{"id":"https://openalex.org/W2923375550","doi":"https://doi.org/10.1021/acs.jcim.9b00022","title":"A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart","display_name":"A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart","publication_year":2019,"publication_date":"2019-03-21","ids":{"openalex":"https://openalex.org/W2923375550","doi":"https://doi.org/10.1021/acs.jcim.9b00022","mag":"2923375550","pmid":"https://pubmed.ncbi.nlm.nih.gov/30897332"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00022","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00022","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/A5040892881","display_name":"Erica Modeste","orcid":"https://orcid.org/0000-0002-2072-129X"},"institutions":[{"id":"https://openalex.org/I158012942","display_name":"University of Richmond","ror":"https://ror.org/03y71xh61","country_code":"US","type":"education","lineage":["https://openalex.org/I158012942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erica Modeste","raw_affiliation_strings":["Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States","institution_ids":["https://openalex.org/I158012942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087539048","display_name":"Lily Mawby","orcid":null},"institutions":[{"id":"https://openalex.org/I158012942","display_name":"University of Richmond","ror":"https://ror.org/03y71xh61","country_code":"US","type":"education","lineage":["https://openalex.org/I158012942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lily Mawby","raw_affiliation_strings":["Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States","institution_ids":["https://openalex.org/I158012942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022921172","display_name":"Bill R. Miller","orcid":"https://orcid.org/0000-0003-4868-7692"},"institutions":[{"id":"https://openalex.org/I199639920","display_name":"Truman State University","ror":"https://ror.org/0396bvs97","country_code":"US","type":"education","lineage":["https://openalex.org/I199639920"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bill Miller","raw_affiliation_strings":["Department of Chemistry, Truman State University, Kirksville, Missouri 63501, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Truman State University, Kirksville, Missouri 63501, United States","institution_ids":["https://openalex.org/I199639920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103611998","display_name":"Eugene Wu","orcid":"https://orcid.org/0000-0002-5189-7036"},"institutions":[{"id":"https://openalex.org/I158012942","display_name":"University of Richmond","ror":"https://ror.org/03y71xh61","country_code":"US","type":"education","lineage":["https://openalex.org/I158012942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eugene Wu","raw_affiliation_strings":["Department of Biology, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States","institution_ids":["https://openalex.org/I158012942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056769433","display_name":"Carol A. Parish","orcid":"https://orcid.org/0000-0003-2878-3070"},"institutions":[{"id":"https://openalex.org/I158012942","display_name":"University of Richmond","ror":"https://ror.org/03y71xh61","country_code":"US","type":"education","lineage":["https://openalex.org/I158012942"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Carol A. Parish","raw_affiliation_strings":["Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States"],"raw_orcid":"https://orcid.org/0000-0003-2878-3070","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, Virginia 23713, United States","institution_ids":["https://openalex.org/I158012942"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056769433"],"corresponding_institution_ids":["https://openalex.org/I158012942"],"apc_list":null,"apc_paid":null,"fwci":0.4143,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.60204614,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"59","issue":"5","first_page":"2423","last_page":"2431"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"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":0.9965999722480774,"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":0.9965999722480774,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/thermostability","display_name":"Thermostability","score":0.94550621509552},{"id":"https://openalex.org/keywords/polymerase","display_name":"Polymerase","score":0.6126288175582886},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5295606255531311},{"id":"https://openalex.org/keywords/dna-polymerase","display_name":"DNA polymerase","score":0.500213623046875},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4488454759120941},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.43238988518714905},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.3685925602912903},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3355211615562439},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24577787518501282},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1625918447971344},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.1619018316268921}],"concepts":[{"id":"https://openalex.org/C2781216036","wikidata":"https://www.wikidata.org/wiki/Q902494","display_name":"Thermostability","level":3,"score":0.94550621509552},{"id":"https://openalex.org/C82381507","wikidata":"https://www.wikidata.org/wiki/Q416878","display_name":"Polymerase","level":3,"score":0.6126288175582886},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5295606255531311},{"id":"https://openalex.org/C2756471","wikidata":"https://www.wikidata.org/wiki/Q206286","display_name":"DNA