A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex
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{"title"=>"A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex", "type"=>"journal", "authors"=>[{"first_name"=>"Kota", "last_name"=>"Kasahara", "scopus_author_id"=>"56001128200"}, {"first_name"=>"Ikuo", "last_name"=>"Fukuda", "scopus_author_id"=>"35776088100"}, {"first_name"=>"Haruki", "last_name"=>"Nakamura", "scopus_author_id"=>"55477600500"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"600483547", "sgr"=>"84911421146", "issn"=>"19326203", "pmid"=>"25380315", "scopus"=>"2-s2.0-84911421146", "doi"=>"10.1371/journal.pone.0112419", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"e1fdfcbe-b770-3276-b7b1-e560742e52bc", "abstract"=>"The dynamic cross correlation (DCC) analysis is a popular method for analyzing the trajectories of molecular dynamics (MD) simulations. However, it is difficult to detect correlative motions that appear transiently in only a part of the trajectory, such as atomic contacts between the side-chains of amino acids, which may rapidly flip. In order to capture these multi-modal behaviors of atoms, which often play essential roles, particularly at the interfaces of macromolecules, we have developed the \"multi-modal DCC (mDCC)\" analysis. The mDCC is an extension of the DCC and it takes advantage of a Bayesian-based pattern recognition technique. We performed MD simulations for molecular systems modeled from the (Ets1)2-DNA complex and analyzed their results with the mDCC method. Ets1 is an essential transcription factor for a variety of physiological processes, such as immunity and cancer development. Although many structural and biochemical studies have so far been performed, its DNA binding properties are still not well characterized. In particular, it is not straightforward to understand the molecular mechanisms how the cooperative binding of two Ets1 molecules facilitates their recognition of Stromelysin-1 gene regulatory elements. A correlation network was constructed among the essential atomic contacts, and the two major pathways by which the two Ets1 molecules communicate were identified. One is a pathway via direct protein-protein interactions and the other is that via the bound DNA intervening two recognition helices. These two pathways intersected at the particular cytosine bases (C110/C11), interacting with the H1, H2, and H3 helices. Furthermore, the mDCC analysis showed that both pathways included the transient interactions at their intermolecular interfaces of Tyr396-C11 and Ala327-Asn380 in multi-modal motions of the amino acid side chains and the nucleotide backbone. Thus, the current mDCC approach is a powerful tool to reveal these complicated behaviors and scrutinize intermolecular communications in a molecular system.", "link"=>"http://www.mendeley.com/research/novel-approach-dynamic-cross-correlation-analysis-molecular-dynamics-simulations-application-ets1-di", "reader_count"=>49, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>10, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>10, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>15, "Pharmacology, Toxicology and Pharmaceutical Science"=>5, "Physics and Astronomy"=>3, "Chemistry"=>5, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>5}}, "reader_count_by_country"=>{"United States"=>1, "United Kingdom"=>1, "South Africa"=>1, "Malaysia"=>1, "Indonesia"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1783899"], "description"=>"<p>The colored bold arrows indicate interactions of important residues that exhibited high Betweenness values. The colors of these arrows are consistent with those in the other figures. The red dashed arrows indicate the intermolecular pairs with highly positive correlations between the Ets1 molecules. The blue dashed arrows indicate the pairs with significant gains of correlations by the loss of the partner Ets1 molecule.</p>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232576, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112419.g005", "stats"=>{"downloads"=>13, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_correlation_network_in_the_Ets1_2_8211_DNA_complex_/1232576", "title"=>"Summary of the correlation network in the (Ets1)<sub>2</sub>–DNA complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-07 03:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1783897"], "description"=>"<p>(A) A simplified correlation network diagram in two-dimension (2D) as a sub-network of the original one shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112419#pone.0112419.s007\" target=\"_blank\">Fig. S7</a>. Each node indicates a residue and each edge indicates a proximal residue pair with a highly positive correlation (the maximum value of mDCC ≥0.5 and the distance between the center positions of the modes <5.0 Å). The two circles correspond to the two Ets1 proteins (chain A and chain B correspond to the left circle and right circles, respectively), and the pink nodes are the DNA. The colors of the Ets1 nodes represent secondary structures: green, orange, and cyan indicate α-helix, β-strand, and others, respectively. The sizes of nodes denote the Betweenness values of residues. Important interactions mentioned in the manuscripts are shown as colored edges with bold arrows. (B) A 3D representation of the core network. The colors of atoms and ribbons represent their Betweenness values, and the atoms in the top 5% Betweenness are shown as spheres. Red lines indicate the shortest paths among all of the spheres. (C) The 3D structure around the recognition (H3) helix and the intermolecular interfaces. The pairs of residues corresponding to colored edges in Fig. 3A are shown as cylinders.