{"id":"https://openalex.org/W7204276167","doi":"https://doi.org/10.1080/07391102.2026.2723209","title":"Transition-metal coordination modulates predicted DNA groove recognition and nucleobase contacts in oligohistidine complexes","display_name":"Transition-metal coordination modulates predicted DNA groove recognition and nucleobase contacts in oligohistidine complexes","publication_year":2026,"publication_date":"2026-08-26","ids":{"openalex":"https://openalex.org/W7204276167","doi":"https://doi.org/10.1080/07391102.2026.2723209","pmid":"https://pubmed.ncbi.nlm.nih.gov/42647108"},"language":"en","primary_location":{"id":"doi:10.1080/07391102.2026.2723209","doi":"https://doi.org/10.1080/07391102.2026.2723209","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.2026.2723209","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomolecular Structure and Dynamics","raw_type":"journal-article"},"volume":null,"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/A5028972055","display_name":"Soykan A\u011far","orcid":"https://orcid.org/0000-0002-9870-6882","observed_orcids":["https://orcid.org/0000-0002-9870-6882"]},"institutions":[{"id":"https://openalex.org/I4387155008","display_name":"Kocaeli Sa\u011fl\u0131k ve Teknoloji \u00dcniversitesi","ror":"https://ror.org/016dcc221","country_code":null,"type":"education","lineage":["https://openalex.org/I4387155008"]}],"countries":[],"is_corresponding":true,"raw_author_name":"Soykan Agar","raw_affiliation_strings":["Faculty of Dentistry, Department of Biochemistry, Kocaeli Health and Technology University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Dentistry, Department of Biochemistry, Kocaeli Health and Technology University","institution_ids":["https://openalex.org/I4387155008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037592402","display_name":"Alparslan Numan Yildiz","orcid":"https://orcid.org/0009-0002-4824-1498","observed_orcids":["https://orcid.org/0009-0002-4824-1498"]},"institutions":[{"id":"https://openalex.org/I42317466","display_name":"Alt\u0131nba\u015f University","ror":"https://ror.org/0145w8333","country_code":"TR","type":"education","lineage":["https://openalex.org/I42317466"]},{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Alparslan Numan Yildiz","raw_affiliation_strings":["Department of Chemistry, Faculty of Arts and Sciences, Istanbul Technical University","Department of Software Engineering, Faculty of Engineering and Architecture, Alt\u0131nba\u015f University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Arts and Sciences, Istanbul Technical University","institution_ids":["https://openalex.org/I48912391"]},{"raw_affiliation_string":"Department of Software Engineering, Faculty of Engineering and Architecture, Alt\u0131nba\u015f University","institution_ids":["https://openalex.org/I42317466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066132054","display_name":"Mine Yurtsever","orcid":"https://orcid.org/0000-0001-6504-7182","observed_orcids":["https://orcid.org/0000-0001-6504-7182"]},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Mine Yurtsever","raw_affiliation_strings":["Department of Chemistry, Faculty of Arts and Sciences, Istanbul Technical University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Arts and Sciences, Istanbul Technical University","institution_ids":["https://openalex.org/I48912391"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028972055","https://openalex.org/A5066132054"],"corresponding_institution_ids":["https://openalex.org/I4387155008","https://openalex.org/I48912391"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.61375828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4595000147819519,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.4595000147819519,"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/T10163","display_name":"Metal complexes synthesis and properties","score":0.3091000020503998,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.06859999895095825,"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/histidine-rich-peptides","display_name":"histidine-rich peptides","score":0.8550000190734863},{"id":"https://openalex.org/keywords/metal-coordination","display_name":"metal coordination","score":0.621999979019165},{"id":"https://openalex.org/keywords/zinc","display_name":"zinc","score":0.49399998784065247},{"id":"https://openalex.org/keywords/nickel","display_name":"nickel","score":1.0},{"id":"https://openalex.org/keywords/copper","display_name":"copper","score":1.0},{"id":"https://openalex.org/keywords/major-groove-binding","display_name":"major groove binding","score":0.7549999952316284},{"id":"https://openalex.org/keywords/minor-groove-binding","display_name":"minor groove binding","score":0.9959999918937683},{"id":"https://openalex.org/keywords/adenine","display_name":"adenine","score":0.5720000267028809},{"id":"https://openalex.org/keywords/guanine","display_name":"guanine","score":0.9990000128746033},{"id":"https://openalex.org/keywords/affinity-purification","display_name":"affinity purification","score":0.4569999873638153},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.5649999976158142},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"molecular