The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study
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{"title"=>"The carboxy terminus of the ligand peptide determines the stability of the MHC class i molecule H-2Kb: A combined molecular dynamics and experimental study", "type"=>"journal", "authors"=>[{"first_name"=>"Esam Tolba", "last_name"=>"Abualrous", "scopus_author_id"=>"55578775700"}, {"first_name"=>"Sunil Kumar", "last_name"=>"Saini", "scopus_author_id"=>"57201596571"}, {"first_name"=>"Venkat Raman", "last_name"=>"Ramnarayan", "scopus_author_id"=>"56004378000"}, {"first_name"=>"Florin Tudor", "last_name"=>"Ilca", "scopus_author_id"=>"56398508700"}, {"first_name"=>"Martin", "last_name"=>"Zacharias", "scopus_author_id"=>"7005598310"}, {"first_name"=>"Sebastian", "last_name"=>"Springer", "scopus_author_id"=>"8773026400"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84942903569", "sgr"=>"84942903569", "pui"=>"606195813", "pmid"=>"26270965", "doi"=>"10.1371/journal.pone.0135421"}, "id"=>"be5eafa3-3aeb-393c-b437-d22364f61a9b", "abstract"=>"Major histocompatibility complex (MHC) class I molecules (proteins) bind peptides of eight to ten amino acids to present them at the cell surface to cytotoxic T cells. The class I binding groove binds the peptide via hydrogen bonds with the peptide termini and via diverse interactions with the anchor residue side chains of the peptide. To elucidate which of these interactions is most important for the thermodynamic and kinetic stability of the peptide-bound state, we have combined molecular dynamics simulations and experimental approaches in an investigation of the conformational dynamics and binding parameters of a murine class I molecule (H-2Kb) with optimal and truncated natural peptide epitopes. We show that the F pocket region dominates the conformational and thermodynamic properties of the binding groove, and that therefore the binding of the C terminus of the peptide to the F pocket region plays a crucial role in bringing about the peptide-bound state of MHC class I.", "link"=>"http://www.mendeley.com/research/carboxy-terminus-ligand-peptide-determines-stability-mhc-class-i-molecule-h2kb-combined-molecular-dy", "reader_count"=>19, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>4, "Other"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>6, "Student > Master"=>4, "Other"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>8, "Physics and Astronomy"=>1, "Chemistry"=>3, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Canada"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2211205"], "description"=>"<p><b>(A)</b> K<sup>b</sup>/β<sub>2</sub>m complexes folded empty or with SIINFEKL-derived peptide as indicated. <b>(B)</b> Analogous experiment, K<sup>b</sup>/β<sub>2</sub>m complexes with FAPGNYPAL-derived peptides. <b>(C) and (D)</b> correlations between ΔΔG values calculated from TDTF T<sub>m</sub> (in A, B) and ΔΔG values from MM/PBSA (<b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135421#pone.0135421.s006\" target=\"_blank\">S1 Table</a></b>).</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510048, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g004", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Thermal_denaturation_measured_by_tryptophan_fluorescence_TDTF_shows_the_T_m_of_K_b_946_2_m_empty_or_in_complex_with_peptide_/1510048", "title"=>"Thermal denaturation measured by tryptophan fluorescence (TDTF) shows the T<sub>m</sub> of K<sup>b</sup>/β<sub>2</sub>m empty or in complex with peptide.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211238", "https://ndownloader.figshare.com/files/2211239", "https://ndownloader.figshare.com/files/2211240", "https://ndownloader.figshare.com/files/2211241", "https://ndownloader.figshare.com/files/2211242", "https://ndownloader.figshare.com/files/2211243", "https://ndownloader.figshare.com/files/2211245"], "description"=>"<div><p>Major histocompatibility complex (MHC) class I molecules (proteins) bind peptides of eight to ten amino acids to present them at the cell surface to cytotoxic T cells. The class I binding groove binds the peptide via hydrogen bonds with the peptide termini and via diverse interactions with the anchor residue side chains of the peptide. To elucidate which of these interactions is most important for the thermodynamic and kinetic stability of the peptide-bound state, we have combined molecular dynamics simulations and experimental approaches in an investigation of the conformational dynamics and binding parameters of a murine class I molecule (H-2K<sup>b</sup>) with optimal and truncated natural peptide epitopes. We show that the F pocket region dominates the conformational and thermodynamic properties of the binding groove, and that therefore the binding of the C terminus of the peptide to the F pocket region plays a crucial role in bringing about the peptide-bound state of MHC class I.