Atomistic Mechanism of MicroRNA Translation Upregulation via Molecular Dynamics Simulations
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{"title"=>"Atomistic mechanism of MicroRNA translation upregulation via molecular dynamics simulations", "type"=>"journal", "authors"=>[{"first_name"=>"Wei", "last_name"=>"Ye", "scopus_author_id"=>"54794598000"}, {"first_name"=>"Fang", "last_name"=>"Qin", "scopus_author_id"=>"57197569671"}, {"first_name"=>"Jian", "last_name"=>"Zhang", "scopus_author_id"=>"7601341506"}, {"first_name"=>"Ray", "last_name"=>"Luo", "scopus_author_id"=>"7202671127"}, {"first_name"=>"Hai Feng", "last_name"=>"Chen", "scopus_author_id"=>"57192534806"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84865442439", "pmid"=>"22952765", "sgr"=>"84865442439", "doi"=>"10.1371/journal.pone.0043788", "isbn"=>"1932-6203", "issn"=>"19326203", "pui"=>"365513924"}, "id"=>"8b4ed320-1f25-346d-897c-df66c0f34638", "abstract"=>"MicroRNAs are endogenous 23-25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0) mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2) are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.", "link"=>"http://www.mendeley.com/research/atomistic-mechanism-microrna-translation-upregulation-via-molecular-dynamics-simulations", "reader_count"=>27, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Master"=>2, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>15, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>1, "Chemistry"=>3, "Psychology"=>1, "Engineering"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Czech Republic"=>1, "United Kingdom"=>1, "France"=>1}, "group_count"=>0}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/585839"], "description"=>"<p>Major secondary structures are indicated. PAZ represents in orange, KH domain in blue, mRNA in magenta, miR369-3 in green.</p>", "links"=>[], "tags"=>["quadruple"], "article_id"=>256333, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_quadruple_complex_for_PAZ_dsRNA_KH_/256333", "title"=>"The quadruple complex for PAZ-dsRNA-KH.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:45:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/311172", "https://ndownloader.figshare.com/files/311257", "https://ndownloader.figshare.com/files/311336", "https://ndownloader.figshare.com/files/311384", "https://ndownloader.figshare.com/files/311477", "https://ndownloader.figshare.com/files/311542", "https://ndownloader.figshare.com/files/311588", "https://ndownloader.figshare.com/files/311649", "https://ndownloader.figshare.com/files/311715"], "description"=>"<div><p>MicroRNAs are endogenous 23–25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0) mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2) are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.</p> </div>", "links"=>[], "tags"=>["atomistic", "microrna", "upregulation", "molecular", "simulations"], "article_id"=>121384, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043788.s001", "https://dx.doi.org/10.1371/journal.pone.0043788.s002", "https://dx.doi.org/10.1371/journal.pone.0043788.s003", "https://dx.doi.org/10.1371/journal.pone.0043788.s004", "https://dx.doi.org/10.1371/journal.pone.0043788.s005", "https://dx.doi.org/10.1371/journal.pone.0043788.s006", "https://dx.doi.org/10.1371/journal.pone.0043788.s007", "https://dx.doi.org/10.1371/journal.pone.0043788.s008", "https://dx.doi.org/10.1371/journal.pone.0043788.s009"], "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Atomistic_Mechanism_of_MicroRNA_Translation_Upregulation_via_Molecular_Dynamics_Simulations/121384", "title"=>"Atomistic Mechanism of MicroRNA Translation Upregulation via Molecular Dynamics Simulations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-27 00:23:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/586611"], "description"=>"<p>The number of base pairs is marked.</p>", "links"=>[], "tags"=>["apo-dsrna", "quadruple"], "article_id"=>257105, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g007", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_between_apo_dsRNA_and_the_quadruple_complex_/257105", "title"=>"Alignment between apo-dsRNA and the quadruple complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:58:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/586438"], "description"=>"<p>Distance between the base of mRNA and mircoRNA for apo-dsRNA, PAZ-dsRNA, KH-dsRNA, complex, and mutant KH-dsRNA.