{"id":"https://openalex.org/W1970624734","doi":"https://doi.org/10.1371/journal.pcbi.1003804","title":"Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA","display_name":"Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA","publication_year":2014,"publication_date":"2014-09-04","ids":{"openalex":"https://openalex.org/W1970624734","doi":"https://doi.org/10.1371/journal.pcbi.1003804","mag":"1970624734","pmid":"https://pubmed.ncbi.nlm.nih.gov/25188490"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003804","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003804","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003804&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003804&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072626733","display_name":"Xiakun Chu","orcid":"https://orcid.org/0000-0003-3166-7070"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiakun Chu","raw_affiliation_strings":["State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100394617","display_name":"Fei Liu","orcid":"https://orcid.org/0000-0002-3567-123X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fei Liu","raw_affiliation_strings":["State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071566821","display_name":"Brian A. Maxwell","orcid":"https://orcid.org/0000-0002-0177-3991"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian A. Maxwell","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100424382","display_name":"Yong Wang","orcid":"https://orcid.org/0000-0001-9156-0377"},"institutions":[{"id":"https://openalex.org/I4210092888","display_name":"Changchun Institute of Applied Chemistry","ror":"https://ror.org/00h52n341","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210092888"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yong Wang","raw_affiliation_strings":["State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China","State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China","institution_ids":["https://openalex.org/I4210092888","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P. R. China","institution_ids":["https://openalex.org/I4210092888","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003952728","display_name":"Zucai Suo","orcid":"https://orcid.org/0000-0003-3871-3420"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zucai Suo","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100419343","display_name":"Haijun Wang","orcid":"https://orcid.org/0000-0001-6058-0121"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haijun Wang","raw_affiliation_strings":["College of Physics, Jilin University, Changchun, Jilin, P.R. China"],"affiliations":[{"raw_affiliation_string":"College of Physics, Jilin University, Changchun, Jilin, P.R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403067","display_name":"Wei Han","orcid":"https://orcid.org/0000-0002-4830-3487"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Han","raw_affiliation_strings":["College of Physics, Jilin University, Changchun, Jilin, P.R. China"],"affiliations":[{"raw_affiliation_string":"College of Physics, Jilin University, Changchun, Jilin, P.R. China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100346147","display_name":"Jin Wang","orcid":"https://orcid.org/0000-0002-2841-4913"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jin Wang","raw_affiliation_strings":["State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China; Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America","Stony Brook University, Stony Brook, United States"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, P.R. China; College of Physics, Jilin University, Changchun, Jilin, P.R. China; Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York, United States of America","institution_ids":[]},{"raw_affiliation_string":"Stony Brook University, Stony Brook, United States","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100346147"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.9965,"has_fulltext":true,"cited_by_count":57,"citation_normalized_percentile":{"value":0.85884386,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"9","first_page":"e1003804","last_page":"e1003804"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-clamp","display_name":"DNA clamp","score":0.5978690385818481},{"id":"https://openalex.org/keywords/dna-polymerase","display_name":"DNA polymerase","score":0.5751359462738037},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5591821670532227},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4637352526187897},{"id":"https://openalex.org/keywords/polymerase","display_name":"Polymerase","score":0.4557272493839264},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.44254639744758606},{"id":"https://openalex.org/keywords/hmg-box","display_name":"HMG-box","score":0.4148562550544739},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3316902816295624},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.2619822323322296},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.16791558265686035},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15949216485023499},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.09901326894760132},{"id":"https://openalex.org/keywords/reverse-transcriptase","display_name":"Reverse