{"id":"https://openalex.org/W4389993993","doi":"https://doi.org/10.1021/acs.jcim.3c01618","title":"Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release","display_name":"Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release","publication_year":2023,"publication_date":"2023-12-20","ids":{"openalex":"https://openalex.org/W4389993993","doi":"https://doi.org/10.1021/acs.jcim.3c01618","pmid":"https://pubmed.ncbi.nlm.nih.gov/38117131"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01618","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01618","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01618","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01618","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022993160","display_name":"Kwangho Nam","orcid":"https://orcid.org/0000-0003-0723-7839"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kwangho Nam","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States"],"raw_orcid":"https://orcid.org/0000-0003-0723-7839","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056831080","display_name":"Abdul Raafik Arattu Thodika","orcid":"https://orcid.org/0009-0001-4973-5265"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abdul Raafik Arattu Thodika","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States"],"raw_orcid":"https://orcid.org/0009-0001-4973-5265","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058031847","display_name":"Christin Grundstr\u00f6m","orcid":"https://orcid.org/0000-0002-6600-7972"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Christin Grundstr\u00f6m","raw_affiliation_strings":["Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden","institution_ids":["https://openalex.org/I90267481"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041455002","display_name":"Uwe H. Sauer","orcid":"https://orcid.org/0000-0002-3420-439X"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Uwe H. Sauer","raw_affiliation_strings":["Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden","institution_ids":["https://openalex.org/I90267481"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073296084","display_name":"Magnus Wolf\u2010Watz","orcid":"https://orcid.org/0000-0002-9098-7974"},"institutions":[{"id":"https://openalex.org/I90267481","display_name":"Ume\u00e5 University","ror":"https://ror.org/05kb8h459","country_code":"SE","type":"education","lineage":["https://openalex.org/I90267481"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Magnus Wolf-Watz","raw_affiliation_strings":["Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-9098-7974","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Ume\u00e5 University, Ume\u00e5 90187, SE, Sweden","institution_ids":["https://openalex.org/I90267481"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022993160"],"corresponding_institution_ids":["https://openalex.org/I189196454"],"apc_list":null,"apc_paid":null,"fwci":1.3623,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.8081259,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"64","issue":"1","first_page":"150","last_page":"163"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12827","display_name":"Biochemical and Molecular Research","score":0.9990000128746033,"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/adenylate-kinase","display_name":"Adenylate kinase","score":0.8706874847412109},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6629929542541504},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6045806407928467},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.546565592288971},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5078533291816711},{"id":"https://openalex.org/keywords/conformational-change","display_name":"Conformational change","score":0.507550835609436},{"id":"https://openalex.org/keywords/adenosine-monophosphate","display_name":"Adenosine monophosphate","score":0.505104124546051},{"id":"https://openalex.org/keywords/adenosine-triphosphate","display_name":"Adenosine triphosphate","score":0.46463659405708313},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4608864486217499},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4068514108657837},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.37506046891212463},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23669365048408508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14492332935333252},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.12849166989326477}],"concepts":[{"id":"https://openalex.org/C180526460","wikidata":"https://www.wikidata.org/wiki/Q356240","display_name":"Adenylate