</p>", "links"=>[], "tags"=>["mrna", "mircorna", "mutant"], "article_id"=>256936, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_between_the_base_of_mRNA_and_mircoRNA_for_apo_dsRNA_PAZ_dsRNA_KH_dsRNA_complex_and_mutant_KH_dsRNA_/256936", "title"=>"Distance between the base of mRNA and mircoRNA for apo-dsRNA, PAZ-dsRNA, KH-dsRNA, complex, and mutant KH-dsRNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:55:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/586324"], "description"=>"<p>A: Distance between Phe69 of PAZ and the base of 3′ terminal of mRNA, U13 in green and U12/U13 in red, respectively. B: The detailed structure near U12/U13 and Phe 69.</p>", "links"=>[], "tags"=>["phe69", "paz", "u12", "u12u13", "dsrna", "paz-dsrna", "quadruqle"], "article_id"=>256811, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g005", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_between_Phe69_of_PAZ_and_U12_or_U12U13_of_dsRNA_and_average_structure_of_PAZ_dsRNA_and_quadruqle_complex_/256811", "title"=>"Distance between Phe69 of PAZ and U12 or U12U13 of dsRNA and average structure of PAZ-dsRNA and quadruqle complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:53:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/586192"], "description"=>"<p>A: apo-dsRNA; B: PAZ-dsRNA; C: KH-dsRNA; D: complex; E: average structure of dsRNA for apo-dsRNA; F: average structure of dsRNA for PAZ-dsRNA; G: average structure of dsRNA for KH-dsRNA; H: average structure of dsRNA for complex.</p>", "links"=>[], "tags"=>["variables", "rmsd", "rg"], "article_id"=>256690, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g004", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Energy_landscape_with_the_variables_of_RMSD_and_Rg_and_average_structure_for_dsRNA_/256690", "title"=>"Energy landscape with the variables of RMSD and Rg and average structure for dsRNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:51:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/586768"], "description"=>"<p>A: Distance between A14 of microRNA and I(N)GKNG motif of KH for WT and mutant KH-dsRNA. B: KH-domain based alignment of WT (blue) and mutant (red) dsRNA-KH complex. C: The detailed interaction between GXXG motif and dsRNA. I/N304–308 is shown in green stick.</p>", "links"=>[], "tags"=>["gxxg", "motif", "kh", "a14", "microrna", "alignment", "wt", "mutant"], "article_id"=>257253, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g008", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_between_GXXG_motif_of_KH_and_A14_of_microRNA_and_structure_alignment_for_WT_and_mutant_KH_dsRNA_/257253", "title"=>"Distance between GXXG motif of KH and A14 of microRNA and structure alignment for WT and mutant KH-dsRNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 02:00:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/585923"], "description"=>"<p>C5’ variation of holo and apo states for dsRNA in five systems.</p>", "links"=>[], "tags"=>["holo", "apo", "states", "dsrna"], "article_id"=>256420, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_C5_8217_variation_of_holo_and_apo_states_for_dsRNA_in_five_systems_/256420", "title"=>"C5’ variation of holo and apo states for dsRNA in five systems.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:47:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/586864"], "description"=>"<p>microRNA up-regulation translation mechanism.</p>", "links"=>[], "tags"=>["up-regulation"], "article_id"=>257362, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_microRNA_up_regulation_translation_mechanism_/257362", "title"=>"microRNA up-regulation translation mechanism.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 02:02:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/586082"], "description"=>"<p>A: Hydrogen bond, hydrophobic, and electrostatic interactions between KH domain and dsRNA for KH-dsRNA and quadruple complex, blue for complex and red for dsRNA-KH. Significant differences for interactions indicate different binding modes. B: The alignment of dsRNA-KH and quadruple complex, blue for complex and red for dsRNA-KH.</p>", "links"=>[], "tags"=>["alignment", "kh-dsrna", "quadruple"], "article_id"=>256575, "categories"=>["Molecular Biology", "Biochemistry", "Biological Sciences", "Biophysics"], "users"=>["Wei Ye", "Fang Qin", "Jian Zhang", "Ray Luo", "Hai-Feng Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043788.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interaction_and_alignment_of_structure_for_KH_dsRNA_and_quadruple_complex_/256575", "title"=>"Interaction and alignment of structure for KH-dsRNA and quadruple complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-27 01:49:35"}

PMC Usage Stats | Further Information

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Relative Metric

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