transcriptase","score":0.07195508480072021}],"concepts":[{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.5978690385818481},{"id":"https://openalex.org/C2756471","wikidata":"https://www.wikidata.org/wiki/Q206286","display_name":"DNA polymerase","level":3,"score":0.5751359462738037},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5591821670532227},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4637352526187897},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.4557272493839264},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.44254639744758606},{"id":"https://openalex.org/C5179208","wikidata":"https://www.wikidata.org/wiki/Q3782057","display_name":"HMG-box","level":5,"score":0.4148562550544739},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3316902816295624},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.2619822323322296},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.16791558265686035},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15949216485023499},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.09901326894760132},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.07195508480072021}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004259","descriptor_name":"DNA-Directed DNA Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1003804","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003804","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003804&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25188490","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25188490","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.785.866","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.785.866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/ea/6b/pcbi.1003804.PMC4154647.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:ef9922a042b4472890b031b9d69a4a56","is_oa":true,"landing_page_url":"https://doaj.org/article/ef9922a042b4472890b031b9d69a4a56","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 9, p e1003804 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3126923","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4154647","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003804","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003804","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003804&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1131331748","display_name":null,"funder_award_id":"91227114","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2717198908","display_name":null,"funder_award_id":"973 project","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5421120092","display_name":null,"funder_award_id":"2010CB933600","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5492191759","display_name":null,"funder_award_id":"11174105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6926952570","display_name":null,"funder_award_id":"21190040","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7033253288","display_name":null,"funder_award_id":"Grants","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309374","display_name":"Ohio State University","ror":"https://ror.org/00rs6vg23"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1970624734.pdf","grobid_xml":"https://content.openalex.org/works/W1970624734.grobid-xml"},"referenced_works_count":118,"referenced_works":["https://openalex.org/W45157614","https://openalex.org/W1479884571","https://openalex.org/W1515096181","https://openalex.org/W1597762634","https://openalex.org/W1829960224","https://openalex.org/W1880349703","https://openalex.org/W1884115821","https://openalex.org/W1953212190","https://openalex.org/W1965127482","https://openalex.org/W1965500179","https://openalex.org/W1966078827","https://openalex.org/W1968437581","https://openalex.org/W1974114013","https://openalex.org/W1978347168","https://openalex.org/W1981369098","https://openalex.org/W1984065492","https://openalex.org/W1985581386","https://openalex.org/W1985746590","https://openalex.org/W1987679703","https://openalex.org/W1990189688","https://openalex.org/W1990507623","https://openalex.org/W1992787746","https://openalex.org/W1994121680","https://openalex.org/W1994756593","https://openalex.org/W2000149219","https://openalex.org/W2006357154","https://openalex.org/W2008233255","https://openalex.org/W2009442572","https://openalex.org/W2010004274","https://openalex.org/W2010041274","https://openalex.org/W2013306140","https://openalex.org/W2017764675","https://openalex.org/W2019455970","https://openalex.org/W2020484461","https://openalex.org/W2022948355","https://openalex.org/W2023231003","https://openalex.org/W2023487073","https://openalex.org/W2023656180","https://openalex.org/W2025102721","https://openalex.org/W2026837912","https://openalex.org/W2026987986","https://openalex.org/W2030239760","https://openalex.org/W2032549034","https://openalex.org/W2034299708","https://openalex.org/W2035747967","https://openalex.org/W2036000659","https://openalex.org/W2036362320","https://openalex.org/W2040295865","https://openalex.org/W2040809566","https://openalex.org/W2041000185","https://openalex.org/W2042336768","https://openalex.org/W2042426030","https://openalex.org/W2045686993","https://openalex.org/W2048855825","https://openalex.org/W2052354390","https://openalex.org/W2053960740","https://openalex.org/