An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
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{"title"=>"An AP endonuclease 1-DNA polymerase β complex: Theoretical prediction of interacting surfaces", "type"=>"journal", "authors"=>[{"first_name"=>"Alexej", "last_name"=>"Abyzov", "scopus_author_id"=>"8732206000"}, {"first_name"=>"Alper", "last_name"=>"Uzun", "scopus_author_id"=>"36851751200"}, {"first_name"=>"Phyllis R.", "last_name"=>"Strauss", "scopus_author_id"=>"7102244754"}, {"first_name"=>"Valentin A.", "last_name"=>"Ilyin", "scopus_author_id"=>"7004649210"}], "year"=>2008, "source"=>"PLoS Computational Biology", "identifiers"=>{"pmid"=>"18437203", "issn"=>"1553734X", "pui"=>"351656712", "sgr"=>"43249110544", "scopus"=>"2-s2.0-43249110544", "doi"=>"10.1371/journal.pcbi.1000066", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)"}, "id"=>"4ed7a0b2-0498-31a9-b8d1-5a72110863f9", "abstract"=>"Abasic (AP) sites in DNA arise through both endogenous and exogenous mechanisms. Since AP sites can prevent replication and transcription, the cell contains systems for their identification and repair. AP endonuclease (APEX1) cleaves the phosphodiester backbone 5' to the AP site. The cleavage, a key step in the base excision repair pathway, is followed by nucleotide insertion and removal of the downstream deoxyribose moiety, performed most often by DNA polymerase beta (pol-beta). While yeast two-hybrid studies and electrophoretic mobility shift assays provide evidence for interaction of APEX1 and pol-beta, the specifics remain obscure. We describe a theoretical study designed to predict detailed interacting surfaces between APEX1 and pol-beta based on published co-crystal structures of each enzyme bound to DNA. Several potentially interacting complexes were identified by sliding the protein molecules along DNA: two with pol-beta located downstream of APEX1 (3' to the damaged site) and three with pol-beta located upstream of APEX1 (5' to the damaged site). Molecular dynamics (MD) simulations, ensuring geometrical complementarity of interfaces, enabled us to predict interacting residues and calculate binding energies, which in two cases were sufficient (approximately -10.0 kcal/mol) to form a stable complex and in one case a weakly interacting complex. Analysis of interface behavior during MD simulation and visual inspection of interfaces allowed us to conclude that complexes with pol-beta at the 3'-side of APEX1 are those most likely to occur in vivo. Additional multiple sequence analyses of APEX1 and pol-beta in related organisms identified a set of correlated mutations of specific residues at the predicted interfaces. Based on these results, we propose that pol-beta in the open or closed conformation interacts and makes a stable interface with APEX1 bound to a cleaved abasic site on the 3' side. The method described here can be used for analysis in any DNA-metabolizing pathway where weak interactions are the principal mode of cross-talk among participants and co-crystal structures of the individual components are available.", "link"=>"http://www.mendeley.com/research/ap-endonuclease-1dna-polymerase-%CE%B2-complex-theoretical-prediction-interacting-surfaces", "reader_count"=>12, "reader_count_by_academic_status"=>{"Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Master"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Medicine and Dentistry"=>1, "Agricultural and Biological Sciences"=>9, "Physics and Astronomy"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Switzerland"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/932785"], "description"=>"<p>(A) Alignment of DNAs co-crystallized with pol-β and APEX1. X stands for the abasic site and x stands for lesion. Notations c1, c2, and c3 mark the alignments used to produce three initial complexes. (B) View of the 3′ complex structure. APEX1 is on the right and pol-β is on the left. The area of protein-protein interaction is circled.</p>", "links"=>[], "tags"=>["apex1"], "article_id"=>603233, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Initial_3_8242_complex_of_APEX1_and_pol_946_closed_conformation_/603233", "title"=>"Initial 3′ complex of APEX1 and pol-β (closed conformation).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:35:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/933397"], "description"=>"<p>Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculate the ratio of “gap volume/interface area” the sum of interface areas in APEX1 and pol-β is used in denominator. The free energy of binding was calculated with FOLD-X server.</p>", "links"=>[], "tags"=>["protein-protein", "interfaces"], "article_id"=>603842, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_of_protein_protein_interfaces_for_the_3_8242_complex_with_pol_946_in_open_conformation_/603842", "title"=>"Parameters of protein-protein interfaces for the 3′ complex (with pol-β in open conformation).