{"id":"https://openalex.org/W4409157057","doi":"https://doi.org/10.1371/journal.pcbi.1012493","title":"Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion","display_name":"Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion","publication_year":2025,"publication_date":"2025-04-04","ids":{"openalex":"https://openalex.org/W4409157057","doi":"https://doi.org/10.1371/journal.pcbi.1012493","pmid":"https://pubmed.ncbi.nlm.nih.gov/40184420"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012493","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1012493","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101332020","display_name":"Chenyang Gu","orcid":"https://orcid.org/0000-0002-0267-0812"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Chenyang Gu","raw_affiliation_strings":["Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-0267-0812","affiliations":[{"raw_affiliation_string":"Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103497775","display_name":"Shoji Takada","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shoji Takada","raw_affiliation_strings":["Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043178611","display_name":"Giovanni B. Brandani","orcid":"https://orcid.org/0000-0003-3379-0187"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Giovanni B. Brandani","raw_affiliation_strings":["Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039427603","display_name":"Tsuyoshi Terakawa","orcid":"https://orcid.org/0000-0002-0151-1123"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tsuyoshi Terakawa","raw_affiliation_strings":["Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan"],"raw_orcid":"https://orcid.org/0000-0002-0151-1123","affiliations":[{"raw_affiliation_string":"Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I22299242"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.5412,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.63632389,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":"21","issue":"4","first_page":"e1012493","last_page":"e1012493"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":1.0,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9994999766349792,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.998199999332428,"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/cohesin","display_name":"Cohesin","score":0.9551286697387695},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.6371762752532959},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5603297352790833},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.5545192360877991},{"id":"https://openalex.org/keywords/dna-clamp","display_name":"DNA clamp","score":0.5225046277046204},{"id":"https://openalex.org/keywords/dna-ligase","display_name":"DNA ligase","score":0.5186940431594849},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4996669292449951},{"id":"https://openalex.org/keywords/hmg-box","display_name":"HMG-box","score":0.46132439374923706},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2951408624649048},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.20687291026115417},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.06826475262641907}],"concepts":[{"id":"https://openalex.org/C115821613","wikidata":"https://www.wikidata.org/wiki/Q21103063","display_name":"Cohesin","level":4,"score":0.9551286697387695},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6371762752532959},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5603297352790833},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5545192360877991},{"id":"https://openalex.org/C31254050","wikidata":"https://www.wikidata.org/wiki/Q22328799","display_name":"DNA clamp","level":5,"score":0.5225046277046204},{"id":"https://openalex.org/C175114707","wikidata":"https://www.wikidata.org/wiki/Q408483","display_name":"DNA ligase","level":3,"score":0.5186940431594849},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4996669292449951},{"id":"https://openalex.org/C5179208","wikidata":"https://www.wikidata.org/wiki/Q3782057","display_name":"HMG-box","level":5,"score":0.46132439374923706},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2951408624649048},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.20687291026115417},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.06826475262641907},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000097722","descriptor_name":"Cohesins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000097722","descriptor_name":"Cohesins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000097722","descriptor_name":"Cohesins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000097722","descriptor_name":"Cohesins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098550","descriptor_name":"Structural Maintenance of Chromosome Protein 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098550","descriptor_name":"Structural Maintenance of Chromosome Protein 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098550","descriptor_name":"Structural Maintenance of Chromosome Protein 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098550","descriptor_name":"Structural Maintenance of Chromosome Protein 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002868","descriptor_name":"Chromosomal Proteins, Non-Histone","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"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":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D018797","descriptor_name":"Cell Cycle Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D021122","descriptor_name":"Protein Subunits","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1012493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012493","pdf_url":null,"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:40184420","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40184420","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:europepmc.org:10783267","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11970657","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.1012493","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012493","pdf_url":null,"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/G1905771739","display_name":null,"funder_award_id":"24H00883","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3354580580","display_name":null,"funder_award_id":"20H0593","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4861608429","display_name":"Characterizing