ligand.</p>", "links"=>[], "tags"=>["ampa-lbd", "hydrogen", "bonding"], "article_id"=>659022, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rearrangement_of_the_AMPA_LBD_hydrogen_bonding_network_/659022", "title"=>"Rearrangement of the AMPA-LBD hydrogen bonding network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:57:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/996454"], "description"=>"<p>For the complexes, the corresponding ligand RMSD-values are depicted as green curves.</p>", "links"=>[], "tags"=>["backbone", "300", "ns", "md", "simulations", "apo-protein", "ampa", "bta"], "article_id"=>659015, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g002", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RMSD_values_for_the_protein_backbone_red_from_300_ns_length_MD_simulations_of_the_apo_protein_top_AMPA_complex_middle_and_BTA_complex_bottom_/659015", "title"=>"RMSD-values for the protein backbone (red) from 300 ns length MD simulations of the apo-protein (top), AMPA complex (middle) and BTA complex (bottom).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:56:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/996482", "https://ndownloader.figshare.com/files/996493", "https://ndownloader.figshare.com/files/996496", "https://ndownloader.figshare.com/files/996497", "https://ndownloader.figshare.com/files/996498"], "description"=>"<div><p>Neurological glutamate receptors are among the most important and intensely studied protein ligand binding systems in humans. They are crucial for the functioning of the central nervous system and involved in a variety of pathologies. Apart from the neurotransmitter glutamate, several artificial, agonistic and antagonistic ligands are known. Of particular interest here are novel photoswitchable agonists that would open the field of optogenetics to glutamate receptors. The receptor proteins are complex, membrane-bound multidomain oligomers that undergo large scale functional conformational changes, making detailed studies of their atomic structure challenging. Therefore, a thorough understanding of the microscopic details of ligand binding and receptor activation remains elusive in many cases. This topic has been successfully addressed by theoretical studies in the past and in this paper, we present extensive molecular dynamics simulation and free energy calculation results on the binding of AMPA and an AMPA derivative, which is the basis for designing light-sensitive ligands. We provide a two-step model for ligand binding domain activation and predict binding free energies for novel compounds in good agreement to experimental observations.</p> </div>", "links"=>[], "tags"=>["computational", "synthetic", "agonist", "ligands", "ionotropic", "glutamate", "receptors"], "article_id"=>659029, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0058774.s001", "https://dx.doi.org/10.1371/journal.pone.0058774.s002", "https://dx.doi.org/10.1371/journal.pone.0058774.s003", "https://dx.doi.org/10.1371/journal.pone.0058774.s004", "https://dx.doi.org/10.1371/journal.pone.0058774.s005"], "stats"=>{"downloads"=>4, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Computational_Study_of_Synthetic_Agonist_Ligands_of_Ionotropic_Glutamate_Receptors__/659029", "title"=>"Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-26 07:00:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/996475"], "description"=>"<p>Both geometric parameters show very similar trends, indicating that the choice of CV for Metadynamics yields a meaningful exploration for functional interdomain motions.</p>", "links"=>[], "tags"=>["interdomain", "cv1", "500", "ns", "metadynamics"], "article_id"=>659028, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g009", "stats"=>{"downloads"=>3, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_time_evolution_of_the_interdomain_angle_black_and_main_collective_variable_CV1_red_over_the_course_of_a_500_ns_length_Metadynamics_simulation_/659028", "title"=>"Comparison of the time evolution of the interdomain angle (black) and main collective variable CV1 (red) over the course of a 500 ns length Metadynamics simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:59:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/996467"], "description"=>"<p>The different free energy curves correspond to sequential 50 ns parts of the per-window total 300 ns simulations. Depicted are the curves for the apo-protein (top), AMPA complex (middle) and BTA complex (bottom). The reaction coordinate is defined as the distance between the backbone center-of-mass of Gly451 and Ser652. For all three simulations, a minimum corresponding to the closed state at ca. 0.5 nm is found. For the two complexes, a second minimum at ca. 0.8 nm corresponding to the half-closed receptor state is observed. For the open state, flat free energy plateaus instead of harmonic minima are found, since the LBD is free to open very wide in our monomeric simulations.</p>", "links"=>[], "tags"=>["curves"], "article_id"=>659025, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g006", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PMF_free_energy_curves_for_the_opening_closing_motion_of_the_LBD_/659025", "title"=>"PMF free energy curves for the opening/closing motion of the LBD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:58:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008112"], "description"=>"<p>Free Energy differences were calculated by taking the differences of the Free Energy values at the corresponding minima in the free energy curve. Metadynamics results correspond to the “US Step 1” calculations.