kinase","level":3,"score":0.8706874847412109},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6629929542541504},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6045806407928467},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.546565592288971},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5078533291816711},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.507550835609436},{"id":"https://openalex.org/C2779876172","wikidata":"https://www.wikidata.org/wiki/Q318369","display_name":"Adenosine monophosphate","level":3,"score":0.505104124546051},{"id":"https://openalex.org/C2779564974","wikidata":"https://www.wikidata.org/wiki/Q80863","display_name":"Adenosine triphosphate","level":2,"score":0.46463659405708313},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4608864486217499},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4068514108657837},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.37506046891212463},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23669365048408508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14492332935333252},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.12849166989326477},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000249","descriptor_name":"Adenosine Monophosphate","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000263","descriptor_name":"Adenylate Kinase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001051","descriptor_name":"Apoenzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.3c01618","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01618","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01618","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38117131","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38117131","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10778088","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10778088","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10778088/pdf/ci3c01618.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.3c01618","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01618","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01618","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8899999856948853,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G447302280","display_name":"Decoding Fundamental Principles in Enzymatic Catalysis","funder_award_id":"2021-04513","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G904804706","display_name":null,"funder_award_id":"R01GM132481","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389993993.pdf","grobid_xml":"https://content.openalex.org/works/W4389993993.grobid-xml"},"referenced_works_count":97,"referenced_works":["https://openalex.org/W1506211024","https://openalex.org/W1967737979","https://openalex.org/W1968127704","https://openalex.org/W1974030600","https://openalex.org/W1976051941","https://openalex.org/W1976499671","https://openalex.org/W1977670956","https://openalex.org/W1978189250","https://openalex.org/W1978193721","https://openalex.org/W1978261861","https://openalex.org/W1980397617","https://openalex.org/W1980571928","https://openalex.org/W1981190811","https://openalex.org/W1985767604","https://openalex.org/W1989161865","https://openalex.org/W1998093640","https://openalex.org/W2005392755","https://openalex.org/W2010867867","https://openalex.org/W2013808431","https://openalex.org/W2014425795","https://openalex.org/W2016466447","https://openalex.org/W2017509211","https://openalex.org/W2017998155","https://openalex.org/W2025153485","https://openalex.org/W2027408247","https://openalex.org/W2027578254","https://openalex.org/W2028968631","https://openalex.org/W2034696427","https://openalex.org/W2035687084","https://openalex.org/W2041000185","https://openalex.org/W2042964041","https://openalex.org/W2043429268","https://openalex.org/W2048822589","https://openalex.org/W2050333027","https://openalex.org/W2055497972","https://openalex.org/W2055939796","https://openalex.org/W2067076385","https://openalex.org/W2067174909","https://openalex.org/W2069643487","https://openalex.org/W2071231667","https://openalex.org/W2075168705","https://openalex.org/W2075609773","https://openalex.org/W2076710572","https://openalex.org/W2079370986","https://openalex.org/W2081555206","https://openalex.org/W2082012059","https://openalex.org/W2097294533","https://openalex.org/W2097412382","https://openalex.org/W2098787719","https://openalex.org/W2106140689","https://openalex.org/W2108921801","https://openalex.org/W2110808180","https://openalex.org/W2115152262","https://openalex.org/W2122502632","https://openalex.org/W2122994276","https://openalex.org/W2124026197","https://openalex.org/W2127362915","https://openalex.org/W2130616267","https://openalex.org/W2131501854","https://openalex.org/W2132262459","https://openalex.org/W2136906292","https://openalex.org/W2137270096","