Using Shifts in Amino Acid Frequency and Substitution Rate to Identify Latent Structural Characters in Base-Excision Repair Enzymes
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{"title"=>"Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes", "type"=>"journal", "authors"=>[{"first_name"=>"Ramiro", "last_name"=>"Barrantes-Reynolds", "scopus_author_id"=>"6504145126"}, {"first_name"=>"Susan S.", "last_name"=>"Wallace", "scopus_author_id"=>"7403227473"}, {"first_name"=>"Jeffrey P.", "last_name"=>"Bond", "scopus_author_id"=>"7402613399"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"362707321", "scopus"=>"2-s2.0-80053598291", "doi"=>"10.1371/journal.pone.0025246", "issn"=>"19326203", "sgr"=>"80053598291"}, "id"=>"00491ac4-f4d1-379e-b5e8-107ea3c21c01", "abstract"=>"Protein evolution includes the birth and death of structural motifs. For example, a zinc finger or a salt bridge may be present in some, but not all, members of a protein family. We propose that such transitions are manifest in sequence phylogenies as concerted shifts in substitution rates of amino acids that are neighbors in a representative structure. First, we identified rate shifts in a quartet from the Fpg/Nei family of base excision repair enzymes using a method developed by Xun Gu and coworkers. We found the shifts to be spatially correlated, more precisely, associated with a flexible loop involved in bacterial Fpg substrate specificity. Consistent with our result, sequences and structures provide convincing evidence that this loop plays a very different role in other family members. Second, then, we developed a method for identifying latent protein structural characters (LSC) given a set of homologous sequences based on Gu's method and proximity in a high-resolution structure. Third, we identified LSC and assigned states of LSC to clades within the Fpg/Nei family of base excision repair enzymes. We describe seven LSC; an accompanying Proteopedia page (http://proteopedia.org/wiki/index.php/Fpg_Nei_Protein_Family) describes these in greater detail and facilitates 3D viewing. The LSC we found provided a surprisingly complete picture of the interaction of the protein with the DNA capturing familiar examples, such as a Zn finger, as well as more subtle interactions. Their preponderance is consistent with an important role as phylogenetic characters. Phylogenetic inference based on LSC provided convincing evidence of independent losses of Zn fingers. Structural motifs may serve as important phylogenetic characters and modeling transitions involving structural motifs may provide a much deeper understanding of protein evolution.", "link"=>"http://www.mendeley.com/research/using-shifts-amino-acid-frequency-substitution-rate-identify-latent-structural-characters-baseexcisi", "reader_count"=>6, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>6}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/727889"], "description"=>"<p>Coefficient of Type I (above diagonal) and Type II (below diagonal) functional divergence for Fpg/Nei clades.</p>", "links"=>[], "tags"=>["ii", "divergence"], "article_id"=>398253, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.t003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coefficient_of_Type_I_above_diagonal_and_Type_II_below_diagonal_functional_divergence_for_Fpg_Nei_clades_/398253", "title"=>"Coefficient of Type I (above diagonal) and Type II (below diagonal) functional divergence for Fpg/Nei clades.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 14:05:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/727955"], "description"=>"<p>Comparison of tree lengths and hypothesis testing of randomness of the loop on all subclades.</p>", "links"=>[], "tags"=>["lengths", "randomness"], "article_id"=>398318, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.t001", "stats"=>{"downloads"=>6, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_tree_lengths_and_hypothesis_testing_of_randomness_of_the_loop_on_all_subclades_/398318", "title"=>"Comparison of tree lengths and hypothesis testing of randomness of the loop on all subclades.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 14:06:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/727745"], "description"=>"<p>Top) Amino acids side chains associated with LSC 1–6 are shown in the context of the protein backbone, DNA backbone, damaged nucleotide, opposite nucleotide, and Zn ion <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Fromme1\" target=\"_blank\">[67]</a>. The green residues in both the structure (top) and the diagram (bottom) correspond to first-shell amino acids conserved in the entire family: R264 (contained in LSC6), N174 (stabilized by LSC1), and K60 (stabilized by LSC3/LSC2) stabilize the phosphate of the damaged base, and P2, E3 and are part of the catalytic residues <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Gilboa1\" target=\"_blank\">[97]</a>. The helix containing P2 and E3 may be stabilized by LSC2 as well. The enzyme everts the damage, and an intercalation loop (LSC4) fills the void and makes contact with the opposite base <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Coste1\" target=\"_blank\">[68]</a>. The damage itself in BaFpg1 is recognized by a recognition complex <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Fromme1\" target=\"_blank\">[67]</a>. Other important residues not included here include H74 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Gilboa1\" target=\"_blank\">[97]</a> and E6 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Kropachev1\" target=\"_blank\">[48]</a>. A DNA binding residue not discussed in the literature corresponds to Tyr242 (part of LSC5).</p>", "links"=>[], "tags"=>["stabilize", "residues", "enzyme-dna"], "article_id"=>398107, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LSCs_supply_or_stabilize_residues_that_participate_in_enzyme_DNA_interactions_/398107", "title"=>"LSCs supply or stabilize residues that participate in enzyme-DNA interactions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:05:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/727860"], "description"=>"<p>1 Length of the reference sequence used to calculate rates for each subfamily.