</p>", "links"=>[], "tags"=>["differences", "calculated", "umbrella", "sampling", "metadynamics"], "article_id"=>668738, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.t002", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Free_Energy_differences_calculated_by_Umbrella_Sampling_and_Metadynamics_in_kcal_mol_/668738", "title"=>"Free Energy differences calculated by Umbrella Sampling and Metadynamics (in kcal/mol).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-25 02:25:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/996464"], "description"=>"<p>The three modes depicted are labeled clamshell (CV1), twisting (CV2) and rocking (CV3) motion, respectively. For a better visualization of the eigenmodes in questions, we have added additional animated movies depicting the conformational changes. See Supplementary Material for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058774#pone.0058774.s003\" target=\"_blank\">Movies S1</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058774#pone.0058774.s004\" target=\"_blank\">S2</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058774#pone.0058774.s005\" target=\"_blank\">S3</a>.</p>", "links"=>[], "tags"=>["eigenvectors", "iglu2", "receptor", "conformational"], "article_id"=>659024, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g005", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Arrow_representation_for_the_three_main_eigenvectors_of_iGlu2_receptor_conformational_motion_/659024", "title"=>"Arrow representation for the three main eigenvectors of iGlu2 receptor conformational motion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:57:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008097"], "description"=>"<p>The X-ray crystal structures used for the closed, half-closed and open states had pdb identifiers 1FTM/2P2A, 1MQG and 1FTO, respectively. A clear correspondence of the observed minima and the receptor conformational states is found. Furthermore, the closed and half-closed receptor states appear consistently more similar to each other than either is to the open state, in good agreement to expectations.</p>", "links"=>[], "tags"=>["nm", "receptor", "conformations", "observed", "pmf"], "article_id"=>668718, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RMSD_values_in_nm_of_receptor_conformations_and_observed_PMF_minima_/668718", "title"=>"RMSD-values in nm of receptor conformations and observed PMF minima.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-25 02:25:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/996452"], "description"=>"<p>Chemical structures of AMPA (left) and 2-BnTetAMPA (right) shown in their zwitterionic state.</p>", "links"=>[], "tags"=>["structures", "ampa", "2-bntetampa", "zwitterionic"], "article_id"=>659013, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g001", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chemical_structures_of_AMPA_left_and_2_BnTetAMPA_right_shown_in_their_zwitterionic_state_/659013", "title"=>"Chemical structures of AMPA (left) and 2-BnTetAMPA (right) shown in their zwitterionic state.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:56:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/996472"], "description"=>"<p>Data from 500 ns of Metadynamics simulations is plotted for each complex. The two minima corresponding to the open and closed state of the LBD are indicated.</p>", "links"=>[], "tags"=>["projected", "variables", "ampa"], "article_id"=>659027, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g008", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_energy_surface_projected_onto_the_first_second_and_third_collective_variables_for_the_opening_closing_transition_of_the_AMPA_complex_/659027", "title"=>"Potential energy surface projected onto the first, second and third collective variables for the opening/closing transition of the AMPA complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:59:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/996470"], "description"=>"<p>The free energy curves correspond to data from 45 US windows using a total of 300 ns simulation length each. Depicted are the curves for the AMPA complex (top) and BTA complex (bottom). The reaction coordinate is defined as center-of-mass distance of the ligand and a group of protein residues, see text for details. For both simulations, a minimum corresponding to the tightly bound ligand at below 0.5 nm is found. During the unbinding process, we see a sharp rise of the free energy curve and a plateau at distances above 0.8 nm.</p>", "links"=>[], "tags"=>["curves", "ligand"], "article_id"=>659026, "categories"=>["Biotechnology", "Physics", "Biochemistry", "Biophysics", "Information And Computing Sciences", "Biological Sciences", "Neuroscience", "Chemistry"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0058774.g007", "stats"=>{"downloads"=>4, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PMF_free_energy_curves_for_the_removal_of_the_ligand_from_the_LBD_/659026", "title"=>"PMF free energy curves for the removal of the ligand from the LBD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-26 06:58:28"}

PMC Usage Stats | Further Information

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Relative Metric

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