W2057750449","https://openalex.org/W2058353811","https://openalex.org/W2059947046","https://openalex.org/W2063006759","https://openalex.org/W2065864578","https://openalex.org/W2065996552","https://openalex.org/W2066790586","https://openalex.org/W2066962978","https://openalex.org/W2069662497","https://openalex.org/W2070183087","https://openalex.org/W2070288144","https://openalex.org/W2074566613","https://openalex.org/W2075702662","https://openalex.org/W2079786703","https://openalex.org/W2079955502","https://openalex.org/W2083265479","https://openalex.org/W2085463974","https://openalex.org/W2087533857","https://openalex.org/W2087667357","https://openalex.org/W2087887622","https://openalex.org/W2088404436","https://openalex.org/W2096929343","https://openalex.org/W2097412382","https://openalex.org/W2098089384","https://openalex.org/W2099650039","https://openalex.org/W2104710588","https://openalex.org/W2104739702","https://openalex.org/W2107238748","https://openalex.org/W2109685531","https://openalex.org/W2110612352","https://openalex.org/W2112154906","https://openalex.org/W2113030357","https://openalex.org/W2113353838","https://openalex.org/W2115273980","https://openalex.org/W2123217482","https://openalex.org/W2123529526","https://openalex.org/W2123559959","https://openalex.org/W2124735489","https://openalex.org/W2126915623","https://openalex.org/W2128380437","https://openalex.org/W2128572087","https://openalex.org/W2136716105","https://openalex.org/W2143970215","https://openalex.org/W2144562104","https://openalex.org/W2147466870","https://openalex.org/W2151497682","https://openalex.org/W2153438491","https://openalex.org/W2155844132","https://openalex.org/W2156865722","https://openalex.org/W2168208027","https://openalex.org/W2171755502","https://openalex.org/W2178631187","https://openalex.org/W2313401558","https://openalex.org/W2325642794","https://openalex.org/W2326269154","https://openalex.org/W2328004490","https://openalex.org/W2329440962","https://openalex.org/W2330598181","https://openalex.org/W2949670980","https://openalex.org/W2953079104","https://openalex.org/W3103586898","https://openalex.org/W4254085062"],"related_works":["https://openalex.org/W1598923468","https://openalex.org/W1968835388","https://openalex.org/W2025103069","https://openalex.org/W2082667042","https://openalex.org/W2107993919","https://openalex.org/W1672783309","https://openalex.org/W2131120052","https://openalex.org/W2109661443","https://openalex.org/W2138180167","https://openalex.org/W2075000512"],"abstract_inverted_index":{"Protein-DNA":[0],"recognition":[1,45,65,109,200],"is":[2,66,110,132,212],"a":[3,18,72,117,134,176],"central":[4],"biological":[5],"process":[6,143,232],"that":[7,107,130,189],"governs":[8],"the":[9,23,39,50,54,59,63,141,145,148,157,160,163,166,169,184,190,218,226,229,234,238],"life":[10],"of":[11,43,53,96,112,147,159,165,193,210,228],"cells.":[12],"A":[13],"protein":[14,31],"will":[15],"often":[16],"undergo":[17],"conformational":[19,32,60,135,170,196],"transition":[20],"to":[21,36,38,76,91,214],"form":[22],"functional":[24,51,78],"complex":[25],"with":[26],"its":[27,89],"target":[28],"DNA.":[29,92],"The":[30],"dynamics":[33,61,79,171,197],"are":[34],"expected":[35],"contribute":[37],"stability":[40],"and":[41,46,98,103,123,144,168,195,254],"specificity":[42],"DNA":[44,83,122,185,207,220,230,257],"therefore":[47],"may":[48],"control":[49],"activity":[52],"protein-DNA":[55,64],"complex.":[56],"Understanding":[57],"how":[58,180,250],"influences":[62],"still":[67],"challenging.":[68],"Here,":[69],"we":[70,105,128,174],"developed":[71,240],"two-basin":[73],"structure-based":[74],"model":[75],"explore":[77],"in":[80,172,198],"Sulfolobus":[81],"solfataricus":[82],"Y-family":[84,219,235],"polymerase":[85],"IV":[86],"(DPO4)":[87],"during":[88,140],"binding":[90,142,153],"With":[93],"explicit":[94],"consideration":[95],"non-specific":[97],"specific":[99,125,256],"interactions":[100],"between":[101,137],"DPO4":[102,131,181],"DNA,":[104],"found":[106,129,213],"DPO4-DNA":[108,199],"comprised":[111],"first":[113],"3D":[114],"diffusion,":[115],"then":[116],"short-range":[118],"adjustment":[119],"sliding":[120],"on":[121,179,249],"finally":[124],"binding.":[126],"Interestingly,":[127],"under":[133],"equilibrium":[136],"multiple":[138],"states":[139],"distributions":[146],"conformations":[149],"vary":[150],"at":[151],"different":[152],"stages.":[154],"By":[155],"modulating":[156],"strength":[158],"electrostatic":[161],"interactions,":[162],"flexibility":[164,194],"linker,":[167],"DPO4,":[173],"drew":[175],"clear":[177],"picture":[178],"dynamically":[182],"regulates":[183],"recognition.":[186],"We":[187],"argue":[188],"unique":[191],"features":[192],"have":[201],"direct":[202],"implications":[203],"for":[204,233,246],"low-fidelity":[205],"translesion":[206],"synthesis,":[208],"most":[209],"which":[211],"be":[215,243],"accomplished":[216],"by":[217],"polymerases.":[221,236],"Our":[222],"results":[223],"help":[224],"complete":[225],"description":[227],"synthesis":[231],"Furthermore,":[237],"methods":[239],"here":[241],"can":[242],"widely":[244],"applied":[245],"future":[247],"investigations":[248],"various":[251],"proteins":[252],"recognize":[253],"bind":[255],"substrates.":[258]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}