{"id":"https://openalex.org/W2500320400","doi":"https://doi.org/10.1021/acs.jcim.6b00153","title":"Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations","display_name":"Understanding the Catalytic Mechanism of Xanthosine Methyltransferase in Caffeine Biosynthesis from QM/MM Molecular Dynamics and Free Energy Simulations","publication_year":2016,"publication_date":"2016-08-02","ids":{"openalex":"https://openalex.org/W2500320400","doi":"https://doi.org/10.1021/acs.jcim.6b00153","mag":"2500320400","pmid":"https://pubmed.ncbi.nlm.nih.gov/27482605"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00153","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00153","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":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/1355886","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046561934","display_name":"Ping Qian","orcid":"https://orcid.org/0000-0002-1724-7339"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I74485261","display_name":"Shandong Agricultural University","ror":"https://ror.org/02ke8fw32","country_code":"CN","type":"education","lineage":["https://openalex.org/I74485261"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Ping Qian","raw_affiliation_strings":["Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China","Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China","institution_ids":["https://openalex.org/I74485261"]},{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042897875","display_name":"Hao\u2010Bo Guo","orcid":"https://orcid.org/0000-0003-1321-1758"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao-Bo Guo","raw_affiliation_strings":["Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hao-Bo Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hao-Bo Guo","raw_affiliation_strings":["Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040130065","display_name":"Yufei Yue","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I74485261","display_name":"Shandong Agricultural University","ror":"https://ror.org/02ke8fw32","country_code":"CN","type":"education","lineage":["https://openalex.org/I74485261"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yufei Yue","raw_affiliation_strings":["Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China","institution_ids":["https://openalex.org/I74485261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001281830","display_name":"Xiaohan Yang","orcid":"https://orcid.org/0000-0001-5207-4210"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I74485261","display_name":"Shandong Agricultural University","ror":"https://ror.org/02ke8fw32","country_code":"CN","type":"education","lineage":["https://openalex.org/I74485261"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Liang Wang","raw_affiliation_strings":["Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China","Biosciences\rDivision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chemistry\rand Material Science Faculty, Shandong Agricultural University, Tai\u2019an 271018, Shandong, People\u2019s Republic of China","institution_ids":["https://openalex.org/I74485261"]},{"raw_affiliation_string":"Biosciences\rDivision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087731954","display_name":"Hong Guo","orcid":"https://orcid.org/0000-0002-5997-5086"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohan Yang","raw_affiliation_strings":["Biosciences\rDivision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences\rDivision, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087731954","display_name":"Hong Guo","orcid":"https://orcid.org/0000-0002-5997-5086"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hong Guo","raw_affiliation_strings":["Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087731954","display_name":"Hong Guo","orcid":"https://orcid.org/0000-0002-5997-5086"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hong Guo","raw_affiliation_strings":["Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States","institution_ids":["https://openalex.org/I75027704"]},{"raw_affiliation_string":"UT/ORNL Center for Molecular\rBiophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046561934","https://openalex.org/A5087731954"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I74485261","https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":1.6084,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84034993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"56","issue":"9","first_page":"1755","last_page":"1761"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12964","display_name":"Diet, Metabolism, and Disease","score":0.9836999773979187,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12964","display_name":"Diet, Metabolism, and Disease","score":0.9836999773979187,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"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/T11924","display_name":"Polyamine Metabolism and