Modeling Transmembrane Domain Dimers/Trimers of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the Membrane
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{"title"=>"Modeling transmembrane domain dimers/trimers of plexin receptors: Implications for mechanisms of signal transmission across the membrane", "type"=>"journal", "authors"=>[{"first_name"=>"Liqun", "last_name"=>"Zhang", "scopus_author_id"=>"55934251700"}, {"first_name"=>"Anton", "last_name"=>"Polyansky", "scopus_author_id"=>"8680534300"}, {"first_name"=>"Matthias", "last_name"=>"Buck", "scopus_author_id"=>"35271219400"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"603600201", "sgr"=>"84926641281", "issn"=>"19326203", "pmid"=>"25837709", "scopus"=>"2-s2.0-84926641281", "doi"=>"10.1371/journal.pone.0121513", "isbn"=>"10.1371/journal.pone.0121513"}, "id"=>"e958e142-43f3-3e24-a55f-04db012258e4", "abstract"=>"Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and -B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, -A3, -A4, -C1 and -D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 - trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.", "link"=>"http://www.mendeley.com/research/modeling-transmembrane-domain-dimerstrimers-plexin-receptors-implications-mechanisms-signal-transmis", "reader_count"=>25, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Master"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Master"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>14, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>1, "Chemistry"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}}, "reader_count_by_country"=>{"Brazil"=>1, "France"=>1, "Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2003251"], "description"=>"<p>RMSD values between the TM regions in the TM only trimers, comparing initial and final structures (a) and RMSD between the TM in the TM only and in the TM-JM structure, both with respect to their own initial (b.1) and with respect to each others final structures (b.2). We also compare the total deviation of the TM-JM structure (initial vs. final) (c) and similarly to a) compare the RMSD of the JM region between initial and final structures (d).</p><p>Plexin-B1 TM-JM trimer RMSD values comparing TM only and TM-JM structures before and after MD.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365837, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.t003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plexin_B1_TM_JM_trimer_RMSD_values_comparing_TM_only_and_TM_JM_structures_before_and_after_MD_/1365837", "title"=>"Plexin-B1 TM-JM trimer RMSD values comparing TM only and TM-JM structures before and after MD.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003233"], "description"=>"<p>a) RMSD values between initial (PREDDIMER predicted) structures across the subfamily of plexins chosen for further simulation. b) RMSD values between the structures (TM+extensions) after MD simulations, showing that the difference between the different subfamilies is essentially preserved.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365819, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g003", "stats"=>{"downloads"=>0, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RMSD_for_initial_and_MD_refined_structures_/1365819", "title"=>"RMSD for initial and MD refined structures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003250"], "description"=>"<p>Schematic illustrating that structures with like-topology can be connected via straight segments, while unlike structures require some bending, either of irregular or of helical structures.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365836, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g009", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_illustrating_that_structures_with_like_topology_can_be_connected_via_straight_segments_while_unlike_structures_require_some_bending_either_of_irregular_or_of_helical_structures_/1365836", "title"=>"Schematic illustrating that structures with like-topology can be connected via straight segments, while unlike structures require some bending, either of irregular or of helical structures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003244"], "description"=>"<p>a) Two TM-JM trimer models for plexin-B1; structures are shown before MD refinement. Final structures are shown in Fig. B in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.s001\" target=\"_blank\">S1 File</a>. Left: extended clock-anticlock; Right: helix connected anticlock-anticlock. Distances of the JM C-terminal region from the membrane are plotted in Fig. F in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.s001\" target=\"_blank\">S1 File</a>. b) RMSF and c) 2> for these plexin-B1 TM-JM trimers plotted as a function of sequence for the same simulations.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365830, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g007", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_structures_and_dynamics_of_plexin_B1_TM_JM_9trimers_/1365830", "title"=>"Model structures and dynamics of plexin-B1 TM-JM 9trimers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003252"], "description"=>"<p>See Legend for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.t003\" target=\"_blank\">Table 3</a>.</p><p>Plexin-C1 TM-JM RMSD values comparing TM only and TM-JM structures before and after MD.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365838, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.t004", "stats"=>{"downloads"=>5, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plexin_C1_TM_JM_RMSD_values_comparing_TM_only_and_TM_JM_structures_before_and_after_MD_/1365838", "title"=>"Plexin-C1 TM-JM RMSD values comparing TM only and TM-JM structures before and after MD.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003249"], "description"=>"<p>a). Two models (c1.2, left and c1.1, right) for the plexin-C1 TM-JM dimer connected by helical segments before 1 μs of MD. b) RMSF and c) 2> both plotted as a function of sequence. Data for helix A in black, helix B in red. Also see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.s002\" target=\"_blank\">S1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.s003\" target=\"_blank\">S2</a> Movies.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365835, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g008", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_structures_and_dynamics_of_plexin_C1_TM_JM_dimers_/1365835", "title"=>"Model structures and dynamics of plexin-C1 TM-JM dimers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003234"], "description"=>"<p>The geometric parameters for the final structures are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.g003\" target=\"_blank\">Fig. 3b</a>. The first AxxxGxxxG dimerization motif is shown in yellow, the alternate motif, QxxxGxxxS in cyan. Models b1.1 and b1.2 are right-handed and b1.3 is left handed.