Computational Exploration of Structural Hypotheses for an Additional Sequence in a Mammalian Mitochondrial Protein
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{"title"=>"Computational exploration of structural hypotheses for an additional sequence in a mammalian mitochondrial protein", "type"=>"journal", "authors"=>[{"first_name"=>"Aymen S.", "last_name"=>"Yassin", "scopus_author_id"=>"20434932800"}, {"first_name"=>"Rajendra K.", "last_name"=>"Agrawal", "scopus_author_id"=>"35496633400"}, {"first_name"=>"Nilesh K.", "last_name"=>"Banavali", "scopus_author_id"=>"6602830466"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21779343", "sgr"=>"79960147079", "doi"=>"10.1371/journal.pone.0021871", "scopus"=>"2-s2.0-79960147079", "pui"=>"362110690", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"35f07247-8b5d-333b-865c-0a22ce84e48c", "abstract"=>"Proteins involved in mammalian mitochondrial translation, when compared to analogous bacterial proteins, frequently have additional sequence regions whose structural or functional roles are not always clear. For example, an additional short insert sequence in the bovine mitochondrial initiation factor 2 (IF2(mt)) seems sufficient to fulfill the added role of eubacterial initiation factor IF1. Prior to our recent cryo-EM study that showed IF2(mt) to structurally occupy both the IF1 and IF2 binding sites, the spatial separation of these sites, and the short length of the insert sequence, posed ambiguity in whether it could perform the role of IF1 through occupation of the IF1 binding site on the ribosome.", "link"=>"http://www.mendeley.com/research/computational-exploration-structural-hypotheses-additional-sequence-mammalian-mitochondrial-protein", "reader_count"=>18, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>3, "Lecturer > Senior Lecturer"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>3, "Lecturer > Senior Lecturer"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>13, "Physics and Astronomy"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Estonia"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/758112"], "description"=>"<p>(A) Final optimized IF2<sub>mt</sub> model bound to the <i>E. coli</i> 70S ribosome. (B) Bacterial IF1 and IF2 bound to the <i>E.coli</i> 70S ribosome, (C) IF2<sub>mt</sub> model bound to the <i>T. thermophilus</i> 30S ribosomal subunit. (D) Bacterial IF1 and IF2 bound to the <i>T. thermophilus</i> 30S ribosomal subunit. Small subunit landmarks indicated: h - head, sh - shoulder, s - spur. Large subunit landmarks indicated: CP - central protuberance, SB - stalk base. The mesh density shown corresponds to the previously published <i>E. coli</i> 70S initiation complex (EMD 1248) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a> and the <i>T. thermophilus</i> 30S initiation complex (EMD 1523) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Simonetti2\" target=\"_blank\">[26]</a>. In (C) and (D), the initiator tRNA density is indicated by an asterisk. The color scheme is as follows: domain G: orange, domain V: green, domain VI-C1: cornflower blue, domain VI-C2: cyan, and insert region: red, bacterial IF1 in dark green, small ribosomal subunit: transparent yellow, and large ribosomal subunit: transparent blue.</p>", "links"=>[], "tags"=>["if1", "if2", "ribosomal", "binding", "sites"], "article_id"=>428480, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g007", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_occupation_of_E_coli_and_T_thermophilus_IF1_and_IF2_ribosomal_binding_sites_by_IF2_mt_/428480", "title"=>"The occupation of <i>E. coli</i> and <i>T. thermophilus</i> IF1 and IF2 ribosomal binding sites by IF2<sub>mt</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:52:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/758184"], "description"=>"<p>Low sequence conservation region indicated by red bar, the first sequence shows the position of the 49 aa insert region as dashes.</p>", "links"=>[], "tags"=>["alignment", "eukaryotic"], "article_id"=>428557, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g008", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_alignment_of_insert_sequence_region_in_representative_eukaryotic_IF2_mt_sequences_/428557", "title"=>"Sequence alignment of insert sequence region in representative eukaryotic IF2<sub>mt</sub> sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:53:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/757994"], "description"=>"<p>A–B represent the optimized IF2<sub>mt</sub> model based on flexible fitting into the excised <i>E. coli</i> IF2 density map <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a>, C–D represent the optimized IF2<sub>mt</sub> model based on flexible fitting into the excised <i>T. thermophilus</i> IF2 density map <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Simonetti2\" target=\"_blank\">[26]</a>. The insert is shown in red and the bacterial IF1 is shown in green. The position of IF1 is predicted based on the manual rigid-body fit of <i>T. thermophilus</i> 30S subunit with bound IF1 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Carter1\" target=\"_blank\">[15]</a>.