How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
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{"title"=>"How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations", "type"=>"journal", "authors"=>[{"first_name"=>"Tomohiro", "last_name"=>"Tanaka", "scopus_author_id"=>"56894664400"}, {"first_name"=>"Naoto", "last_name"=>"Hori", "scopus_author_id"=>"55202495800"}, {"first_name"=>"Shoji", "last_name"=>"Takada", "scopus_author_id"=>"7202611424"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "sgr"=>"84938675284", "doi"=>"10.1371/journal.pcbi.1004356", "scopus"=>"2-s2.0-84938675284", "pmid"=>"26158498", "pui"=>"605505676"}, "id"=>"0b35534b-bde1-34b5-a9ac-7ed7aa6ba175", "abstract"=>"Co-translational folding (CTF) facilitates correct folding in vivo, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional state. Here, to gain structural insights on the underlying mechanisms, we performed comparative molecular simulations of SufI that mimic CTF as well as refolding schemes. A CTF scheme that relied on a codon-based prediction of translational rates exhibited folding probability markedly higher than that by the refolding scheme. When the CTF schedule is speeded up, the success rate dropped. These agree with experiments. Structural investigation clarified that misfolding of the middle domain was much more frequent in the refolding scheme than that in the codon-based CTF scheme. The middle domain is less stable and can fold via interactions with the folded N-terminal domain. Folding pathway networks showed the codon-based CTF gives narrower pathways to the native state than the refolding scheme.", "link"=>"http://www.mendeley.com/research/cotranslational-folding-multidomain-protein-affected-elongation-schedule-molecular-simulations", "reader_count"=>35, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>9, "Materials Science"=>1, "Agricultural and Biological Sciences"=>12, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>7, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>7}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "Argentina"=>1, "Japan"=>1, "China"=>1, "United Kingdom"=>2, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2168895"], "description"=>"<p>Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478144, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.t004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_Kolmogorov_Smirnov_tests_to_check_the_difference_of_the_histograms_of_N_domain_8217_s_Q_scores_of_the_final_structures_/1478144", "title"=>"Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168893"], "description"=>"<p>Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of Q<sub>total</sub>-scores of the final structures.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478142, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.t002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_Kolmogorov_Smirnov_tests_to_check_the_difference_of_the_histograms_of_Q_total_scores_of_the_final_structures_/1478142", "title"=>"Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of Q<sub>total</sub>-scores of the final structures.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168890"], "description"=>"<p>The refolding network possesses 3284 nodes, while the codon-based CTF has only 820 nodes. The size of nodes represent their probabilities. The darkness of the node represents native-ness. The darker one is closer to the native. Diamonds, triangle, and stars indicate that N-, M-, and C-domains are pre-dominantly unfolded, respectively. When pre-dominantly unfolded domains are no uniquely decided, circles are used.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478139, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.g004", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SufI_folding_networks_for_refolding_A_and_for_the_codon_based_CTF_B_/1478139", "title"=>"SufI folding networks for refolding (A) and for the codon-based CTF (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168889"], "description"=>"<p>A) Fractions of misfolded domains at the end of simulations in four different schemes; the refolding (black), the CTF<sub>fast</sub> (red), the CTF<sub>slow</sub> (green), and the CTF<sub>codon</sub> (blue). B) Representative final structures of misfolding. i) structure that is misfolded in N-domain. ii) Misfolded in M-domain. iii) (right) Misfolded in C-domain. (left) Native structure for comparison. See text for the explanation of the block arrows.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478138, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Misfolding_in_SufI_domains_/1478138", "title"=>"Misfolding in SufI domains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168901", "https://ndownloader.figshare.com/files/2168902", "https://ndownloader.figshare.com/files/2168903", "https://ndownloader.figshare.com/files/2168904", "https://ndownloader.figshare.com/files/2168905", "https://ndownloader.figshare.com/files/2168906", "https://ndownloader.figshare.com/files/2168907"], "description"=>"<div><p>Co-translational folding (CTF) facilitates correct folding <i>in vivo</i>, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional state. Here, to gain structural insights on the underlying mechanisms, we performed comparative molecular simulations of SufI that mimic CTF as well as refolding schemes. A CTF scheme that relied on a codon-based prediction of translational rates exhibited folding probability markedly higher than that by the refolding scheme. When the CTF schedule is speeded up, the success rate dropped. These agree with experiments. Structural investigation clarified that misfolding of the middle domain was much more frequent in the refolding scheme than that in the codon-based CTF scheme. The middle domain is less stable and can fold via interactions with the folded N-terminal domain. Folding pathway networks showed the codon-based CTF gives narrower pathways to the native state than the refolding scheme.</p></div>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478150, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004356.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s004", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s005", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s006", "https://dx.doi.org/10.1371/journal.pcbi.1004356.s007"], "stats"=>{"downloads"=>14, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_How_Co_translational_Folding_of_Multi_domain_Protein_Is_Affected_by_Elongation_Schedule_Molecular_Simulations_/1478150", "title"=>"How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168898"], "description"=>"<p>Pairwise Mann-Whitney U tests tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478147, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.t007", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_Mann_Whitney_U_tests_tests_to_check_the_difference_of_the_histograms_of_N_domain_8217_s_Q_scores_of_the_final_structures_/1478147", "title"=>"Pairwise Mann-Whitney U tests tests to check the difference of the histograms of N-domain’s Q-scores of the final structures.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168897"], "description"=>"<p>Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of C-domain’s Q-scores of the final structures.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478146, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.t006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_Kolmogorov_Smirnov_tests_to_check_the_difference_of_the_histograms_of_C_domain_8217_s_Q_scores_of_the_final_structures_/1478146", "title"=>"Pairwise Kolmogorov-Smirnov tests to check the difference of the histograms of C-domain’s Q-scores of the final structures.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168892"], "description"=>"<p><sup>a</sup> For the judgement of folding, the stringent criterion was used.</p><p>Number of successful folding cases<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004356#t001fn001\" target=\"_blank\"><sup>a</sup></a> out of 100 trajectories.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478141, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_successful_folding_cases_a_out_of_100_trajectories_/1478141", "title"=>"Number of successful folding cases<sup>a</sup> out of 100 trajectories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-07-09 02:50:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/2168891"], "description"=>"<p>A) The degree of folding acquisition Δ<i>Q</i><sub><i>i</i></sub> after averaging over the window size 5. B) One over the translation rate computed from the Spencer <i>et al</i>.’s algorithm [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004356#pcbi.1004356.ref043\" target=\"_blank\">43</a>]. Experimentally-detected translational attenuation regions, 33-40kDa (281-326th residues) and 25-28kDa (214-240th residues), are shaded in grey [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004356#pcbi.1004356.ref016\" target=\"_blank\">16</a>]. C) The scattered plot of the translation time and the degree of folding. Here, residues 200–350 are used. The correlation coefficient was 0.51.</p>", "links"=>[], "tags"=>["ctf", "refolding scheme", "middle domain"], "article_id"=>1478140, "categories"=>["Biological Sciences"], "users"=>["Tomohiro Tanaka", "Naoto Hori", "Shoji Takada"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004356.g005", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_correlation_between_the_inverse_of_elongation_rate_and_the_degree_of_folding_in_SufI_/1478140", "title"=>"The correlation between the inverse of elongation rate and the degree of folding in SufI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-09 02:50:04"}
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  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"5", "full-text"=>"7", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"3", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}

Relative Metric

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