{"id":"https://openalex.org/W3047616326","doi":"https://doi.org/10.1021/acs.jcim.0c00159","title":"Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases","display_name":"Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases","publication_year":2020,"publication_date":"2020-08-05","ids":{"openalex":"https://openalex.org/W3047616326","doi":"https://doi.org/10.1021/acs.jcim.0c00159","mag":"3047616326","pmid":"https://pubmed.ncbi.nlm.nih.gov/32786702"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00159","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00159","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/A5066833582","display_name":"Jingyuan Zhuang","orcid":"https://orcid.org/0000-0003-1148-9721"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingyuan Zhuang","raw_affiliation_strings":["School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100403435","display_name":"Fan Zhang","orcid":"https://orcid.org/0000-0002-0953-7416"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Zhang","raw_affiliation_strings":["School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056409326","display_name":"Jingwei Zhou","orcid":"https://orcid.org/0000-0001-5382-1134"},"institutions":[{"id":"https://openalex.org/I117532281","display_name":"Guangzhou University of Chinese Medicine","ror":"https://ror.org/03qb7bg95","country_code":"CN","type":"education","lineage":["https://openalex.org/I117532281"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jingwei Zhou","raw_affiliation_strings":["Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, P. R. China"],"raw_orcid":"https://orcid.org/0000-0001-5382-1134","affiliations":[{"raw_affiliation_string":"Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, P. R. China","institution_ids":["https://openalex.org/I117532281"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111886119","display_name":"Wenbin Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wenbin Deng","raw_affiliation_strings":["School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P. R. China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065291000","display_name":"Ruibo Wu","orcid":"https://orcid.org/0000-0002-1984-046X"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruibo Wu","raw_affiliation_strings":["School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-1984-046X","affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056409326","https://openalex.org/A5111886119"],"corresponding_institution_ids":["https://openalex.org/I117532281","https://openalex.org/I157773358"],"apc_list":null,"apc_paid":null,"fwci":0.2441,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5307517,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"60","issue":"10","first_page":"4985","last_page":"4994"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":1.0,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":1.0,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9975000023841858,"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"}},{"id":"https://openalex.org/T11385","display_name":"Natural product bioactivities and synthesis","score":0.9918000102043152,"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/active-site","display_name":"Active site","score":0.7034903764724731},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6100826263427734},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.5989338755607605},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.5870165228843689},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5747781991958618},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16794970631599426},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.15050408244132996},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.12267377972602844}],"concepts":[{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.7034903764724731},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6100826263427734},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.5989338755607605},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5870165228843689},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5747781991958618},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16794970631599426},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.15050408244132996},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.12267377972602844}],"mesh":[{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003500","descriptor_name":"Cyclization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013729","descriptor_name":"Terpenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013729","descriptor_name":"Terpenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013729","descriptor_name":"Terpenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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.0c00159","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00159","