</p>", "links"=>[], "tags"=>["optimized", "composite", "models", "excised", "if2", "cryo-em", "densities", "overlay", "49", "aa", "bacterial"], "article_id"=>428359, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g006", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Final_optimized_composite_IF2_mt_models_showing_fit_into_excised_IF2_cryo_EM_densities_and_the_structural_overlay_of_the_49_aa_insert_with_bacterial_IF1_/428359", "title"=>"Final optimized composite IF2<sub>mt</sub> models showing fit into excised IF2 cryo-EM densities and the structural overlay of the 49 aa insert with bacterial IF1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:51:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/757872"], "description"=>"<p>A–C represent flexible fitting into the excised cryo-EM map of <i>E. coli</i> IF2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a>, D–F represent flexible fitting into the excised cryo-EM map of <i>T. thermophilus</i> IF2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Simonetti2\" target=\"_blank\">[26]</a>. (A) <i>E. coli</i> IF2 model from <i>Allen et al.</i> 2005 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a>. (B, E) Rigid body docked IF2<sub>mt</sub> models without insert. (C, F) Flexibly fit IF2<sub>mt</sub> models without insert. (D) <i>T. thermophilus</i> IF2 model (since this model is not deposited in the PDB, it was recreated using MODELLER based on the Simonettie <i>et al.</i> 2008 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Simonetti2\" target=\"_blank\">[26]</a> sequence alignment and flexibly fit using MDFF protocol 5). The color scheme is the same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone-0021871-g002\" target=\"_blank\">Figure 2</a>.</p>", "links"=>[], "tags"=>["fitting", "composite", "models"], "article_id"=>428245, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g005", "stats"=>{"downloads"=>4, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flexible_fitting_of_composite_IF2_mt_models_without_insert_/428245", "title"=>"Flexible fitting of composite IF2<sub>mt</sub> models without insert.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:51:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/757743"], "description"=>"<p>(A) Five secondary structure prediction protocols: JPRED <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Cole1\" target=\"_blank\">[35]</a>, SCRATCH <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Cheng1\" target=\"_blank\">[36]</a>, PSIPRED <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-McGuffin1\" target=\"_blank\">[37]</a>, PREDICTPROTEIN <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Rost1\" target=\"_blank\">[38]</a>, and NETSURFP <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Petersen1\" target=\"_blank\">[39]</a>; were used to predict the internal secondary structure of the 49 aa insert region in IF2<sub>mt</sub>. H represents α-Helix, C represents Coil, and E represents Extended strand. (B) Tertiary structure of the 49 aa insert as predicted by I-TASSER.</p>", "links"=>[], "tags"=>["tertiary", "49", "aa"], "article_id"=>428119, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Secondary_and_tertiary_structure_prediction_of_the_49_aa_insert_region_in_IF2_mt_/428119", "title"=>"Secondary and tertiary structure prediction of the 49 aa insert region in IF2<sub>mt</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:50:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/757674"], "description"=>"<p>A–C represent flexible fits in excised map of <i>E. coli</i> IF2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a>. D–F represent flexible fits in excised map of <i>T. thermophilus</i> IF2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Simonetti2\" target=\"_blank\">[26]</a>. A and D are automated MODELLER IF2<sub>mt</sub> models, B and E are automated I-TASSER models, and C and F are automated SWISS-MODEL models. All models are flexibly fit using MDFF protocol 5 (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#s4\" target=\"_blank\">Methods</a> section) and cross correlation coefficient (CCC) values of the fit are indicated next to each depicted model. The color scheme is as follows: domain G: orange, domain V: green, domain VI-C1: cornflower blue, domain VI-C2: cyan, and insert region: red. The black asterisk in panel A indicates the region of additional density originally assigned to the structurally unresolved N-terminal region of <i>E. coli</i> IF2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Allen2\" target=\"_blank\">[24]</a>, and the higher CCC values in panels B and C are probably due to the enforced fit of the insert into this empty non-insert density.