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:39:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/932887"], "description"=>"<p>The initial complex is shown in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-g002\" target=\"_blank\">Figure 2</a>. Subdomains of pol-β are colored by different colors and named. The protein-protein interface consists of three spatially distinct segments. Residues with correlated mutations (for segment #2: Arg<sup>221</sup> of APEX1 and Gln<sup>31</sup> of pol-β) are colored in cyan (see also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-g006\" target=\"_blank\">Figure 6</a>).</p>", "links"=>[], "tags"=>["interface", "apex1", "ns", "md"], "article_id"=>603332, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_interface_of_APEX1_and_pol_946_closed_conformation_in_3_8242_complex_after_0_2_ns_of_MD_simulation_/603332", "title"=>"The interface of APEX1 and pol-β (closed conformation) in 3′ complex after 0.2 ns of MD simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:36:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/933423"], "description"=>"<p>The residues assembling the majority of the interface are highlighted in bold. The columns “Seg” refers to the discrete interface segments where the listed residues are located (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-g003\" target=\"_blank\">Figure 3</a>). The column “Interface Area” displays range of interface area represented by a residue during MD simulation (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-t001\" target=\"_blank\">Table 1</a>).</p>", "links"=>[], "tags"=>["residues", "apex1"], "article_id"=>603873, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interface_residues_of_APEX1_and_pol_946_closed_conformation_in_the_3_8242_complex_/603873", "title"=>"Interface residues of APEX1 and pol-β (closed conformation) in the 3′ complex.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:39:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/933057"], "description"=>"<p>(A) Alignment of 12-mer template DNA and DNAs co-crystallized with pol-β and APEX1. X stands for the abasic site and x stands for lesion. (B) View of the structure of the complex. APEX1 is on the right and pol-β is on the left. The area of protein-protein interaction is circled.</p>", "links"=>[], "tags"=>["apex1", "constructed"], "article_id"=>603499, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Initial_5_8242_complex_of_APEX1_and_pol_946_open_conformation_constructed_on_a_straight_DNA_/603499", "title"=>"Initial 5′ complex of APEX1 and pol-β (open conformation) constructed on a straight DNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:37:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/933506"], "description"=>"<p>Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculate the ratio of “gap volume/interface area” the sum of interface areas in APEX1 and pol-β is used in denominator. The free energy of binding was calculated with FOLD-X server.</p>", "links"=>[], "tags"=>["protein-protein", "interfaces", "conformation"], "article_id"=>603951, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_of_protein_protein_interfaces_for_the_5_8242_complex_with_pol_946_in_open_conformation_and_straight_DNA_/603951", "title"=>"Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation and straight DNA).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:39:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/933130"], "description"=>"<p>Only alignment for fragments of interacting regions in the 3′ complexes (with open and closed conformation of pol-β) is shown. Residues at the interfaces are in bold; neighboring residues are in normal font. Interacting residues include residues from segments #1, #2, and #3 and adjacent residues (see text), found at interface only in the complex with open conformation of pol-β. Adjacent residues are termed (where possible) AR. Correlated mutations of interacting residues are highlighted in cyan and orange. Other variations in interacting residues are highlighted in red.</p>", "links"=>[], "tags"=>["alignment", "apex1"], "article_id"=>603576, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_sequence_alignment_of_APEX1_and_pol_946_/603576", "title"=>"Multiple sequence alignment of APEX1 and pol-β.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:37:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/933569"], "description"=>"<p>Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculate the ratio of “gap volume/interface area” the sum of interface areas in APEX1 and pol-β is used in denominator. The free energy of binding was calculated with FOLD-X server.