Computational Analysis of siRNA Recognition by the Ago2 PAZ Domain and Identification of the Determinants of RNA-Induced Gene Silencing
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{"title"=>"Computational Analysis of siRNA Recognition by the Ago2 PAZ Domain and Identification of the Determinants of RNA-Induced Gene Silencing", "type"=>"journal", "authors"=>[{"first_name"=>"Mahmoud", "last_name"=>"Kandeel", "scopus_author_id"=>"22937486100"}, {"first_name"=>"Yukio", "last_name"=>"Kitade", "scopus_author_id"=>"7005896406"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23441235", "sgr"=>"84874153367", "doi"=>"10.1371/journal.pone.0057140", "scopus"=>"2-s2.0-84874153367", "pui"=>"368381774", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"82da4dd2-2dcf-36db-b729-208a85a39122", "abstract"=>"RNA interference (RNAi) is a highly specialized process of protein-siRNA interaction that results in the regulation of gene expression and cleavage of target mRNA. The PAZ domain of the Argonaute proteins binds to the 3' end of siRNA, and during RNAi the attaching end of the siRNA switches between binding and release from its binding pocket. This biphasic interaction of the 3' end of siRNA with the PAZ domain is essential for RNAi activity; however, it remains unclear whether stronger or weaker binding with PAZ domain will facilitate or hinder the overall RNAi process. Here we report the correlation between the binding of modified siRNA 3' overhang analogues and their in vivo RNAi efficacy. We found that higher RNAi efficacy was associated with the parameters of lower Ki value, lower total intermolecular energy, lower free energy, higher hydrogen bonding, smaller total surface of interaction and fewer van der Waals interactions. Electrostatic interaction was a minor contributor to compounds recognition, underscoring the presence of phosphate groups in the modified analogues. Thus, compounds with lower binding affinity are associated with better gene silencing. Lower binding strength along with the smaller interaction surface, higher hydrogen bonding and fewer van der Waals interactions were among the markers for favorable RNAi activity. Within the measured parameters, the interaction surface, van der Waals interactions and inhibition constant showed a statistically significant correlation with measured RNAi efficacy. The considerations provided in this report will be helpful in the design of new compounds with better gene silencing ability.", "link"=>"http://www.mendeley.com/research/computational-analysis-sirna-recognition-ago2-paz-domain-identification-determinants-rnainduced-gene", "reader_count"=>27, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Student > Doctoral Student"=>4, "Researcher"=>5, "Student > Ph. D. Student"=>6, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Student > Doctoral Student"=>4, "Researcher"=>5, "Student > Ph. D. Student"=>6, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>4, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>16, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/487499"], "description"=>"<p>The output data included total energy (Kcal/mol), van der Waals interactions (Kcal/mol), hydrogen bonding (Kcal/mol), electrostatic interactions (Kcal/mol) and average conpair plotted against RL/FL) and plotted against <i>Renilla</i> luciferace expression normalized by firefly luciferase data).</p>", "links"=>[], "tags"=>["paz", "domain-ligands", "forces", "idemdock"], "article_id"=>158025, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dissection_of_PAZ_domain_ligands_interaction_forces_data_is_obtained_from_iDEMDOCK_software_/158025", "title"=>"Dissection of PAZ domain-ligands interaction forces (data is obtained from iDEMDOCK software).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:15:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/486992"], "description"=>"<p>Fig. 2A is a representative diagram showing the docked poses in the binding site of PAZ domain. From the docked poses, the best pose with the lowest energy was used to align with other compounds in the binding site of PAZ domain. The docking profiles of compounds ordered by total interaction energy are shown in Fig. 2B. The numerical values of data can be viewed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057140#pone-0057140-t001\" target=\"_blank\">Table 1</a>. The clustering of compounds is shown in Fig. 2C. The dendrogram is generated by iGEMDOCK post analysis tools and viewed by tree view software.</p>", "links"=>[], "tags"=>["poses", "compounds", "paz"], "article_id"=>157512, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Docked_poses_of_compounds_with_PAZ_domain_/157512", "title"=>"Docked poses of compounds with PAZ domain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:13:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/487194"], "description"=>"<p>Free energy (Kcal/mol), inhibition constant (µM), van der Waals interactions, hydrogen bonding and desolvation energy (Kcal/mol), electrostatic energy (Kcal/mol) and interaction surface were plotted against RL/FL (<i>Renilla</i> luciferace expression normalized by firefly luciferase data).</p>", "links"=>[], "tags"=>["paz", "domain-ligands", "forces", "docking"], "article_id"=>157717, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dissection_of_the_PAZ_domain_ligands_interaction_forces_data_is_obtained_from_the_docking_server_/157717", "title"=>"Dissection of the PAZ domain-ligands interaction forces (data is obtained from the docking server).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:14:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/486921"], "description"=>"<p>The figure is generated by ChemBioDraw ultra 12.0 (CambridgeSoft, USA).