</p>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232574, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112419.g003", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_correlation_network_in_Ets1_2_8211_DNA_model_/1232574", "title"=>"A correlation network in (Ets1)<sub>2</sub>–DNA model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-07 03:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1783896"], "description"=>"<p>(A, B, and C) Interactions among the Nδ atom of the Asn380B side-chain, and the Cβ atoms of Ala324A and Ala327A. (A) The time course of interatomic distances, where red and blue plots denote Ala324A–Asn380B and Ala327A–Asn380B, respectively. (B) Spatial distributions of the coordinates of the three atoms. Color gradations of the plots, green to blue, yellow to red, and cyan to magenta, correspond to the time evolution of the simulation from 10 to 200 ns, for Ala324A, Ala327A, and Asn380B, respectively. (C) Contours of probability density functions of the Gaussian mixture models learned from the distributions in (B). The green, red and cyan meshes denote the contours for Ala324A, Ala327A, and Asn380B, respectively. (D, E, and F) Interactions among the Oη atom of Tyr396B, the backbone nitrogen atom of Leu337B, and an oxygen atom of the phosphate group of C11. (D) Time course of interatomic distances, where red, blue, and green plots denote Tyr396B–C11, Leu337B–Tyr396, and Leu337B–C11 pairs, respectively. (E) Contours of probability density functions of the Gaussian mixture models. The cyan, red, and blue meshes denote the contours of Tyr396B, Leu337B, and C11, respectively. (F) Snapshots at 0 ns (green) and 200 ns (cyan). The structures of the three residues focused on here are shown as sticks.</p>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232573, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112419.g002", "stats"=>{"downloads"=>8, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_transiently_formed_intermolecular_interactions_/1232573", "title"=>"Examples of transiently formed intermolecular interactions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-07 03:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1783895"], "description"=>"<p>(A) The maps of mDCC values and their differences from the DCC values (the upper and lower triangles, respectively). The color gradation from blue to red corresponds to mDCC values and their differences from DCC values from −1.0 to 1.0. The horizontal and vertical axes denote residues in the system, including two Ets1 molecules and a double-stranded DNA. The colored bars along each axis provided a guide for the secondary structures of residues: green, orange, cyan, and pink denote α-helix, β-strand, loop or turn, and DNA, respectively. Parts marked by the rectangles a–j, and residues marked at the top and right of the map are discussed in the main text. (B) Histogram of residue-wise mDCC and DCC values, shown in pink and cyan, respectively.</p>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232572, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112419.g001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_mDCC_and_DCC_among_residues_of_the_Ets1_2_8211_DNA_complex_/1232572", "title"=>"mDCC and DCC among residues of the (Ets1)<sub>2</sub>–DNA complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-07 03:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1783900", "https://ndownloader.figshare.com/files/1783901", "https://ndownloader.figshare.com/files/1783902", "https://ndownloader.figshare.com/files/1783903", "https://ndownloader.figshare.com/files/1783904", "https://ndownloader.figshare.com/files/1783905", "https://ndownloader.figshare.com/files/1783906", "https://ndownloader.figshare.com/files/1783907", "https://ndownloader.figshare.com/files/1783908", "https://ndownloader.figshare.com/files/1783909", "https://ndownloader.figshare.com/files/1783910", "https://ndownloader.figshare.com/files/1783911", "https://ndownloader.figshare.com/files/1783912", "https://ndownloader.figshare.com/files/1783913", "https://ndownloader.figshare.com/files/1783914", "https://ndownloader.figshare.com/files/1783915"], "description"=>"<div><p>The dynamic cross correlation (DCC) analysis is a popular