Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
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{"title"=>"Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases", "type"=>"journal", "authors"=>[{"first_name"=>"Bradley", "last_name"=>"Kossmann", "scopus_author_id"=>"56311060200"}, {"first_name"=>"Ivaylo", "last_name"=>"Ivanov", "scopus_author_id"=>"35576835900"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-84905457969", "sgr"=>"84905457969", "issn"=>"15537358", "doi"=>"10.1371/journal.pcbi.1003704", "pui"=>"373701164"}, "id"=>"7d176b0a-2814-3758-aac9-d1b99bd9a5b4", "abstract"=>"Alkylpurine glycosylase D (AlkD) exhibits a unique base excision strategy. Instead of interacting directly with the lesion, the enzyme engages the non-lesion DNA strand. AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression. Since this strategy leaves the alkylated base solvent exposed, the means to achieve enzymatic cleavage had remained unclear. We determined a minimum energy path for flipping out a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the energetics of base extrusion. We show that AlkD acts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state. These states are almost equivalent in free energy and separated by low barriers. Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA. N-glycosidic bond scission is then facilitated by a backbone phosphate group proximal to the alkylated base.", "link"=>"http://www.mendeley.com/research/alkylpurine-glycosylase-d-employs-dna-sculpting-strategy-extrude-excise-damaged-bases", "reader_count"=>5, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1579251"], "description"=>"<p>A) Overall architecture of the AlkD-DNA complex with residues contacting the DNA backbone shown explicitly and labelled; B) The mode of recognition of the extrahelical thymine base opposite to the 3 mA lesion. DNA is shown in stick representation and as a transparent colored surface. AlkD is shown in cartoon representation.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "recognizes"], "article_id"=>1092737, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003704.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AlkD_recognizes_DNA_through_HEAT_repeat_motifs_/1092737", "title"=>"AlkD recognizes DNA through HEAT repeat motifs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-03 02:48:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1579270"], "description"=>"<p>A) DNA substrate in the initial (red), intermediate (gray) and final (blue) states of AlkD base extrusion. AlkD is represented in cyan. Minimal side chain movement is sufficient to accommodate the DNA conformational transitions; B) Shift in hydrogen bonding contacts from the intermediate to the final state. Two AlkD residues, Arg43 and Thr39, making direct contacts to the lesion strand shift their binding positions along the DNA backbone.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "provides", "scaffold", "conformations", "degrees"], "article_id"=>1092738, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003704.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AlkD_provides_a_scaffold_to_accommodate_multiple_DNA_conformations_with_different_degrees_of_bending_/1092738", "title"=>"AlkD provides a scaffold to accommodate multiple DNA conformations with different degrees of bending.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-03 02:48:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1579271"], "description"=>"<p>Phosphate groups are numbered starting from the 3 mA lesion at position 0.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "hydrogen", "bonding", "observed", "ma", "phosphate", "-2", "lesion"], "article_id"=>1092739, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003704.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Persistent_hydrogen_bonding_contact_observed_between_the_3_mA_base_and_the_phosphate_in_position_2_along_the_lesion_strand_/1092739", "title"=>"Persistent hydrogen bonding contact observed between the 3 mA base and the phosphate in position -2 along the lesion strand.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-03 02:48:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1579272", "https://ndownloader.figshare.com/files/1579273", "https://ndownloader.figshare.com/files/1579274"], "description"=>"<div><p>Alkylpurine glycosylase D (AlkD) exhibits a unique base excision strategy. Instead of interacting directly with the lesion, the enzyme engages the non-lesion DNA strand. AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression. Since this strategy leaves the alkylated base solvent exposed, the means to achieve enzymatic cleavage had remained unclear. We determined a minimum energy path for flipping out a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the energetics of base extrusion. We show that AlkD acts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state. These states are almost equivalent in free energy and separated by low barriers. Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA. <i>N</i>-glycosidic bond scission is then facilitated by a backbone phosphate group proximal to the alkylated base.</p></div>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "glycosylase", "employs", "sculpting", "extrude", "excise", "damaged"], "article_id"=>1092740, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003704.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003704.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003704.s003"], "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alkylpurine_Glycosylase_D_Employs_DNA_Sculpting_as_a_Strategy_to_Extrude_and_Excise_Damaged_Bases_/1092740", "title"=>"Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-03 02:48:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1579246"], "description"=>"<p>Effective free energy profiles for base flipping in the presence (red line) and absence (blue line) of AlkD. The rmsd-based reaction coordinate, ξ was normalized to vary from 0 to 1.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "binding", "flattens", "lesion", "extrusion"], "article_id"=>1092734, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003704.g001", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AlkD_binding_flattens_the_free_energy_landscape_for_lesion_extrusion_from_DNA_/1092734", "title"=>"AlkD binding flattens the free energy landscape for lesion extrusion from DNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-03 02:48:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/1579247"], "description"=>"<p>The three stable states in the AlkD/3 mA-DNA PMF. A) initial state; B) kinked intermediate state; and C) fully extruded (final) state. DNA bending is shown schematically in black.</p>", "links"=>[], "tags"=>["Biochemistry", "dna", "DNA repair", "Nucleic acids", "biophysics", "Biophysical simulations", "chemistry", "computational chemistry", "molecular dynamics", "sculpting", "substrate", "conformations", "flipping"], "article_id"=>1092735, "categories"=>["Biological Sciences"], "users"=>["Bradley Kossmann", "Ivaylo Ivanov"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003704.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AlkD_s_sculpting_of_the_DNA_substrate_results_in_three_stable_conformations_along_the_flipping_pathway_/1092735", "title"=>"AlkD's sculpting of the DNA substrate results in three stable conformations along the flipping pathway.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-03 02:48:16"}

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