{"id":"https://openalex.org/W1999263344","doi":"https://doi.org/10.1021/ci500657d","title":"Molecular Dynamics Study of the Recognition of Dimethylated CpG Sites by MBD1 Protein","display_name":"Molecular Dynamics Study of the Recognition of Dimethylated CpG Sites by MBD1 Protein","publication_year":2015,"publication_date":"2015-02-06","ids":{"openalex":"https://openalex.org/W1999263344","doi":"https://doi.org/10.1021/ci500657d","mag":"1999263344","pmid":"https://pubmed.ncbi.nlm.nih.gov/25658035"},"language":"en","primary_location":{"id":"doi:10.1021/ci500657d","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500657d","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103599155","display_name":"Caterina Bianca Neve Aurora Bianchi","orcid":null},"institutions":[{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Caterina Bianchi","raw_affiliation_strings":["Department\rof Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Guip\u00fazcoa, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Guip\u00fazcoa, Spain","institution_ids":["https://openalex.org/I169108374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016053493","display_name":"Ronen Zangi","orcid":"https://orcid.org/0000-0001-5332-885X"},"institutions":[{"id":"https://openalex.org/I110594554","display_name":"Ikerbasque","ror":"https://ror.org/01cc3fy72","country_code":"ES","type":"other","lineage":["https://openalex.org/I110594554"]},{"id":"https://openalex.org/I169108374","display_name":"University of the Basque Country","ror":"https://ror.org/000xsnr85","country_code":"ES","type":"education","lineage":["https://openalex.org/I169108374"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Ronen Zangi","raw_affiliation_strings":["Department\rof Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Guip\u00fazcoa, Spain","IKERBASQUE, Basque\rFoundation for Science, 48013 Bilbao, Bizkaia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Guip\u00fazcoa, Spain","institution_ids":["https://openalex.org/I169108374"]},{"raw_affiliation_string":"IKERBASQUE, Basque\rFoundation for Science, 48013 Bilbao, Bizkaia, Spain","institution_ids":["https://openalex.org/I110594554"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016053493"],"corresponding_institution_ids":["https://openalex.org/I110594554","https://openalex.org/I169108374"],"apc_list":null,"apc_paid":null,"fwci":0.4434,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.64926103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"55","issue":"3","first_page":"636","last_page":"644"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9997000098228455,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9997000098228455,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9851999878883362,"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/T11482","display_name":"RNA modifications and cancer","score":0.9829999804496765,"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/cpg-site","display_name":"CpG site","score":0.7974044680595398},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.7570173740386963},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6345271468162537},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.6060142517089844},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5493568181991577},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5310713648796082},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.4619174003601074},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.4314527213573456},{"id":"https://openalex.org/keywords/cytosine","display_name":"Cytosine","score":0.4294436275959015},{"id":"https://openalex.org/keywords/hmg-box","display_name":"HMG-box","score":0.42771440744400024},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.3802416920661926},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.34847667813301086},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3248705565929413},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.32461583614349365},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32269126176834106},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29515671730041504},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.1813848316669464},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15924635529518127},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.12900829315185547}],"concepts":[{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.7974044680595398},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.7570173740386963},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6345271468162537},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.6060142517089844},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5493568181991577},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5310713648796082},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.4619174003601074},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4314527213573456},{"id":"https://openalex.org/C2776023528","wikidata":"https://www.wikidata.org/wiki/Q178425","display_name":"Cytosine","level":3,"score":0.4294436275959015},{"id":"https://openalex.org/C5179208","wikidata":"https://www.wikidata.org/wiki/Q3782057","display_name":"HMG-box","level":5,"score":0.42771440744400024},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.3802416920661926},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.34847667813301086},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3248705565929413},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.32461583614349365},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32269126176834106},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29515671730041504},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.1813848316669464},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15924635529518127},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.12900829315185547}],"mesh":[{"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":"D003596","descriptor_name":"Cytosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","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},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci500657d","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci500657d","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:25658035","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25658035","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4299747794","display_name":null,"funder_award_id":"247485","funder_id":"https://openalex.org/F4320332197","funder_display_name":"Directorate-General