</p>", "links"=>[], "tags"=>["protein-protein", "interfaces"], "article_id"=>604023, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_of_protein_protein_interfaces_for_the_5_8242_complex_with_pol_946_in_open_conformation_/604023", "title"=>"Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:40:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/933474"], "description"=>"<p>The residues assembling the majority of the interface are highlighted in bold. The columns “Seg” refers to the discrete interface segments where the listed residues are located. The column “Interface Area” displays range of interface area represented by a residue during MD simulation (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-t006\" target=\"_blank\">Table 6</a>).</p>", "links"=>[], "tags"=>["residues", "apex1"], "article_id"=>603928, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interface_residues_of_APEX1_and_pol_946_open_conformation_in_the_5_8242_complex_with_straight_DNA_/603928", "title"=>"Interface residues of APEX1 and pol-β (open conformation) in the 5′ complex with straight DNA.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:39:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/933299"], "description"=>"<p>Movement of thumb and 8-kDa subdomains of pol-β changes interface with APEX1 and may trigger complex dissociation. (A) shows 3′ complex APEX1 and pol-β complex with pol-β in open conformation. (B) shows the complex with pol-β in closed conformation. Area of protein-protein interface is circled. Arrows show the direction of thumb and 8-kDa subdomain movement.</p>", "links"=>[], "tags"=>["apex1"], "article_id"=>603745, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g007", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Suggested_mechanism_of_APEX1_and_pol_946_interaction_/603745", "title"=>"Suggested mechanism of APEX1 and pol-β interaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:38:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/933450"], "description"=>"<p>Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculate the ratio of “gap volume/interface area,” the sum of interface areas in APEX1 and pol-β is used in denominator. The free energy of binding was calculated with FOLD-X server.</p>", "links"=>[], "tags"=>["protein-protein", "interfaces"], "article_id"=>603899, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_of_protein_protein_interfaces_for_the_3_8242_complex_with_pol_946_in_closed_conformation_/603899", "title"=>"Parameters of protein-protein interfaces for the 3′ complex (with pol-β in closed conformation).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:39:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/932964"], "description"=>"<p>(A) Alignment of DNAs co-crystallized with pol-β and APEX1. X stands for the abasic site and x stands for lesion. Notations c4, c5, and c6 mark the alignments used to produce three initial complexes. (B) View of the 5′ complex structure. APEX1 is on the left and pol-β is on the right. The area of protein-protein interaction is circled.</p>", "links"=>[], "tags"=>["apex1"], "article_id"=>603417, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Initial_5_8242_complex_of_APEX1_and_pol_946_closed_conformation_/603417", "title"=>"Initial 5′ complex of APEX1 and pol-β (closed conformation).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:36:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/933532"], "description"=>"<p>The residues assembling the majority of the interface are highlighted in bold. The column “Interface Area” displays range of interface area represented by a residue during MD simulation (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000066#pcbi-1000066-t004\" target=\"_blank\">Table 4</a>).</p>", "links"=>[], "tags"=>["residues", "apex1"], "article_id"=>603983, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.t005", "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interface_residues_of_APEX1_and_pol_946_in_the_5_8242_complex_/603983", "title"=>"Interface residues of APEX1 and pol-β in the 5′ complex.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:40:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/932689"], "description"=>"<p>Comments underneath each picture reflect the conclusion made about each complex after analysis.</p>", "links"=>[], "tags"=>["diagram"], "article_id"=>603135, "categories"=>["Medicine", "Computational Biology"], "users"=>["Alexej Abyzov", "Alper Uzun", "Phyllis R. Strauss", "Valentin A. Ilyin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000066.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_diagram_of_initial_complex_construction_/603135", "title"=>"Schematic diagram of initial complex construction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:35:07"}

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Relative Metric

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