Applications","score":0.9595999717712402,"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/T10414","display_name":"Cannabis and Cannabinoid Research","score":0.9531000256538391,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deprotonation","display_name":"Deprotonation","score":0.7072439789772034},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.7020571231842041},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6871969699859619},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6822870373725891},{"id":"https://openalex.org/keywords/biosynthesis","display_name":"Biosynthesis","score":0.5981886386871338},{"id":"https://openalex.org/keywords/methyltransferase","display_name":"Methyltransferase","score":0.5926921367645264},{"id":"https://openalex.org/keywords/catalytic-cycle","display_name":"Catalytic cycle","score":0.5422341227531433},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.5176613926887512},{"id":"https://openalex.org/keywords/substrate","display_name":"Substrate (aquarium)","score":0.477545827627182},{"id":"https://openalex.org/keywords/qm/mm","display_name":"QM/MM","score":0.4728848338127136},{"id":"https://openalex.org/keywords/caffeine","display_name":"Caffeine","score":0.4468890428543091},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4116235375404358},{"id":"https://openalex.org/keywords/methyl-group","display_name":"Methyl group","score":0.4102437198162079},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.38535094261169434},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.37334465980529785},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3159672021865845},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.14646583795547485},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10163173079490662}],"concepts":[{"id":"https://openalex.org/C118629725","wikidata":"https://www.wikidata.org/wiki/Q2686738","display_name":"Deprotonation","level":3,"score":0.7072439789772034},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.7020571231842041},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6871969699859619},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6822870373725891},{"id":"https://openalex.org/C553450214","wikidata":"https://www.wikidata.org/wiki/Q851162","display_name":"Biosynthesis","level":3,"score":0.5981886386871338},{"id":"https://openalex.org/C91965660","wikidata":"https://www.wikidata.org/wiki/Q415875","display_name":"Methyltransferase","level":4,"score":0.5926921367645264},{"id":"https://openalex.org/C63338738","wikidata":"https://www.wikidata.org/wiki/Q287862","display_name":"Catalytic cycle","level":3,"score":0.5422341227531433},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.5176613926887512},{"id":"https://openalex.org/C2777289219","wikidata":"https://www.wikidata.org/wiki/Q7632154","display_name":"Substrate (aquarium)","level":2,"score":0.477545827627182},{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.4728848338127136},{"id":"https://openalex.org/C2778500429","wikidata":"https://www.wikidata.org/wiki/Q60235","display_name":"Caffeine","level":2,"score":0.4468890428543091},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4116235375404358},{"id":"https://openalex.org/C2778565081","wikidata":"https://www.wikidata.org/wiki/Q4407","display_name":"Methyl group","level":3,"score":0.4102437198162079},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.38535094261169434},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.37334465980529785},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3159672021865845},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.14646583795547485},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10163173079490662},{"id":"https://openalex.org/C2780263894","wikidata":"https://www.wikidata.org/wiki/Q335268","display_name":"Alkyl","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002110","descriptor_name":"Caffeine","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D002110","descriptor_name":"Caffeine","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D002110","descriptor_name":"Caffeine","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008780","descriptor_name":"Methyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012263","descriptor_name":"Ribonucleosides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012263","descriptor_name":"Ribonucleosides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012263","descriptor_name":"Ribonucleosides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014970","descriptor_name":"Xanthines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014970","descriptor_name":"Xanthines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014970","descriptor_name":"Xanthines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055162","descriptor_name":"Biocatalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.6b00153","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00153","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:27482605