</p>", "links"=>[], "tags"=>["fits", "automated", "models", "if2", "cryo-em"], "article_id"=>428046, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flexible_fits_of_automated_complete_IF2_mt_models_into_IF2_cryo_EM_maps_/428046", "title"=>"Flexible fits of automated complete IF2<sub>mt</sub> models into IF2 cryo-EM maps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:50:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/758256"], "description"=>"<p>(A) Comparison of IF2<sub>mt</sub> model obtained by fitting into the <i>E. coli</i> IF2 cryo-EM map (in blue, left) with recently published IF2<sub>mt</sub> model obtained by fitting into the IF2<sub>mt</sub> cryo-EM map <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Yassin1\" target=\"_blank\">[27]</a> (in red, right). The initial CCC value with the IF2<sub>mt</sub> cryo-EM map is 0.73, but flexible fitting improves the CCC value to 0.84 (blue, center). (B) An alternate topologically variant model for IF2<sub>mt</sub> (blue, left) and secondary structure differences between the alternate model (center) and the recently published IF2<sub>mt</sub> model (right) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021871#pone.0021871-Yassin1\" target=\"_blank\">[27]</a>. The alternate model is obtained through reorientation of an α-helix (residues 446–460, in region indicated by red arrow) that results in additional helices being maintained in the insert region (indicated by a blue arrow). Color scheme for secondary structure: α-helices in purple, β-sheets in yellow, loops in cyan or white, and alternate helices in blue.</p>", "links"=>[], "tags"=>["quasi-atomic", "models", "fitting", "cryo-em"], "article_id"=>428633, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g009", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Computationally_predicted_quasi_atomic_IF2_mt_models_and_their_flexible_fitting_into_the_IF2_mt_cryo_EM_map_/428633", "title"=>"Computationally predicted quasi-atomic IF2<sub>mt</sub> models and their flexible fitting into the IF2<sub>mt</sub> cryo-EM map.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:53:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/757813"], "description"=>"<p>If X is the number of dynamics steps and Y is the number of subsequent minimization steps, the six different MDFF protocols tested are: (1) X = 5000, Y = 700, (2) X = 10000, Y = 1200, (3) X = 20000, Y = 2200, (4) X = 50000, Y = 5200, (5) X = 100000, Y = 10200, (6) X = 150000, Y = 15200. MDFF protocol 0 represents the rigid-body docked initial models without any MDFF flexible fitting. The solid black line and the dotted green line represent cross correlation coefficients after X dynamics steps and only the first 200 minimization steps in the <i>E. coli</i> and <i>T. thermophilus</i> density maps, respectively. The solid red and dotted blue lines represent these values after all dynamics and minimization steps for the <i>E. coli</i> and <i>T. thermophilus</i> density maps, respectively.</p>", "links"=>[], "tags"=>["fitting", "mdff"], "article_id"=>428183, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g004", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimization_of_flexible_fitting_MDFF_protocols_/428183", "title"=>"Optimization of flexible fitting MDFF protocols.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:51:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/757581"], "description"=>"<p>(A) Depiction of domain alignment with the IF2<sub>mt</sub> insert region shown in red. (B) The manually adjusted ClustalW sequence alignment; the red arrow indicates the 49 aa insert sequence.</p>", "links"=>[], "tags"=>["alignment"], "article_id"=>427955, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Aymen S. Yassin", "Rajendra K. Agrawal", "Nilesh K. Banavali"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0021871.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Domain_architecture_and_sequence_alignment_of_IF2_mt_and_M_thermoautotrophicum_IF2_/427955", "title"=>"Domain architecture and sequence alignment of IF2<sub>mt</sub> and <i>M. thermoautotrophicum</i> IF2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 16:49:37"}

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