for Research and Innovation"},{"id":"https://openalex.org/G4817628247","display_name":null,"funder_award_id":"S-PE12UN014","funder_id":"https://openalex.org/F4320321705","funder_display_name":"Eusko Jaurlaritza"}],"funders":[{"id":"https://openalex.org/F4320321705","display_name":"Eusko Jaurlaritza","ror":"https://ror.org/00pz2fp31"},{"id":"https://openalex.org/F4320332197","display_name":"Directorate-General for Research and Innovation","ror":"https://ror.org/01ef4as46"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1567517848","https://openalex.org/W1820104986","https://openalex.org/W1966078827","https://openalex.org/W1970973025","https://openalex.org/W1975325714","https://openalex.org/W1975572122","https://openalex.org/W1976499671","https://openalex.org/W1983271674","https://openalex.org/W1983910978","https://openalex.org/W2003117591","https://openalex.org/W2003297982","https://openalex.org/W2015353463","https://openalex.org/W2019127737","https://openalex.org/W2021958912","https://openalex.org/W2023592911","https://openalex.org/W2024819383","https://openalex.org/W2027703149","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2038818360","https://openalex.org/W2045179023","https://openalex.org/W2053504434","https://openalex.org/W2057477511","https://openalex.org/W2058244371","https://openalex.org/W2064779454","https://openalex.org/W2067174909","https://openalex.org/W2078617491","https://openalex.org/W2080972330","https://openalex.org/W2084822564","https://openalex.org/W2090250026","https://openalex.org/W2103945336","https://openalex.org/W2114150529","https://openalex.org/W2115147255","https://openalex.org/W2118813986","https://openalex.org/W2121417064","https://openalex.org/W2122199548","https://openalex.org/W2123693419","https://openalex.org/W2128572087","https://openalex.org/W2136729627","https://openalex.org/W2137154596","https://openalex.org/W2138100316","https://openalex.org/W2139401049","https://openalex.org/W2144288821","https://openalex.org/W2149263899","https://openalex.org/W2153900602","https://openalex.org/W2163408209","https://openalex.org/W2165056748","https://openalex.org/W2167388443","https://openalex.org/W2170533290","https://openalex.org/W2172197806","https://openalex.org/W3017082821"],"related_works":["https://openalex.org/W2586219588","https://openalex.org/W2030922238","https://openalex.org/W1870851597","https://openalex.org/W2099901107","https://openalex.org/W1776902257","https://openalex.org/W2148072770","https://openalex.org/W1926921733","https://openalex.org/W1974642429","https://openalex.org/W2028056900","https://openalex.org/W2052894840"],"abstract_inverted_index":{"The":[0,44,153,287,347],"cell":[1],"is":[2,29,54,90,113,136,167,180,193,243,264,293,345,367],"able":[3,77,114],"to":[4,8,70,78,87,101,115,129,142,161,185,354],"regulate":[5],"which":[6,106,220,308],"genes":[7],"express":[9],"via":[10],"chemical":[11,49,362],"marks":[12,50],"on":[13,17,26,51,289,364],"the":[14,18,24,27,35,40,52,73,103,107,124,144,158,162,203,221,226,236,239,253,257,270,285,290,299,312,317,320,328,335,343,358,361,365,370],"DNA":[15,28,53,80,131,146,366],"and":[16,170,231,267,284,305,331],"histone":[19],"proteins.":[20],"In":[21,93,212],"all":[22],"vertebrates,":[23],"modification":[25],"methylation":[30],"at":[31,256],"position":[32],"5":[33],"of":[34,59,111,127,155,157,248,269,277,298,319,334,357],"two":[36,204],"cytosines":[37],"present":[38],"in":[39,164,219,307,311,350],"dinucleotide":[41],"sequence":[42],"CpG.":[43],"information":[45],"encoded":[46],"by":[47,56,105,138,196,210,225,245,295,369],"these":[48],"processed":[55],"a":[57,63,130,177,187,190,249,261,265,275,278],"family":[58],"protein":[60],"factors":[61],"containing":[62,81,132],"conserved":[64,227,301,336],"methyl-CpG":[65],"binding":[66,86,109,125,143,174,186,254],"domain":[67,110],"(MBD).":[68],"Essential":[69],"their":[71,200],"function,":[72],"MBD":[74],"proteins":[75],"are":[76,207,340],"bind":[79,116],"dimethylated":[82,118,133,178],"CpG":[83,119,134,151],"sites,":[84],"whereas":[85],"unmethylated":[88,150],"sites":[89],"not":[91],"observed.":[92],"this":[94,173,351],"paper,":[95],"we":[96],"perform":[97],"molecular":[98],"dynamics":[99],"simulations":[100],"investigate":[102],"mechanism":[104],"mCpG":[108],"MBD1":[112,128],"specifically":[117],"sites.":[120],"We":[121],"find":[122],"that":[123,192,339],"affinity":[126,175],"site":[135,255],"stronger":[137],"26.4":[139],"kJ/mol":[140],"relative":[141,184],"same":[145],"but":[147],"with":[148,327],"an":[149,246],"site.":[152],"contribution":[154],"each":[156],"methyl":[159,205,321],"groups":[160,206],"change":[163],"free":[165],"energy":[166],"very":[168],"similar":[169],"additive.":[171],"Therefore,":[172],"(to":[176],"DNA)":[179],"halved":[181],"when":[182,342],"considered":[183],"hemimethylated":[188],"DNA,":[189],"result":[191],"also":[194],"supported":[195],"experimental":[197],"observations.":[198],"Despite":[199],"equal":[201],"contributions,":[202],"recognized":[208,294,368],"differently":[209],"MBD1.":[211],"one":[213],"case,":[214],"demethylation":[215],"induces":[216],"conformational":[217,296],"changes":[218,297],"hydrophobic":[222,302],"patch":[223],"formed":[224],"residues":[228],"Val20,":[229],"Arg22,":[230],"Tyr34":[232,283],"moves":[233],"away":[234],"from":[235],"(methyl)cytosine,":[237],"weakening":[238],"DNA-protein":[240],"interactions.":[241],"This":[242],"accompanied":[244],"intrusion":[247],"bulk":[250],"water":[251],"into":[252],"protein-DNA":[258,271],"interface.":[259],"As":[260],"consequence,":[262],"there":[263],"reduction":[266],"rearrangements":[268],"hydrogen":[272,280,325],"bonds":[273,326],"including":[274],"loss":[276],"crucial":[279],"bond":[281],"between":[282],"(methyl)cytosine.":[286],"methylcytosine":[288],"opposite":[291],"strand":[292],"surrounding":[300],"residues,":[303],"Arg44":[304,309],"Ser45,":[306],"participate":[310],"5mC-Arg-G":[313],"triad.":[314],"More":[315],"specifically,":[316],"hydrogens":[318],"group":[322,330],"form":[323],"weak":[324],"guanidino":[329],"backbone":[332],"carbonyl":[333],"Arg44,":[337],"interactions":[338],"absent":[341],"cytosine":[344],"unmethylated.":[346],"results":[348],"presented":[349],"paper":[352],"contribute":[353],"our":[355],"knowledge":[356],"different":[359],"ways":[360],"mark":[363],"epigenetic":[371],"machinery.":[372]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