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365820, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_final_structures_for_plexin_B1_models_b1_1_b1_2_and_b1_3_after_all_atom_MD_simulation_/1365820", "title"=>"The final structures for plexin-B1 models b1.1, b1.2 and b1.3 after all-atom MD simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003220"], "description"=>"<p>RMSD (top), crossing (middle) and helix rotation angles (bottom panel), calculated as in [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.ref009\" target=\"_blank\">9</a>]. Rotation angles for helix A in black, helix B in red. The data (see also <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#sec020\" target=\"_blank\">methods</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.t002\" target=\"_blank\">Table 2</a>) suggest that 1 μs MD simulations are typically sufficient for the refinement. However, slower reversible changes are seen in simulation B1.1 which was continued to 2 μs. Standard deviations of RMSD and geometric parameters over the last 250 ns of the simulations were used to confirm equilibration.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365817, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_variations_of_plexin_B1_models_b1_1_b1_2_and_b1_3_panels_a_b_c_respectively_in_MD_simulations_TM_flanking_residue_simulations_/1365817", "title"=>"Structural variations of plexin-B1 models b1.1, b1.2 and b1.3 (panels a,b,c respectively) in MD simulations (TM + flanking residue simulations).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003303", "https://ndownloader.figshare.com/files/2003307", "https://ndownloader.figshare.com/files/2003308"], "description"=>"<div><p>Single-pass transmembrane (TM) receptors transmit signals across lipid bilayers by helix association or by configurational changes within preformed dimers. The structure determination for such TM regions is challenging and has mostly been accomplished by NMR spectroscopy. Recently, the computational prediction of TM dimer structures is becoming recognized for providing models, including alternate conformational states, which are important for receptor regulation. Here we pursued a strategy to predict helix oligomers that is based on packing considerations (using the PREDDIMER webserver) and is followed by a refinement of structures, utilizing microsecond all-atom molecular dynamics simulations. We applied this method to plexin TM receptors, a family of 9 human proteins, involved in the regulation of cell guidance and motility. The predicted models show that, overall, the preferences identified by PREDDIMER are preserved in the unrestrained simulations and that TM structures are likely to be diverse across the plexin family. Plexin-B1 and –B3 TM helices are regular and tend to associate, whereas plexin-A1, -A2, –A3, -A4, -C1 and –D1 contain sequence elements, such as poly-Glycine or aromatic residues that distort helix conformation and association. Plexin-B2 does not form stable dimers due to the presence of TM prolines. No experimental structural information on the TM region is available for these proteins, except for plexin-C1 dimeric and plexin-B1 – trimeric structures inferred from X-ray crystal structures of the intracellular regions. Plexin-B1 TM trimers utilize Ser and Thr sidechains for interhelical contacts. We also modeled the juxta-membrane (JM) region of plexin-C1 and plexin-B1 and show that it synergizes with the TM structures. The structure and dynamics of the JM region and TM-JM junction provide determinants for the distance and distribution of the intracellular domains, and for their binding partners relative to the membrane. The structures suggest experimental tests and will be useful for the interpretation of future studies.</p></div>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365879, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0121513.s001", "https://dx.doi.org/10.1371/journal.pone.0121513.s002", "https://dx.doi.org/10.1371/journal.pone.0121513.s003"], "stats"=>{"downloads"=>12, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modeling_Transmembrane_Domain_Dimers_Trimers_of_Plexin_Receptors_Implications_for_Mechanisms_of_Signal_Transmission_across_the_Membrane_/1365879", "title"=>"Modeling Transmembrane Domain Dimers/Trimers of Plexin Receptors: Implications for Mechanisms of Signal Transmission across the Membrane", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003219"], "description"=>"<p>a). Modes for transmitting information across the cellular membrane in single pass TM receptors: Translation (monomer-dimer association); Piston (sliding of helices to change register); Pivot (change in interhelix crossing angles); and Rotation (change of helix interacting surfaces). b). Amino-acid sequence alignment of TM and TM proximal regions of all 9 human plexins: TM regions shaded grey, extra N- and C-terminal extensions underlined in red/blue for peptides, for which all-atom simulations were carried out, the juxta-membrane (JM) region is shown in blue for plexin-B1 and plexin-C1. The number after the plexin name corresponds to the first residue shown in the alignment. c). Comparison of plexin-B1 TM only peptide structure obtained from PREDDIMER (Left) and the same peptide with helix N- and C-terminal extensions (Right) embedded in lipid bilayer (structures of model b1.2 are shown); the peptide is shown as ribbon representation; the lipids are given in all-atom line representation on the right and the implicit bilayer is shown for the PREDDIMER prediction as orange lines on left.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365816, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Models_of_plexin_TM_dimer_receptor_signaling_structure_and_sequence_comparison_/1365816", "title"=>"Models of plexin TM dimer receptor signaling, structure and sequence comparison.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003239"], "description"=>"<p>See legend for <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121513#pone.0121513.g004\" target=\"_blank\">Fig. 4</a>.</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365825, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g006", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Models_for_plexin_B1_trimer_TM_region_in_the_TM_JM_models_before_a_c_on_top_panel_and_after_MD_simulations_b_d_on_bottom_panel_/1365825", "title"=>"Models for plexin-B1 trimer TM region in the TM-JM models before (a,c on top panel) and after MD simulations (b,d on bottom panel).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/2003237"], "description"=>"<p>Models with clockwise (a,c) and anti-clockwise (b,d) helix packing, looking from N-terminus into membrane. Helix A is on upper side, then B and C clockwise for clockwise, C and B for anti-clockwise. Ser and Thr sidechains are shown in stick (orange) and location of small residues (AxxxGxxxG) in the center of the TM region are indicated (in yellow).</p>", "links"=>[], "tags"=>["jm", "PREDDIMER", "TM dimer structures", "TM structures", "region", "nmr", "plexin TM receptors"], "article_id"=>1365823, "categories"=>["Biological Sciences"], "users"=>["Liqun Zhang", "Anton Polyansky", "Matthias Buck"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121513.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Models_for_plexin_B1_trimer_TM_region_before_a_c_and_after_the_simulations_b_d_/1365823", "title"=>"Models for plexin-B1 trimer TM region before (a,c) and after the simulations (b,d).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-02 14:46:19"}

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