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:32786702","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32786702","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/G2255234378","display_name":"\u500d\u534a\u841c\u73af\u5316\u9176(ATAS\u548cTEAS)\u50ac\u5316\u673a\u5236\u7814\u7a76\u53ca\u5176\u86cb\u767d\u6d3b\u6027\u91cd\u8bbe\u8ba1","funder_award_id":"21773313","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3667467801","display_name":null,"funder_award_id":"81772449","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5588845597","display_name":null,"funder_award_id":"81971081","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7440495871","display_name":null,"funder_award_id":"81803436","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1463493509","https://openalex.org/W1866679460","https://openalex.org/W1976161355","https://openalex.org/W1976499671","https://openalex.org/W1984186737","https://openalex.org/W1986607177","https://openalex.org/W1992400377","https://openalex.org/W1994525974","https://openalex.org/W1997638680","https://openalex.org/W2008708467","https://openalex.org/W2008865353","https://openalex.org/W2022205995","https://openalex.org/W2024305976","https://openalex.org/W2032478862","https://openalex.org/W2034402891","https://openalex.org/W2046886711","https://openalex.org/W2050816664","https://openalex.org/W2056400844","https://openalex.org/W2062528838","https://openalex.org/W2062743073","https://openalex.org/W2073073672","https://openalex.org/W2080690387","https://openalex.org/W2083164919","https://openalex.org/W2085475030","https://openalex.org/W2098750284","https://openalex.org/W2103935727","https://openalex.org/W2106140689","https://openalex.org/W2109678534","https://openalex.org/W2117109978","https://openalex.org/W2147993766","https://openalex.org/W2148532595","https://openalex.org/W2149125081","https://openalex.org/W2152835591","https://openalex.org/W2163915395","https://openalex.org/W2170242620","https://openalex.org/W2177638519","https://openalex.org/W2317863386","https://openalex.org/W2330673149","https://openalex.org/W2334782546","https://openalex.org/W2377402880","https://openalex.org/W2592452129","https://openalex.org/W2593210325","https://openalex.org/W2742677840","https://openalex.org/W2750432728","https://openalex.org/W2761747373","https://openalex.org/W2938271636","https://openalex.org/W2967824457","https://openalex.org/W2971082441"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Microbe":[0],"class":[1,72,193,220],"I":[2,73,194,221],"terpene":[3],"cyclases":[4],"(TPCs)":[5],"are":[6,55,177],"responsible":[7],"for":[8,215],"deriving":[9],"numerous":[10],"functionally":[11],"and":[12,50,76,99,140,174,185,188,209],"structurally":[13],"diverse":[14],"groups":[15],"of":[16,23,64,92,108,117,127,137,146,153,163,171,201,218],"terpenoid":[17],"natural":[18],"products.":[19],"The":[20],"conformational":[21],"change":[22],"their":[24],"active":[25,47,82,138,147,202],"pockets":[26],"from":[27],"\"open\"":[28],"state":[29,32],"to":[30,45,158,190],"\"closed\"":[31],"upon":[33],"substrate":[34,144],"binding":[35],"has":[36],"been":[37],"clarified.":[38],"However,":[39],"the":[40,62,65,81,89,104,115,123,128,134,143,151,154,161,164,182,199],"key":[41],"structural":[42,95,166,212],"basis":[43,63,213],"relevant":[44],"this":[46,59],"pocket":[48,83,139,148,203],"dynamics":[49,67,84,200],"its":[51],"detailed":[52],"molecular":[53,66],"mechanism":[54],"still":[56],"unclear.":[57],"In":[58],"work,":[60],"on":[61,69,88],"(MD)":[68],"two":[70,93,165,168],"microbe":[71,192,219],"TPCs":[74,222],"(SdS":[75],"bCinS),":[77],"we":[78,112],"propose":[79],"that":[80,114],"is":[85,120],"highly":[86],"dependent":[87],"residue":[90,125],"orientation":[91,126],"conserved":[94],"bases":[96],"R-D":[97,183],"dyad":[98,184],"X-R-D":[100,129,155,186],"triad,":[101,130],"rather":[102],"than":[103],"previously":[105],"suggested":[106],"flexibility":[107,116],"kink":[109,118],"region.":[110],"Actually,":[111],"considered":[113],"region":[119],"synchronous":[121],"with":[122,223],"R":[124],"which":[131],"could":[132],"regulate":[133],"entrance":[135],"size":[136],"thus":[141],"affect":[142],"selectivity":[145],"by":[149],"utilizing":[150],"promiscuity":[152],"triad.":[156],"Furthermore,":[157],"better":[159],"understand":[160],"function":[162],"bases,":[167],"intelligible":[169],"models":[170],"\"PPi":[172],"catcher-locker\"":[173],"\"selector-PPi":[175],"sensor-orienter\"":[176],"proposed":[178],"to,":[179],"respectively,":[180],"describe":[181],"triad":[187],"broadened":[189],"more":[191],"TPCs.":[195],"These":[196],"findings":[197],"exhibit":[198],"inaccessible":[204],"in":[205],"static":[206],"crystal":[207],"structures":[208],"provide":[210],"useful":[211],"knowledge":[214],"further":[216],"design":[217],"different":[224],"cyclization":[225],"ability.":[226]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