polymerase","level":3,"score":0.500213623046875},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4488454759120941},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.43238988518714905},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.3685925602912903},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3355211615562439},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24577787518501282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1625918447971344},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.1619018316268921}],"mesh":[{"descriptor_ui":"D003080","descriptor_name":"Cold Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003080","descriptor_name":"Cold Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003080","descriptor_name":"Cold Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004795","descriptor_name":"Enzyme Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004795","descriptor_name":"Enzyme Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004795","descriptor_name":"Enzyme Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":true},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013824","descriptor_name":"Thermus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D013824","descriptor_name":"Thermus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D013824","descriptor_name":"Thermus","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019914","descriptor_name":"Taq Polymerase","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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00022","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00022","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:30897332","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30897332","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/G3804823648","display_name":null,"funder_award_id":"CHE-1800014","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G7731961781","display_name":null,"funder_award_id":"CHE-1213271","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320309424","display_name":"Thomas F. and Kate Miller Jeffress Memorial Trust","ror":"https://ror.org/006tvg625"},{"id":"https://openalex.org/F4320332454","display_name":"American Chemical Society Petroleum Research Fund","ror":"https://ror.org/059dqb057"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1537950146","https://openalex.org/W1986534666","https://openalex.org/W2001278481","https://openalex.org/W2009447971","https://openalex.org/W2013754612","https://openalex.org/W2029667189","https://openalex.org/W2035650458","https://openalex.org/W2076949721","https://openalex.org/W2084309802","https://openalex.org/W2091984642","https://openalex.org/W2099386490","https://openalex.org/W2106140689","https://openalex.org/W2126552603","https://openalex.org/W2149410625","https://openalex.org/W2332712348","https://openalex.org/W4248096216"],"related_works":["https://openalex.org/W2398277866","https://openalex.org/W2074011169","https://openalex.org/W2077167296","https://openalex.org/W1936051282","https://openalex.org/W2031882707","https://openalex.org/W2076445634","https://openalex.org/W2025103069","https://openalex.org/W1972765689","https://openalex.org/W2624814344","https://openalex.org/W2418031828"],"abstract_inverted_index":{"DNA":[0,8,42,70,95,115,142,232],"polymerase":[1,13,43,71,96,116,143],"I":[2],"from":[3],"Thermus":[4],"aquaticus":[5],"(":[6],"Taq":[7,41,69,94,114,141,231],"polymerase)":[9],"is":[10],"useful":[11],"for":[12,229],"chain":[14],"reactions":[15],"because":[16],"of":[17,30,34,86,156,197,207,218],"its":[18,22],"exceptional":[19],"thermostability;":[20],"however,":[21],"activity":[23,178],"at":[24,44,72,100,107,123,148,159,183,222],"low":[25,45,126,151,160],"temperatures":[26],"can":[27],"cause":[28],"amplification":[29,50],"unintended":[31],"products.":[32],"Mutation":[33],"isoleucine":[35],"707":[36],"to":[37,52,77,176,180,212],"leucine":[38],"(I707L)":[39],"slows":[40],"temperatures,":[46],"which":[47],"decreases":[48],"unwanted":[49],"due":[51],"mispriming.":[53],"In":[54],"this":[55,173],"work,":[56],"unrestrained":[57],"molecular":[58],"dynamics":[59,122],"(MD)":[60],"simulations":[61],"were":[62],"performed":[63],"on":[64,137],"I707L":[65,93,139],"and":[66,74,103,125,150,172,201],"wild-type":[67],"(WT)":[68],"341":[73,223],"298":[75,184],"K":[76],"determine":[78],"how":[79],"the":[80,83,87,108,112,138,157,164,169,181,191,198,208,219],"mutation":[81,192],"affects":[82],"dynamic":[84,146],"nature":[85,206],"protein.":[88],"The":[89,153],"results":[90,129,136,193],"suggest":[91],"that":[92,144,163,190],"remains":[97,166],"relatively":[98],"immobile":[99],"room":[101],"temperature":[102,161],"becomes":[104],"more":[105],"flexible":[106,215],"higher":[109],"temperature,":[110],"while":[111],"WT":[113,182,230],"demonstrates":[117],"less":[118],"substantial":[119],"differences":[120,147],"in":[121,131,168,194],"high":[124,149],"temperatures.":[127,152],"These":[128],"are":[130],"agreement":[132],"with":[133],"previous":[134],"experimental":[135],"mutant":[140,158,165,209],"show":[145],"decreased":[154],"mobility":[155],"suggests":[162],"longer":[167],"blocked":[170],"conformation,":[171],"may":[174],"lead":[175],"reduced":[177],"relative":[179],"K.":[185],"Principal":[186],"component":[187],"analysis":[188],"revealed":[189],"decoupled":[195,205],"movements":[196],"Q":[199,220],"helix":[200,221],"fingers":[202],"domain.":[203],"This":[204],"gives":[210],"way":[211],"an":[213],"increasingly":[214],"N-terminal":[216],"end":[217],"K,":[224],"a":[225],"characteristic":[226],"not":[227],"seen":[228],"polymerase.":[233]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}