</p>", "links"=>[], "tags"=>["modified", "nucleotides", "analogues", "docking"], "article_id"=>157442, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_of_modified_nucleotides_or_nucleotides_analogues_used_in_the_docking_studies_/157442", "title"=>"Structure of modified nucleotides or nucleotides analogues used in the docking studies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:12:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/487611"], "description"=>"<p>*Pearson's correlation coefficient is calculated by STATA. Data showing significant correlation at 0.05 level are marked by asterisk.</p>", "links"=>[], "tags"=>["rnai", "parameters", "produced"], "article_id"=>158140, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_analysis_for_RNAi_activity_and_the_measured_parameters_produced_by_iGEMDOCK_/158140", "title"=>"Correlation analysis for RNAi activity and the measured parameters produced by iGEMDOCK.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:16:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/487070"], "description"=>"<p>A Hierarchical clustering and the profile of interactions of various compounds with PAZ domain is represented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057140#pone-0057140-g003\" target=\"_blank\">Fig 3A</a>. The compounds are ranked according to pharmacological and energy-based scoring function. E, H and V indicate electrostatic, hydrogen bonding and vdW interactions, respectively. The vdW interactions are coloured in green when the energy is less than -4. The hydrogen bonding and electrostatic interactions are coloured in green if the energy is ≤ −4. M and S indicates main chain or side chain of interacting residues. The residues showing important hydrogen bonding interactions with docked compounds is given in Fig. 3B. Hydrogen bonds are represented as green dashed lines A two dimensional figure of binding of compounds with PAZ domain is shown in Fig. 3C. The ligand is compound tt, residues sharing with hydrogen bonding is shown in pink.</p>", "links"=>[], "tags"=>["parameters", "compounds", "paz"], "article_id"=>157593, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interaction_parameters_of_compounds_with_the_PAZ_domain_/157593", "title"=>"Interaction parameters of compounds with the PAZ domain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:13:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/487584"], "description"=>"<p>*Pearson's correlation coefficient is calculated by STATA. Data showing significant correlation at 0.05 level are marked by asterisk.</p>", "links"=>[], "tags"=>["rnai", "parameters", "produced", "docking"], "article_id"=>158103, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.t004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_analysis_for_RNAi_activity_and_the_measured_parameters_produced_by_the_docking_server_/158103", "title"=>"Correlation analysis for RNAi activity and the measured parameters produced by the docking server.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:16:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/487640"], "description"=>"<p>The ligands are ordered as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057140#pone-0057140-g001\" target=\"_blank\">Fig. 1</a>). The output data included free energy (Kcal/mol), inhibition constant (µM),van der Waals interactions, Hydrogen bonding and desolvation energy (Kcal/mol), electrostatic energy (Kcal/mol) and interaction surface. RL/FL indicates <i>Renilla</i> luciferace expression normalized by firefly luciferase data.</p>", "links"=>[], "tags"=>["docking"], "article_id"=>158168, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_docking_results_by_using_the_docking_server_/158168", "title"=>"The docking results by using the docking server.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:16:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/487400"], "description"=>"<p>The phosphate groups of siRNA are marked by red colour opposing the surface of PAZ domain in blue.</p>", "links"=>[], "tags"=>["interactions", "sirna", "paz"], "article_id"=>157921, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electrostatic_interactions_of_siRNA_with_PAZ_domain_/157921", "title"=>"Electrostatic interactions of siRNA with PAZ domain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 15:15:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/487672"], "description"=>"<p>The ligands are ordered as shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057140#pone-0057140-g001\" target=\"_blank\">Fig. 1</a>). The output data included total energy (Kcal/mol), van der Waals interactions (VDW, Kcal/mol), Hydrogen bonding (HBond, Kcal/mol), electrostatic interactions (elec, Kcal/mol) and average conpair. RL/FL indicates <i>Renilla</i> luciferace expression normalized by firefly luciferase data.</p>", "links"=>[], "tags"=>["docking"], "article_id"=>158201, "categories"=>["Physics", "Biochemistry", "Biophysics", "Molecular Biology", "Chemistry", "Genetics"], "users"=>["Mahmoud Kandeel", "Yukio Kitade"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057140.t001", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_docking_results_by_using_iGEMDOCK_/158201", "title"=>"The docking results by using iGEMDOCK.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 15:16:41"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
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  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "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"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"1", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[247, 429, 544, 647, 747, 842, 929, 1012, 1099, 1179, 1263, 1339, 1409]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[254, 421, 527, 626, 720, 813, 900, 983, 1063, 1136, 1210, 1283, 1342]}]}
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