dynamics","score":0.9319999814033508}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6460000276565552},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.6046000123023987},{"id":"https://openalex.org/C61234307","wikidata":"https://www.wikidata.org/wiki/Q422960","display_name":"Nucleobase","level":3,"score":0.6025999784469604},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4334999918937683},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.367900013923645},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3637000024318695},{"id":"https://openalex.org/C2779472054","wikidata":"https://www.wikidata.org/wiki/Q2377973","display_name":"Groove (engineering)","level":2,"score":0.33239999413490295},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.30230000615119934},{"id":"https://openalex.org/C191961535","wikidata":"https://www.wikidata.org/wiki/Q2360205","display_name":"A-DNA","level":3,"score":0.28439998626708984},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.2653999924659729},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.26170000433921814},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.25110000371932983}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1080/07391102.2026.2723209","doi":"https://doi.org/10.1080/07391102.2026.2723209","is_oa":false,"landing_page_url":"https://doi.org/10.1080/07391102.2026.2723209","pdf_url":null,"source":{"id":"https://openalex.org/S178711970","display_name":"Journal of Biomolecular Structure and Dynamics","issn_l":"0739-1102","issn":["0739-1102","1538-0254"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1"],"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547","https://openalex.org/P4310320449"],"host_organization_lineage_names":["Taylor & Francis","Informa"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomolecular Structure and Dynamics","raw_type":"journal-article"},{"id":"pmid:42647108","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42647108","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,"listed_in":[],"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 biomolecular structure & dynamics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1972758026","https://openalex.org/W2000339616","https://openalex.org/W2014168875","https://openalex.org/W2031873338","https://openalex.org/W2035843576","https://openalex.org/W2036323471","https://openalex.org/W2065992606","https://openalex.org/W2067110039","https://openalex.org/W2097771231","https://openalex.org/W2100095805","https://openalex.org/W2102067176","https://openalex.org/W2143981217","https://openalex.org/W2313948371","https://openalex.org/W2898962162","https://openalex.org/W3168436232","https://openalex.org/W3210430327","https://openalex.org/W3216980468","https://openalex.org/W4399739181","https://openalex.org/W4408080010","https://openalex.org/W7117990669"],"related_works":[],"abstract_inverted_index":{"Histidine-rich":[0],"peptides":[1],"are":[2,176],"widely":[3],"used":[4,64,86],"in":[5,33],"affinity-based":[6],"purification":[7],"because":[8],"imidazole":[9],"donors":[10],"can":[11],"coordinate":[12],"transition-metal":[13],"ions.":[14],"To":[15],"examine":[16],"how":[17],"fixed":[18],"metal-coordination":[19],"models":[20,130,160,182],"may":[21,208],"alter":[22],"the":[23,42,51,60,76,105,149,167,171,179,184],"predicted":[24,89],"DNA-contacting":[25],"behavior":[26],"of":[27,124,142,213],"a":[28,31,73,112,120,204],"histidine":[29],"hexamer,":[30],"fully":[32],"silico":[34],"comparison":[35,206],"was":[36],"performed":[37],"using":[38],"metal-free":[39,109,168],"His6":[40,110],"and":[41,48,67,82,100,119,145,152,158,183],"tri-metal":[43,128],"model":[44],"complexes":[45],"[Zn3(His6)]6+,":[46],"[Ni3(His6)]6+,":[47],"[Cu3(His6)]6+":[49],"against":[50],"canonical":[52],"B-DNA":[53],"dodecamer":[54],"1BNA":[55,107,185],"[d(CGCGAATTCGCG)].":[56],"The":[57,127,156,201],"formulas":[58],"denote":[59],"neutral-terminal/neutral-imidazole":[61],"computational":[62,181],"representation":[63],"for":[65,148],"docking":[66,81,98,122,140],"molecular":[68],"dynamics":[69],"(MD),":[70],"rather":[71],"than":[72,166],"claim":[74],"concerning":[75],"dominant":[77,113,132],"solution-phase":[78,198],"species.":[79],"Molecular":[80],"MD":[83],"simulations":[84],"were":[85],"to":[87,178],"compare":[88],"groove":[90],"localization,":[91],"recurrent":[92],"nucleobase-associated":[93],"contacts,":[94,137],"hydrogen-bond":[95],"patterns,":[96],"relative":[97,139],"scores,":[99],"trajectory-based":[101],"structural":[102],"persistence.":[103],"Within":[104],"examined":[106],"model,":[108],"produced":[111,131],"major-groove":[114],"pose":[115],"with":[116,135,138],"adenine-associated":[117],"contacts":[118],"Vina":[121],"score":[123],"\u22128.9":[125],"kcal/mol.":[126],"coordination":[129],"minor-groove":[133],"poses":[134],"guanine-associated":[136],"scores":[141],"\u22129.5,":[143],"\u221213.5,":[144],"\u221210.8":[146],"kcal/mol":[147],"Zn(II),":[150],"Ni(II),":[151],"Cu(II)":[153],"models,":[154],"respectively.":[155],"Ni(II)-":[157],"Cu(II)-containing":[159],"also":[161],"displayed":[162],"lower":[163],"RMSD":[164],"levels":[165],"complex":[169],"over":[170],"sampled":[172],"trajectories.":[173],"These":[174],"observations":[175],"restricted":[177],"defined":[180],"sequence;":[186],"they":[187],"do":[188],"not":[189],"establish":[190],"experimental":[191,211],"binding":[192],"affinities,":[193],"universal":[194],"nucleobase":[195],"selectivity,":[196],"or":[197],"metal":[199],"speciation.":[200],"work":[202],"provides":[203],"hypothesis-generating":[205],"that":[207],"guide":[209],"future":[210],"investigation":[212],"metal-coordinated":[214],"oligohistidine-DNA":[215],"interactions.":[216]},"counts_by_year":[],"updated_date":"2026-09-23T05:00:35.095934","created_date":"2026-08-27T00:00:00"}