method for analyzing the trajectories of molecular dynamics (MD) simulations. However, it is difficult to detect correlative motions that appear transiently in only a part of the trajectory, such as atomic contacts between the side-chains of amino acids, which may rapidly flip. In order to capture these multi-modal behaviors of atoms, which often play essential roles, particularly at the interfaces of macromolecules, we have developed the “multi-modal DCC (mDCC)” analysis. The mDCC is an extension of the DCC and it takes advantage of a Bayesian-based pattern recognition technique. We performed MD simulations for molecular systems modeled from the (Ets1)<sub>2</sub>–DNA complex and analyzed their results with the mDCC method. Ets1 is an essential transcription factor for a variety of physiological processes, such as immunity and cancer development. Although many structural and biochemical studies have so far been performed, its DNA binding properties are still not well characterized. In particular, it is not straightforward to understand the molecular mechanisms how the cooperative binding of two Ets1 molecules facilitates their recognition of Stromelysin-1 gene regulatory elements. A correlation network was constructed among the essential atomic contacts, and the two major pathways by which the two Ets1 molecules communicate were identified. One is a pathway via direct protein-protein interactions and the other is that via the bound DNA intervening two recognition helices. These two pathways intersected at the particular cytosine bases (C110/C11), interacting with the H1, H2, and H3 helices. Furthermore, the mDCC analysis showed that both pathways included the transient interactions at their intermolecular interfaces of Tyr396–C11 and Ala327–Asn380 in multi-modal motions of the amino acid side chains and the nucleotide backbone. Thus, the current mDCC approach is a powerful tool to reveal these complicated behaviors and scrutinize intermolecular communications in a molecular system.</p></div>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232577, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0112419.s001", "https://dx.doi.org/10.1371/journal.pone.0112419.s002", "https://dx.doi.org/10.1371/journal.pone.0112419.s003", "https://dx.doi.org/10.1371/journal.pone.0112419.s004", "https://dx.doi.org/10.1371/journal.pone.0112419.s005", "https://dx.doi.org/10.1371/journal.pone.0112419.s006", "https://dx.doi.org/10.1371/journal.pone.0112419.s007", "https://dx.doi.org/10.1371/journal.pone.0112419.s008", "https://dx.doi.org/10.1371/journal.pone.0112419.s009", "https://dx.doi.org/10.1371/journal.pone.0112419.s010", "https://dx.doi.org/10.1371/journal.pone.0112419.s011", "https://dx.doi.org/10.1371/journal.pone.0112419.s012", "https://dx.doi.org/10.1371/journal.pone.0112419.s013", "https://dx.doi.org/10.1371/journal.pone.0112419.s014", "https://dx.doi.org/10.1371/journal.pone.0112419.s015", "https://dx.doi.org/10.1371/journal.pone.0112419.s016"], "stats"=>{"downloads"=>23, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Novel_Approach_of_Dynamic_Cross_Correlation_Analysis_on_Molecular_Dynamics_Simulations_and_Its_Application_to_Ets1_Dimer_8211_DNA_Complex_/1232577", "title"=>"A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-11-07 03:12:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1783898"], "description"=>"<p>The upper triangle shows mDCC values in the single Ets1–DNA model, with the color gradation from blue to red corresponding to mDCC values from −1.0 to 1.0. The lower triangle shows differences of the mDCC values in the single Ets1–DNA model from those in the (Ets1)<sub>2</sub>–DNA model with the color gradation corresponding from−0.7 to 0.7. For the lower triangle, negative values (blue) indicate correlations that decreased by the removal of the partner Ets1 molecule.</p>", "links"=>[], "tags"=>["Ets 1", "mDCC method", "Dynamic Cross Correlation Analysis", "cancer development", "Molecular Dynamics Simulations", "acid side chains", "novel approach", "interface", "interaction", "DNA Binding Properties", "pathways intersected", "mDCC analysis", "Ets 1 molecules", "mDCC approach", "nucleotide backbone", "MD simulations", "correlative motions", "transcription factor", "cytosine bases", "recognition helices", "contact", "correlation network", "H 3 helices"], "article_id"=>1232575, "categories"=>["Biological Sciences", "Science Policy"], "users"=>["Kota Kasahara", "Ikuo Fukuda", "Haruki Nakamura"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112419.g004", "stats"=>{"downloads"=>2, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_of_mDCC_maps_between_the_Ets1_2_8211_DNA_and_single_Ets1_8211_DNA_models_/1232575", "title"=>"Comparisons of mDCC maps between the (Ets1)<sub>2</sub>–DNA and single Ets1–DNA models.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-07 03:12:06"}

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Relative Metric

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