{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T10:51:50Z","timestamp":1773658310587,"version":"3.50.1"},"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2008,4,25]],"date-time":"2008-04-25T00:00:00Z","timestamp":1209081600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000066","type":"journal-article","created":{"date-parts":[[2008,4,24]],"date-time":"2008-04-24T18:11:47Z","timestamp":1209060707000},"page":"e1000066","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":17,"title":["An AP Endonuclease 1\u2013DNA Polymerase \u03b2 Complex: Theoretical Prediction of Interacting Surfaces"],"prefix":"10.1371","volume":"4","author":[{"given":"Alexej","family":"Abyzov","sequence":"first","affiliation":[]},{"given":"Alper","family":"Uzun","sequence":"additional","affiliation":[]},{"given":"Phyllis R.","family":"Strauss","sequence":"additional","affiliation":[]},{"given":"Valentin A.","family":"Ilyin","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2008,4,25]]},"reference":[{"key":"ref1","article-title":"DNA Repair And Mutagenesis","author":"EC Friedberg","year":"2006"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.dnarep.2006.11.004","article-title":"Role of active site tyrosines in dynamic aspects of DNA binding by AP endonuclease.","volume":"6","author":"LF Melo","year":"2007","journal-title":"DNA Repair (Amst)"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1074\/jbc.272.2.1302","article-title":"Substrate binding by human apurinic\/apyrimidinic endonuclease indicates a Briggs-Haldane mechanism.","volume":"272","author":"PR Strauss","year":"1997","journal-title":"J Biol Chem"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1016\/j.dnarep.2006.10.017","article-title":"The mechanics of base excision repair, and its relationship to aging and disease.","volume":"6","author":"DM Wilson 3rd","year":"2007","journal-title":"DNA Repair (Amst)"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S0076-6879(06)08007-4","article-title":"Activities and mechanism of DNA polymerase beta.","volume":"408","author":"WA Beard","year":"2006","journal-title":"Methods Enzymol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"7166","DOI":"10.1073\/pnas.94.14.7166","article-title":"Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway.","volume":"94","author":"RA Bennett","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"9127","DOI":"10.1073\/pnas.88.20.9127","article-title":"Cloning and characterization of a 3-methyladenine DNA glycosylase cDNA from human cells whose gene maps to chromosome 16.","volume":"88","author":"L Samson","year":"1991","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/0092-8674(95)90489-1","article-title":"The Epstein-Barr virus transforming protein LMP1 engages signaling proteins for the tumor necrosis factor receptor family.","volume":"80","author":"G Mosialos","year":"1995","journal-title":"Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1101\/gad.7.4.555","article-title":"The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit.","volume":"7","author":"T Durfee","year":"1993","journal-title":"Genes Dev"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"16000","DOI":"10.1074\/jbc.271.27.16000","article-title":"Specific interaction of DNA polymerase beta and DNA ligase I in a multiprotein base excision repair complex from bovine testis.","volume":"271","author":"R Prasad","year":"1996","journal-title":"J Biol Chem"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"13532","DOI":"10.1074\/jbc.M611295200","article-title":"Coordination of steps in single-nucleotide base excision repair mediated by apurinic\/apyrimidinic endonuclease 1 and DNA polymerase beta.","volume":"282","author":"Y Liu","year":"2007","journal-title":"J Biol Chem"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/35000249","article-title":"DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected].","volume":"403","author":"CD Mol","year":"2000","journal-title":"Nature"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1016\/j.str.2006.01.011","article-title":"Magnesium-induced assembly of a complete DNA polymerase catalytic complex.","volume":"14","author":"VK Batra","year":"2006","journal-title":"Structure"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"11205","DOI":"10.1021\/bi9703812","article-title":"Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.","volume":"36","author":"MR Sawaya","year":"1997","journal-title":"Biochemistry"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1002\/pro.5560010117","article-title":"Calculation of the free energy of association for protein complexes.","volume":"1","author":"N Horton","year":"1992","journal-title":"Protein Sci"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1002\/prot.10074","article-title":"In silico two-hybrid system for the selection of physically interacting protein pairs.","volume":"47","author":"F Pazos","year":"2002","journal-title":"Proteins"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"36242","DOI":"10.1074\/jbc.M306065200","article-title":"Modulation of the 3\u2032\u21925\u2032-exonuclease activity of human apurinic endonuclease (Ape1) by its 5\u2032-incised Abasic DNA product.","volume":"278","author":"D Wong","year":"2003","journal-title":"J Biol Chem"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3408","DOI":"10.1074\/jbc.M002884200","article-title":"DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase beta. Implication for the identity of the rate-limiting conformational change.","volume":"276","author":"BJ Vande Berg","year":"2001","journal-title":"J Biol Chem"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"15263","DOI":"10.1074\/jbc.273.24.15263","article-title":"Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.","volume":"273","author":"R Prasad","year":"1998","journal-title":"J Biol Chem"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"16553","DOI":"10.1021\/bi9907429","article-title":"Human apurinic\/apyrimidinic endonuclease is processive.","volume":"38","author":"DC Carey","year":"1999","journal-title":"Biochemistry"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1093\/nar\/30.8.1817","article-title":"A quantitative model of human DNA base excision repair. I. Mechanistic insights.","volume":"30","author":"BA Sokhansanj","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"12778","DOI":"10.1021\/bi960790i","article-title":"Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.","volume":"35","author":"H Pelletier","year":"1996","journal-title":"Biochemistry"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/nsb0897-657","article-title":"The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.","volume":"4","author":"JR Huth","year":"1997","journal-title":"Nat Struct Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1107\/S0567739476001873","article-title":"A solution for the best rotation to relate two sets of vectors.","volume":"32","author":"W Kabsch","year":"1976","journal-title":"Acta Crystallographica Section A"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3677","DOI":"10.1093\/bioinformatics\/bti602","article-title":"Friend, an integrated analytical front-end application for bioinformatics.","volume":"21","author":"A Abyzov","year":"2005","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1110\/ps.04672604","article-title":"Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point.","volume":"13","author":"VA Ilyin","year":"2004","journal-title":"Protein Sci"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: fast, flexible, and free.","volume":"26","author":"D Van Der Spoel","year":"2005","journal-title":"J Comput Chem"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1073\/pnas.93.1.13","article-title":"Principles of protein-protein interactions.","volume":"93","author":"S Jones","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/S0022-2836(02)00442-4","article-title":"Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.","volume":"320","author":"R Guerois","year":"2002","journal-title":"J Mol Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0968-0004(98)01285-7","article-title":"Multiple sequence alignment with Clustal X.","volume":"23","author":"F Jeanmougin","year":"1998","journal-title":"Trends Biochem Sci"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000066","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T12:01:41Z","timestamp":1540296101000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000066"}},"subtitle":[],"editor":[{"given":"Michael","family":"Levitt","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2008,4,25]]},"references-count":31,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2008,4,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000066","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,4,25]]}}}