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27482605","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":"pmid:27790913","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27790913","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:osti.gov:1355886","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1355886","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1355886","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1355886","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"awards":[{"id":"https://openalex.org/G1719536385","display_name":null,"funder_award_id":"DE-AC05-00OR22725","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4886405875","display_name":null,"funder_award_id":"201408370020","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G5027417669","display_name":null,"funder_award_id":"817940","funder_id":"https://openalex.org/F4320337397","funder_display_name":"Division of Molecular and Cellular Biosciences"},{"id":"https://openalex.org/G8507318371","display_name":null,"funder_award_id":"20903063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320337397","display_name":"Division of Molecular and Cellular Biosciences","ror":"https://ror.org/002jdaq33"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1485501298","https://openalex.org/W1970815841","https://openalex.org/W1976499671","https://openalex.org/W1981396672","https://openalex.org/W1983493485","https://openalex.org/W1989753444","https://openalex.org/W1992892547","https://openalex.org/W2006758041","https://openalex.org/W2009493983","https://openalex.org/W2022696619","https://openalex.org/W2025732137","https://openalex.org/W2027408247","https://openalex.org/W2027815611","https://openalex.org/W2034102180","https://openalex.org/W2038120864","https://openalex.org/W2059203673","https://openalex.org/W2063447602","https://openalex.org/W2075399298","https://openalex.org/W2090540659","https://openalex.org/W2102376488","https://openalex.org/W2110049118","https://openalex.org/W2112154906","https://openalex.org/W2115676532","https://openalex.org/W2119575116","https://openalex.org/W2132262459","https://openalex.org/W2162166182","https://openalex.org/W2314638436","https://openalex.org/W2327581403"],"related_works":["https://openalex.org/W2030642920","https://openalex.org/W2059012543","https://openalex.org/W2341079287","https://openalex.org/W2229620774","https://openalex.org/W1996734722","https://openalex.org/W3020911676","https://openalex.org/W4389099184","https://openalex.org/W4388672154","https://openalex.org/W2073776364","https://openalex.org/W2073829535"],"abstract_inverted_index":{"S-Adenosyl-l-methionine":[0],"(SAM)":[1],"dependent":[2],"xanthosine":[3,83,115,158,178,209],"methyltransferase":[4],"(XMT)":[5],"is":[6,100,126,150,169,203],"the":[7,12,17,23,36,42,46,75,79,94,97,104,111,128,131,138,141,146,154,161,172,187,197,207],"key":[8],"enzyme":[9],"that":[10,102,125,137],"catalyzes":[11],"first":[13,142],"methyl":[14,105],"transfer":[15],"in":[16,45,145,181,186],"caffeine":[18,147,217],"biosynthesis":[19,148,218],"pathway":[20,149],"to":[21,73,110,152],"produce":[22],"intermediate":[24],"7-methylxanthosine":[25],"(7mXR).":[26],"Although":[27],"XMT":[28],"has":[29],"been":[30],"a":[31,117],"subject":[32],"of":[33,41,65,78,114,157,177,213],"extensive":[34],"discussions,":[35],"catalytic":[37,76],"mechanism":[38,77],"and":[39,61,84,184,192,200],"nature":[40],"substrate":[43,139],"involved":[44],"catalysis":[47],"are":[48,71,91,219],"still":[49],"unclear.":[50],"In":[51],"this":[52,214],"paper,":[53],"quantum":[54],"mechanical/molecular":[55],"mechanical":[56],"(QM/MM)":[57],"molecular":[58],"dynamics":[59,193],"(MD)":[60],"free":[62,119],"energy":[63,120],"(potential":[64],"mean":[66],"force":[67],"or":[68],"PMF)":[69],"simulations":[70,202],"undertaken":[72],"determine":[74],"XMT-catalyzed":[80],"reaction.":[81],"Both":[82],"its":[85],"monoanionic":[86,112,155,208],"form":[87,113,156,163],"with":[88,116,206],"N3":[89,176],"deprotonated":[90],"used":[92],"as":[93,164],"substrates":[95],"for":[96,130,140,216],"methylation.":[98],"It":[99],"found":[101],"while":[103],"group":[106],"can":[107],"be":[108,153],"transferred":[109],"reasonable":[118],"barrier":[121],"(about":[122],"17":[123],"kcal/mol),":[124],"not":[127],"case":[129],"neutral":[132,162],"xanthosine.":[133],"The":[134,190,211],"results":[135],"suggest":[136],"methylation":[143],"step":[144],"likely":[151],"rather":[159],"than":[160],"widely":[165],"adopted.":[166],"This":[167],"conclusion":[168,215],"supported":[170],"by":[171],"pKa":[173],"value":[174],"on":[175],"both":[179,196],"measured":[180],"aqueous":[182],"phase":[183],"calculated":[185],"enzymatic":[188],"environment.":[189],"structural":[191],"information":[194],"from":[195],"X-ray":[198],"structure":[199],"MD":[201],"also":[204],"consistent":[205],"scenario.":[210],"implications":[212],"discussed.":[220]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-19T07:52:34.831488","created_date":"2016-08-23T00:00:00"}
