Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain
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{"title"=>"Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain", "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"=>"Dirk", "last_name"=>"Trauner", "scopus_author_id"=>"7006165081"}, {"first_name"=>"Marcus", "last_name"=>"Elstner", "scopus_author_id"=>"7004554960"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"372971536", "doi"=>"10.1371/journal.pone.0092716", "sgr"=>"84899499184", "scopus"=>"2-s2.0-84899499184", "pmid"=>"24713651"}, "id"=>"65450849-d15b-3107-962e-0c379fa88b27", "abstract"=>"Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs). We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.", "link"=>"http://www.mendeley.com/research/ligand-photoisomerization-triggers-conformational-changes-iglur2-ligand-binding-domain", "reader_count"=>15, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2, "Other"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2, "Other"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>2, "Chemistry"=>6}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>6}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Portugal"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1454907"], "description"=>"<p>Seven protein X-ray crystal structures (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092716#s2\" target=\"_blank\">Methods</a> for references) are listed along with their co-crystallized compounds. ‘RMSD’ gives the root mean square deviation of the best ligand placement compared to the crystal structure position, ‘Score’ the corresponding binding strength prediction and ‘Rank’ the number of the best solution among all docking results for a complex.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "ligand", "docking", "calculations", "redocking", "co-crystallized", "ligands", "binding"], "article_id"=>991117, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.t001", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_ligand_docking_calculations_for_redocking_co_crystallized_ligands_into_their_binding_pockets_/991117", "title"=>"Summary of ligand docking calculations for redocking co-crystallized ligands into their binding pockets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454906"], "description"=>"<p>The blue protein structure is taken after equilibration run. The red protein structure is caused by <i>cis</i>-ATA-3 (grey bulk) in position 2. a) Front view; b) Side view.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "helix"], "article_id"=>991116, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g010", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_push_down_of_helix_H_/991116", "title"=>"Illustration of the push down of helix H.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454903"], "description"=>"<p>a) 900 ns after the isomerization to <i>cis</i>; b) 900 ns after back-isomerization to <i>trans</i>.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "azobenzene", "binding", "describes", "translocation"], "article_id"=>991113, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g007", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distance_between_the_azobenzene_and_the_binding_pocket_that_describes_the_translocation_from_position_1_to_position_2_/991113", "title"=>"The distance between the azobenzene and the binding pocket, that describes the translocation from position 1 to position 2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454901"], "description"=>"<p>The distance between G451 and S651 describes the opening of the LBD (a+c). The distance between E402 and T686 maps the formation of a hydrogen between the two residues (b+d).</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "equilibration", "md", "pos1", "pos2"], "article_id"=>991111, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_properties_along_the_equilibration_MD_for_POS1_a_b_and_POS2_c_d_/991111", "title"=>"Structural properties along the equilibration MD for POS1 (a+b) and POS2 (c+d).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454902"], "description"=>"<p>The distance between Gly451 and Ser651 describes the opening of the LBD (a+c). The distance between E402 and T686 maps the formation of a hydrogen between the two residues (b+d).</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "isomerization", "pos1", "pos2"], "article_id"=>991112, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_properties_after_the_isomerization_to_cis_for_POS1_a_b_and_POS2_c_d_/991112", "title"=>"Structural properties after the isomerization to <i>cis</i> for POS1 (a+b) and POS2 (c+d).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454900"], "description"=>"<p>a) LBD dimer with different colored monomers. The cyan spheres depict the center of mass of G451 and S651 within a monomer. The green spheres depict the center of mass of P632. b) LBD monomer. G451 and S651 are depicted by cyan spheres, P632 by a green sphere and the functional groups of E402 and T686 are depicted in blue.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics"], "article_id"=>991110, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_4_/991110", "title"=>"Figure 4", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454897"], "description"=>"<p>Chemical structure of <i>cis</i>-ATA-3.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics"], "article_id"=>991107, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g001", "stats"=>{"downloads"=>1, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chemical_structure_of_cis_ATA_3_/991107", "title"=>"Chemical structure of <i>cis</i>-ATA-3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454908"], "description"=>"<div><p>Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs). We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.</p></div>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "photo-isomerization", "triggers", "conformational", "iglur2", "ligand", "binding"], "article_id"=>991118, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ligand_Photo_Isomerization_Triggers_Conformational_Changes_in_iGluR2_Ligand_Binding_Domain_/991118", "title"=>"Ligand Photo-Isomerization Triggers Conformational Changes in iGluR2 Ligand Binding Domain", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454905"], "description"=>"<p>The vertical orange lines depict the isomerization. a) G451-S651 distance; b) P632 distance; c) Distance between the azobenzene and the pocket; d) distance between helix H and helix B.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics"], "article_id"=>991115, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g009", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Different_structural_properties_along_the_three_consecutive_MDs_/991115", "title"=>"Different structural properties along the three consecutive MDs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454904"], "description"=>"<p>a) The distance between Gly451 and Ser651 after the back-isomerization to <i>trans</i>; b) The distance between E402 and T686 after back-isomerization.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics"], "article_id"=>991114, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g008", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_8_/991114", "title"=>"Figure 8", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454899"], "description"=>"<p>(a) Position 1; (b) Position 2.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "binding", "positions"], "article_id"=>991109, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g003", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_two_proposed_binding_positions_for_ATA_3_/991109", "title"=>"The two proposed binding positions for ATA-3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1454898"], "description"=>"<p>The solid lines depict the adiabatic states. The dotted line shows the force field potential and the dashed line represents the switching potential, that mimics the isomerization.</p>", "links"=>[], "tags"=>["Biochemistry", "hormones", "Peptide hormones", "neuropeptides", "Neurochemistry", "Neurochemicals", "neurotransmitters", "proteins", "protein structure", "Protein folding", "Protein chemistry", "biophysics", "Biophysical simulations", "biotechnology", "Computational biology", "computational neuroscience", "molecular biology", "Macromolecular structure analysis", "neuroscience", "Sensory systems", "pharmacology", "Drug research and development", "drug discovery", "chemistry", "computational chemistry", "molecular dynamics", "Molecular mechanics", "torsion"], "article_id"=>991108, "categories"=>["Biological Sciences"], "users"=>["Tino Wolter", "Thomas Steinbrecher", "Dirk Trauner", "Marcus Elstner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0092716.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_picture_of_the_potential_energy_along_the_torsion_around_the_N_8202_8202_N_double_bond_/991108", "title"=>"Schematic picture of the potential energy along the torsion around the N = N double bond.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-08 03:57:23"}

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