</p>", "links"=>[], "tags"=>["subfamily", "alignments"], "article_id"=>398220, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.t004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Features_of_the_subfamily_alignments_and_trees_/398220", "title"=>"Features of the subfamily alignments and trees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 14:05:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/727413"], "description"=>"<p>An LSC can have multiple states. A) State of LSC1 in the B. stearothermophilus MutM structure <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Fromme1\" target=\"_blank\">[67]</a>. N174 (in pink), part of the helix-two-turn-helix (H2TH) motif along with two other amino acids (including the key amino acid R264, in blue) functions in the orientation and kinking of the DNA <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Zharkov2\" target=\"_blank\">[70]</a>. K160 (blue) helps keep the proper arrangement between the zinc finger and the H2TH <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Sugahara1\" target=\"_blank\">[69]</a>. B) Sequence logos for the each of the nine LSC1 amino acids in each of the three clades as well as MvNei1. Column headings indicate the aligned position in both the B. stearothermophilus MutM and E. coli Nei sequences. The sequence logos associated with 1R2Y K160 suggest that in three of the nine clades (BaFpg1, BaFpg2 and PFNei) the arrangement between the zinc finger and the H2TH is stabilized by a lysine in the same manner as in the B. stearothermophilus MutM protein. C) State of LSC1 in the E. coli Nei structure (62, PDB 1K3W). R171 hydrogen bonds to the other beta-sheet of the zinc-finger, presumably playing a role analogous to 1R2Y K160, which originates on a different helix. The sequence logos associated with R171 suggests that in six subfamilies (AcNei1 and AcNei2, PrNei and all vertebrate subfamilies), the arrangement between the zinc finger and the H2TH is maintained by an arginine or lysine in the same manner as in the E. coli Nei protein. For the subfamilies of BaFpg1 and PrNei, sites 160 and 266 are a type I, 174 and 264 are a type 0, and the rest are type II.</p>", "links"=>[], "tags"=>["states", "solutions"], "article_id"=>397774, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_States_of_an_LSC_Two_solutions_to_the_same_problem_/397774", "title"=>"Multiple States of an LSC: Two solutions to the same problem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:03:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/727641"], "description"=>"<p>Substitution rates of individual aligned amino acid positions can differ between clades of orthologs from actinomycetes (left, Pearson correlation 0.47) or eukaryotes (right, 0.19). Each axis reflects amino acid variation rate in one of the replicate organism trees described in the legend to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone-0025246-g004\" target=\"_blank\">Figure 4</a>. Each point is an aligned amino acid sequence position. Sites that have experienced a rate-shift (Type I) are green while those that exhibit an amino acid frequency-shift (Type II) are red.</p>", "links"=>[], "tags"=>["rates", "aligned", "amino", "positions", "clades"], "article_id"=>398001, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Substitution_rates_of_individual_aligned_amino_acid_positions_can_differ_between_clades_of_orthologs_/398001", "title"=>"Substitution rates of individual aligned amino acid positions can differ between clades of orthologs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:04:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/727341"], "description"=>"<p>Type I sites, amino acids that shift in substitution rate among two clades (BaFpg1, and PFNei), are colored in green in the B. stearothermophilus MutM structure <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025246#pone.0025246-Fromme1\" target=\"_blank\">[67]</a> (1R2Y). Three structural clusters (LSCs) are shown, the (a) zinc finger (BaFpg1), zincless finger (PFNei); b) two highly conserved glycines on Fpg which mark the beginning and end of the recognition loop, and which have a higher rate on PFNei, suggesting that the loop does not perform the same role in recognition and c) a triad that stabilizes the DNA and the opposite base which allows for more variability on PFNei.</p>", "links"=>[], "tags"=>["clustering"], "article_id"=>397698, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_structural_clustering_of_type_I_sites_/397698", "title"=>"Example of structural clustering of type I sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:02:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/727923"], "description"=>"<p>Seven LSCs from the Fpg/Nei protein family.</p>", "links"=>[], "tags"=>["lscs"], "article_id"=>398288, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seven_LSCs_from_the_Fpg_Nei_protein_family_/398288", "title"=>"Seven LSCs from the Fpg/Nei protein family.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 14:05:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/727571"], "description"=>"<p>Each column corresponds to one of the three organismal phylogenies. Each entry in a column (paired blue and green bars) represents an instance of the organismal phylogeny in the Fpg/Nei family protein phylogeny. The blue bars correspond to the number of substitutions from the last common ancestor (LCA) of each replicate tree to the present while the green bars correspond to the number of substitutions from the LCA of the phylogeny of replicate trees to the LCA of the each replicate tree.</p>", "links"=>[], "tags"=>["replicate", "eukaryote"], "article_id"=>397934, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rate_variation_does_not_differ_dramatically_between_replicate_Proteobacterium_Actinomycete_or_Eukaryote_organism_tree_topologies_/397934", "title"=>"Rate variation does not differ dramatically between replicate Proteobacterium, Actinomycete, or Eukaryote organism tree topologies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:04:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/727491"], "description"=>"<p>The most parsimonious protein phylogeny consistent with the states of the six LSCs is shown with the changes in LSCs annotated as red bars. The choice of the root results in one of its children (BaFpg1, BaFpg2) represents well the diversity of bacteria while the other represents plants, fungi, and metazoans.</p>", "links"=>[], "tags"=>["states", "lscs", "infer"], "article_id"=>397851, "categories"=>["Molecular Biology", "Biological Sciences"], "users"=>["Ramiro Barrantes-Reynolds", "Susan S. Wallace", "Jeffrey P. Bond"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025246.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_states_of_LSCs_can_be_used_to_infer_the_Fpg_Nei_family_phylogeny_/397851", "title"=>"The states of LSCs can be used to infer the Fpg/Nei family phylogeny.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 14:03:42"}

PMC Usage Stats | Further Information

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  • {"month"=>"1", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"1", "year"=>"2012", "pdf"=>"1", "unique-ip"=>"3", "figure"=>"3", "scanned-summary"=>"0", "supp-data"=>"0"}
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  • {"unique-ip"=>"8", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2012", "month"=>"7"}
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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"4"}
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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
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  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"0", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
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