</p></div>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510061, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0135421.s001", "https://dx.doi.org/10.1371/journal.pone.0135421.s002", "https://dx.doi.org/10.1371/journal.pone.0135421.s003", "https://dx.doi.org/10.1371/journal.pone.0135421.s004", "https://dx.doi.org/10.1371/journal.pone.0135421.s005", "https://dx.doi.org/10.1371/journal.pone.0135421.s006", "https://dx.doi.org/10.1371/journal.pone.0135421.s007"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Carboxy_Terminus_of_the_Ligand_Peptide_Determines_the_Stability_of_the_MHC_Class_I_Molecule_H_2K_b_A_Combined_Molecular_Dynamics_and_Experimental_Study/1510061", "title"=>"The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2K<sup>b</sup>: A Combined Molecular Dynamics and Experimental Study", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211203"], "description"=>"<p>The empty molecule and the K<sup>b</sup>/C-terminally truncated peptide complex show high flexibility of the alpha helices lining the F pocket.</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510046, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Color_coded_view_of_the_configurational_flexibility_of_K_b_binding_groove_and_peptide_calculated_as_root_mean_square_fluctuations_RMSF_for_each_individual_residue_of_the_protein_from_two_independent_MD_simulations_of_complexes_with_peptide_derived_from_t/1510046", "title"=>"Color-coded view of the configurational flexibility of K<sup>b</sup> binding groove and peptide calculated as root mean square fluctuations (RMSF) for each individual residue of the protein from two independent MD simulations of complexes with peptide derived from the (A) K<sup>b</sup>/SIINFEKL or (B) K<sup>b</sup>/FAPGNYPAL structures and depicted as a color (blue to red) on a cartoon representation of K<sup>b</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211200"], "description"=>"<p>The values were calculated from frames of two independent MD simulations. <b>(A)</b> RMSD time course for trajectories of the complexes derived from the K<sup>b</sup>/SIINFEKL crystal structure. <b>(B)</b> RMSD probability distribution of all trajectories for each molecule. <b>(C)</b> RMSD time course for the trajectories of the complexes derived from the K<sup>b</sup>/FAPGNYPAL crystal structure. <b>(D)</b> RMSD probability distribution calculated over the trajectories for each molecule.</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510043, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Root_mean_square_deviation_RMSD_of_the_binding_groove_of_H_2K_b_residues_1_8211_180_gray_bound_to_the_indicated_peptides_/1510043", "title"=>"Root mean square deviation (RMSD) of the binding groove of H-2K<sup>b</sup> (residues 1–180, gray), bound to the indicated peptides.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211199"], "description"=>"<p><b>(A)</b> Cartoon representation of class I heavy chain (gray) and the light chain β<sub>2</sub>m (pink). <b>(B)</b> Top view of the H-2K<sup>b</sup> binding groove bound to an octamer antigenic peptide, SIINFEKL, represented as sticks of the peptide backbone (green carbon, red oxygen, and blue nitrogen). The hydrogen bonds between the peptide C and N termini and the binding groove are shown as red dashes. <b>(C)</b> The molecular surface of the F pocket (red) and the A pocket (yellow) of the H-2K<sup>b</sup> binding groove (gray).</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510042, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystal_structure_of_the_luminal_domain_of_H_2K_b_/1510042", "title"=>"Crystal structure of the luminal domain of H-2K<sup>b</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211213"], "description"=>"<p>Free energy changes were extracted from simulations of complexes with peptides derived from K<sup>b</sup>/SIINFEKL (<b>B</b>) or K<sup>b</sup>/FAPGNYPAL (<b>C</b>) structures. The start point and end point reaction coordinates are shown in the supporting material (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0135421#pone.0135421.s003\" target=\"_blank\">S3 Fig</a>).