the mechanism of chromatin remodeling by molecular dynamics simulations","funder_award_id":"20K06587","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5174230046","display_name":"\u7d30\u80de\u5185\u8907\u96d1\u74b0\u5883\u4e0b\u306e\u76f8\u5206\u96e2\u306b\u3088\u308b\u751f\u4f53\u5206\u5b50\u51dd\u7e2e\u4f53\u5f62\u6210\u306e\u751f\u7269\u7269\u7406","funder_award_id":"24K01991","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5363867960","display_name":"Development of next-generation coarse-grained simulations towards analysis of cellular-scale assembly","funder_award_id":"21H02441","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320309807","display_name":"Takeda Science Foundation","ror":"https://ror.org/02y123g31"},{"id":"https://openalex.org/F4320316984","display_name":"Kyoto University Foundation","ror":null},{"id":"https://openalex.org/F4320322210","display_name":"Inamori Foundation","ror":"https://ror.org/00ht8je70"},{"id":"https://openalex.org/F4320323365","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1523490929","https://openalex.org/W1750015149","https://openalex.org/W1966431081","https://openalex.org/W1992225546","https://openalex.org/W2000332333","https://openalex.org/W2003673194","https://openalex.org/W2010713749","https://openalex.org/W2029582401","https://openalex.org/W2045533286","https://openalex.org/W2047005748","https://openalex.org/W2059287705","https://openalex.org/W2069662497","https://openalex.org/W2090037139","https://openalex.org/W2103653834","https://openalex.org/W2136464549","https://openalex.org/W2141807666","https://openalex.org/W2144362290","https://openalex.org/W2150329841","https://openalex.org/W2162980545","https://openalex.org/W2174021414","https://openalex.org/W2277909096","https://openalex.org/W2328563019","https://openalex.org/W2510475640","https://openalex.org/W2700512636","https://openalex.org/W2731784911","https://openalex.org/W2775505403","https://openalex.org/W2899721502","https://openalex.org/W2951976277","https://openalex.org/W2963275370","https://openalex.org/W2989713781","https://openalex.org/W2991248607","https://openalex.org/W2997323475","https://openalex.org/W3025316148","https://openalex.org/W3046933533","https://openalex.org/W3048619043","https://openalex.org/W3099479137","https://openalex.org/W3125756628","https://openalex.org/W3136389052","https://openalex.org/W3164690700","https://openalex.org/W3177828909","https://openalex.org/W3184281134","https://openalex.org/W3186803894","https://openalex.org/W3201478141","https://openalex.org/W3204390956","https://openalex.org/W4205560910","https://openalex.org/W4211156111","https://openalex.org/W4211196614","https://openalex.org/W4225783793","https://openalex.org/W4281793572","https://openalex.org/W4295242589","https://openalex.org/W4366594168","https://openalex.org/W4387079461","https://openalex.org/W4392501799","https://openalex.org/W4399731408","https://openalex.org/W6650253663"],"related_works":["https://openalex.org/W2793868219","https://openalex.org/W3161304531","https://openalex.org/W1983939771","https://openalex.org/W2968205299","https://openalex.org/W2020633581","https://openalex.org/W4228998207","https://openalex.org/W2126856425","https://openalex.org/W2152011623","https://openalex.org/W2889776493","https://openalex.org/W2124426699"],"abstract_inverted_index":{"The":[0,128],"SMC":[1],"complex":[2,89,133],"cohesin":[3,39,88,154],"mediates":[4],"interphase":[5],"chromatin":[6],"structural":[7,35,83],"formation":[8],"in":[9,152,173,189,208],"eukaryotic":[10],"cells":[11],"through":[12],"DNA":[13,52,56,70,95,124,136,144,150,174,185,192],"loop":[14,175,193],"extrusion.":[15,176],"Here,":[16],"we":[17,30,54,80,109],"sought":[18],"to":[19,69],"investigate":[20],"its":[21],"mechanism":[22],"using":[23,71],"molecular":[24],"dynamics":[25],"simulations.":[26],"To":[27],"achieve":[28],"this,":[29],"first":[31],"constructed":[32,81],"the":[33,38,64,82,86,92,99,102,106,115,131,153,158,198,202,209],"amino-acid-residue-resolution":[34],"models":[36],"of":[37,66,85,105,130,184,201],"subunits,":[40],"SMC1,":[41,116],"SMC3,":[42,117],"STAG1,":[43,118],"and":[44,62,90,119,146,160,196,206],"NIPBL.":[45],"By":[46],"simulating":[47],"these":[48,67,166],"subunits":[49,121,204],"with":[50,134],"double-stranded":[51,135],"molecules,":[53],"predicted":[55,93,107],"binding":[57,96,186],"patches":[58,68,97,113],"on":[59,98,114],"each":[60],"subunit":[61],"quantified":[63],"affinities":[65],"their":[72],"dissociation":[73],"rate":[74],"constants":[75],"as":[76,170],"a":[77,123,149],"proxy.":[78],"Then,":[79],"model":[84],"whole":[87,132],"mapped":[91],"high-affinity":[94],"structure.":[100],"From":[101],"spatial":[103],"relations":[104],"patches,":[108],"identified":[110,169],"that":[111,139],"multiple":[112],"NIPBL":[120,207],"form":[122],"clamping":[125],"patch":[126,141],"group.":[127],"simulations":[129],"molecules":[137],"suggest":[138],"this":[140,178],"group":[142],"facilitates":[143],"bending":[145],"helps":[147],"capture":[148],"segment":[151],"ring":[155],"formed":[156],"by":[157],"SMC1":[159],"SMC3":[161],"subunits.":[162],"In":[163],"previous":[164],"studies,":[165],"have":[167],"been":[168],"critical":[171],"steps":[172],"Therefore,":[177],"study":[179],"provides":[180],"experimentally":[181],"testable":[182],"predictions":[183],"sites":[187],"implicated":[188],"previously":[190],"proposed":[191],"extrusion":[194],"mechanisms":[195],"highlights":[197],"essential":[199],"roles":[200],"accessory":[203],"STAG1":[205],"mechanism.":[210]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}