https://openalex.org/W2140147242","https://openalex.org/W2143171629","https://openalex.org/W2146890570","https://openalex.org/W2154197653","https://openalex.org/W2160294964","https://openalex.org/W2252883583","https://openalex.org/W2311509164","https://openalex.org/W2326269154","https://openalex.org/W2463220226","https://openalex.org/W2473350337","https://openalex.org/W2511991795","https://openalex.org/W2520728390","https://openalex.org/W2522558972","https://openalex.org/W2619720316","https://openalex.org/W2786992197","https://openalex.org/W2791252992","https://openalex.org/W2793141467","https://openalex.org/W2883581091","https://openalex.org/W2949223833","https://openalex.org/W2963680108","https://openalex.org/W3080779913","https://openalex.org/W3083132420","https://openalex.org/W3158381884","https://openalex.org/W3178812772","https://openalex.org/W3213993419","https://openalex.org/W4210309881","https://openalex.org/W4210521569","https://openalex.org/W4225157634","https://openalex.org/W4248872320","https://openalex.org/W4304688442","https://openalex.org/W4309647628","https://openalex.org/W4321436177","https://openalex.org/W4322582051","https://openalex.org/W4366816468","https://openalex.org/W4382048734"],"related_works":["https://openalex.org/W2864987764","https://openalex.org/W2803517866","https://openalex.org/W1520098196","https://openalex.org/W1860746711","https://openalex.org/W3001593310","https://openalex.org/W1963693682","https://openalex.org/W1696727162","https://openalex.org/W4247873571","https://openalex.org/W1802649109","https://openalex.org/W2508599875"],"abstract_inverted_index":{"This":[0,164],"study":[1],"explores":[2],"ligand-driven":[3,179],"conformational":[4,16,162,180],"changes":[5,181],"in":[6,166,198,258],"adenylate":[7],"kinase":[8],"(AK),":[9],"which":[10,57],"is":[11,99,110,219],"known":[12],"for":[13,35,133,175],"its":[14,122,205],"open-to-close":[15],"transitions":[17],"upon":[18],"ligand":[19,40,54,71,123,138],"binding":[20,139],"and":[21,39,42,73,121,233,251,277],"release.":[22,114],"By":[23],"utilizing":[24],"string":[25],"free":[26,32,131,235],"energy":[27,33,132,236],"simulations,":[28],"we":[29,185],"determine":[30,186],"the":[31,48,60,63,77,96,107,117,129,137,167,176,199,210,215,222,228,234,247,269,284,289],"profiles":[34,46],"both":[36],"enzyme":[37,134],"opening":[38,61,75,120,241,250],"release":[41,55,72,124],"compare":[43],"them":[44],"with":[45,59,173,238,243,246,260],"from":[47],"apoenzyme.":[49],"Results":[50],"reveal":[51],"a":[52,265],"three-step":[53],"process,":[56],"initiates":[58],"of":[62,76,182,190,201,212,217,268,288],"adenosine":[64,78],"triphosphate-binding":[65],"subdomain":[66,80],"(ATP":[67],"lid),":[68],"followed":[69],"by":[70,102,112,154],"concomitant":[74],"monophosphate-binding":[79],"(AMP":[81],"lid).":[82],"The":[83],"ligands":[84],"then":[85],"transition":[86],"to":[87,128,283],"nonspecific":[88],"positions":[89],"before":[90],"complete":[91],"dissociation.":[92],"In":[93,115,209],"these":[94],"processes,":[95],"first":[97,226],"step":[98,109],"energetically":[100],"driven":[101,111],"ATP":[103,113,158,229,239],"lid":[104,119,146,159,224,230,240],"opening,":[105,214],"whereas":[106,157],"second":[108],"contrast,":[116],"AMP":[118,145,155,223],"make":[125],"minor":[126],"contributions":[127],"total":[130],"opening.":[135],"Regarding":[136],"mechanism,":[140],"our":[141,261],"results":[142],"suggest":[143],"that":[144,194,280],"closure":[147,160,168],"occurs":[148],"via":[149],"an":[150,171,187,191],"induced-fit":[151],"mechanism":[152],"triggered":[153],"binding,":[156],"follows":[161],"selection.":[163],"difference":[165],"mechanisms":[169],"provides":[170,264],"explanation":[172],"implications":[174],"debate":[177],"on":[178],"AK.":[183],"Additionally,":[184],"X-ray":[188],"structure":[189],"AK":[192,249],"variant":[193],"exhibits":[195],"significant":[196],"rearrangements":[197],"stacking":[200],"catalytic":[202,207,278,286],"arginines,":[203],"explaining":[204],"reduced":[206],"activity.":[208],"context":[211],"apoenzyme":[213],"sequence":[216],"events":[218],"different.":[220],"Here,":[221],"opens":[225],"while":[227],"remains":[231],"closed,":[232],"associated":[237],"varies":[242],"orientation,":[244],"aligning":[245],"reported":[248],"closing":[252],"rate":[253],"heterogeneity.":[254],"Finally,":[255],"this":[256],"study,":[257],"conjunction":[259],"previous":[262],"research,":[263],"comprehensive":[266],"view":[267],"intricate":[270],"interplay":[271],"between":[272],"various":[273],"structural":[274],"elements,":[275],"ligands,":[276],"residues":[279],"collectively":[281],"contribute":[282],"robust":[285],"power":[287],"enzyme.":[290]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