</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510056, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g008", "stats"=>{"downloads"=>1, "page_views"=>83, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculated_free_energy_change_potential_of_mean_force_PMF_obtained_from_umbrella_sampling_simulations_along_the_distance_between_the_alpha_carbon_of_the_P_969_and_the_bottom_of_the_F_pocket_/1510056", "title"=>"Calculated free energy change (potential of mean force, PMF) obtained from umbrella sampling simulations along the distance between the alpha carbon of the Pω and the bottom of the F pocket.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211211"], "description"=>"<p>RMA-S cells were incubated overnight at 25°C, then 10 μM peptide (as indicated) was added to the medium, and cells were transferred to 37°C. H-2K<sup>b</sup> surface levels were determined at each time point with MAb Y3 and flow cytometry. Averages ± SEM (n = 3) are normalized to initial mean fluorescence intensity (MFI).</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510054, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g007", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_K_b_C_terminally_truncated_peptide_complex_shows_the_lowest_stability_on_the_cell_surface_in_a_BFA_decay_experiment_/1510054", "title"=>"The K<sup>b</sup>/C-terminally truncated peptide complex shows the lowest stability on the cell surface in a BFA decay experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211208"], "description"=>"<p>K<sup>b</sup>/β<sub>2</sub>m complexes derived from the SIINFEKL (<b>A</b>) or the FAPGNYPAL (<b>B</b>) structures were folded empty and then incubated for 5 minutes with different concentrations of full-length, truncated, or modified peptides. The Pω truncated peptide shows the highest IC<sub>50</sub> value. Numerical IC<sub>50</sub> values: SIINFEKL, 0.19 μM; IINFEKL, 0.43 μM; SIINFEK, 7.7 μM; SIINFEKA, 0.12 μM; FAPGNYPAL, 0.16 μM; APGNYPAL, 0.15 μM; FAPGNYPA, 18.0 μM; FAPGNYPAA, 0.22 μM. Binding curves (left) are of one representative experiment, and the IC<sub>50</sub> values (right) are the average of three experiments.</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510051, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Half_maximal_concentration_of_peptide_IC_50_required_to_inhibit_the_binding_of_the_high_affinity_peptide_SIINFEK_TAMRA_L_/1510051", "title"=>"Half-maximal concentration of peptide (IC<sub>50</sub>) required to inhibit the binding of the high affinity peptide SIINFEK<sub>TAMRA</sub>L.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211206"], "description"=>"<p><b>(A)</b> Region I (black, A pocket region, residues 50–59 and 165–176), Region II (gray, C pocket region, residues 60–72 and 152–164), and Region III (red, F pocket region, residues 73–84 and 139–150). <b>(B) and (C)</b> Width variance of each region measured as the distance of the centers of masses of the α carbons of respective opposing helical segments for complex derived from the SIINFEKL <b>(B)</b> and FAPGNYPAL <b>(C)</b> crystal structures. Error bars represent standard deviation.</p>", "links"=>[], "tags"=>["F pocket region", "Experimental Study Major histocompatibility", "cytotoxic T cells", "anchor residue side chains", "peptide", "mhc", "binding groove", "Ligand Peptide Determines"], "article_id"=>1510049, "categories"=>["Biological Sciences"], "users"=>["Esam Tolba Abualrous", "Sunil Kumar Saini", "Venkat Raman Ramnarayan", "Florin Tudor Ilca", "Martin Zacharias", "Sebastian Springer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135421.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variation_of_the_binding_groove_width_in_MD_simulations_/1510049", "title"=>"Variation of the binding groove width in MD simulations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:51:42"}

PMC Usage Stats | Further Information

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Relative Metric

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