{"id":"https://openalex.org/W2984542651","doi":"https://doi.org/10.3390/e21111130","title":"Dynamical Behavior of \u03b2-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution","display_name":"Dynamical Behavior of \u03b2-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution","publication_year":2019,"publication_date":"2019-11-19","ids":{"openalex":"https://openalex.org/W2984542651","doi":"https://doi.org/10.3390/e21111130","mag":"2984542651"},"language":"en","primary_location":{"id":"doi:10.3390/e21111130","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e21111130","pdf_url":"https://www.mdpi.com/1099-4300/21/11/1130/pdf?version=1574141738","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1099-4300/21/11/1130/pdf?version=1574141738","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001888109","display_name":"Feng Wang","orcid":"https://orcid.org/0000-0001-7808-7538"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feng Wang","raw_affiliation_strings":["Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA"],"raw_orcid":"https://orcid.org/0000-0001-7808-7538","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100783219","display_name":"Hong-Yu Zhou","orcid":"https://orcid.org/0000-0002-1256-7050"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyu Zhou","raw_affiliation_strings":["Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100722142","display_name":"Xinlei Wang","orcid":"https://orcid.org/0000-0002-8561-6511"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinlei Wang","raw_affiliation_strings":["Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistical Science, Southern Methodist University, Dallas, TX 75275, USA","institution_ids":["https://openalex.org/I178169726"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010373442","display_name":"Peng Tao","orcid":"https://orcid.org/0000-0002-2488-0239"},"institutions":[{"id":"https://openalex.org/I178169726","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378","country_code":"US","type":"education","lineage":["https://openalex.org/I178169726"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peng Tao","raw_affiliation_strings":["Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA"],"raw_orcid":"https://orcid.org/0000-0002-2488-0239","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX 75275, USA","institution_ids":["https://openalex.org/I178169726"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010373442"],"corresponding_institution_ids":["https://openalex.org/I178169726"],"apc_list":{"value":2000,"currency":"CHF","value_usd":2165},"apc_paid":{"value":2000,"currency":"CHF","value_usd":2165},"fwci":0.58,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.66604899,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"11","first_page":"1130","last_page":"1130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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":0.9987999796867371,"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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":0.9922000169754028,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/penicillin-binding-proteins","display_name":"Penicillin binding proteins","score":0.8226751685142517},{"id":"https://openalex.org/keywords/penicillin","display_name":"Penicillin","score":0.7051491141319275},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5656467080116272},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.510555624961853},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.4838658571243286},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.48151764273643494},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4755660891532898},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4517176151275635},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.43539342284202576},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43151259422302246},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4235355854034424},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.42247626185417175},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2795577943325043},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21423032879829407}],"concepts":[{"id":"https://openalex.org/C2776653525","wikidata":"https://www.wikidata.org/wiki/Q7162855","display_name":"Penicillin binding proteins","level":4,"score":0.8226751685142517},{"id":"https://openalex.org/C174802600","wikidata":"https://www.wikidata.org/wiki/Q12190","display_name":"Penicillin","level":3,"score":0.7051491141319275},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5656467080116272},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.510555624961853},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.4838658571243286},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.48151764273643494},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4755660891532898},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4517176151275635},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.43539342284202576},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43151259422302246},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4235355854034424},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.42247626185417175},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2795577943325043},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21423032879829407}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/e21111130","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e21111130","pdf_url":"https://www.mdpi.com/1099-4300/21/11/1130/pdf?version=1574141738","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:dcffdffa2cba46c4b99d31f4e34e95fb","is_oa":true,"landing_page_url":"https://doaj.org/article/dcffdffa2cba46c4b99d31f4e34e95fb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy, Vol 21, Iss 11, p 1130 (2019)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/1099-4300/21/11/1130/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/e21111130","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7514474","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7514474","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Entropy (Basel)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/e21111130","is_oa":true,"landing_page_url":"https://doi.org/10.3390/e21111130","pdf_url":"https://www.mdpi.com/1099-4300/21/11/1130/pdf?version=1574141738","source":{"id":"https://openalex.org/S195231649","display_name":"Entropy","issn_l":"1099-4300","issn":["1099-4300"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Entropy","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G7462042259","display_name":"CAREER: New strategy to outsmart antimicrobial resistance: Mastering evolution of beta-lactamases catalytic mechanism through reaction pathways alignment, simulation, and analysis","funder_award_id":"1753167","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320318036","display_name":"Southern Methodist University","ror":"https://ror.org/042tdr378"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2984542651.pdf","grobid_xml":"https://content.openalex.org/works/W2984542651.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W585413800","https://openalex.org/W1621941250","https://openalex.org/W1701997017","https://openalex.org/W1970229608","https://openalex.org/W1972561608","https://openalex.org/W1973858832","https://openalex.org/W1976499671","https://openalex.org/W1979070806","https://openalex.org/W1984084871","https://openalex.org/W1986043460","https://openalex.org/W1987938525","https://openalex.org/W1993400812","https://openalex.org/W1998828560","https://openalex.org/W1998933192","https://openalex.org/W1999858937","https://openalex.org/W2004235085","https://openalex.org/W2006727669","https://openalex.org/W2010089917","https://openalex.org/W2015639754","https://openalex.org/W2023236836","https://openalex.org/W2028702957","https://openalex.org/W2032592607","https://openalex.org/W2036411010","https://openalex.org/W2042640333","https://openalex.org/W2045301115","https://openalex.org/W2047709322","https://openalex.org/W2048167567","https://openalex.org/W2051323767","https://openalex.org/W2053696392","https://openalex.org/W2054111366","https://openalex.org/W2055530511","https://openalex.org/W2060872117","https://openalex.org/W2063893529","https://openalex.org/W2067174909","https://openalex.org/W2070753604","https://openalex.org/W2072511197","https://openalex.org/W2073703928","https://openalex.org/W2075610521","https://openalex.org/W2077760098","https://openalex.org/W2079750630","https://openalex.org/W2084292396","https://openalex.org/W2084367350","https://openalex.org/W2086699924","https://openalex.org/W2088647884","https://openalex.org/W2091701505","https://openalex.org/W2092269506","https://openalex.org/W2106140689","https://openalex.org/W2111038162","https://openalex.org/W2125838338","https://openalex.org/W2134253205","https://openalex.org/W2143592395","https://openalex.org/W2143986312","https://openalex.org/W2153255945","https://openalex.org/W2153856953","https://openalex.org/W2155192732","https://openalex.org/W2155267446","https://openalex.org/W2155816874","https://openalex.org/W2156500885","https://openalex.org/W2224158481","https://openalex.org/W2226825552","https://openalex.org/W2265661434","https://openalex.org/W2292301738","https://openalex.org/W2315297180","https://openalex.org/W2402945284","https://openalex.org/W2565971407","https://openalex.org/W2781967430","https://openalex.org/W2787360936","https://openalex.org/W2894143091","https://openalex.org/W2949223833","https://openalex.org/W2959300111","https://openalex.org/W2963426504","https://openalex.org/W3100312042","https://openalex.org/W3100810942","https://openalex.org/W4298082496"],"related_works":["https://openalex.org/W1528942931","https://openalex.org/W2419608298","https://openalex.org/W2413675266","https://openalex.org/W2330255377","https://openalex.org/W1852497695","https://openalex.org/W2091078308","https://openalex.org/W2071988704","https://openalex.org/W1991833505","https://openalex.org/W2125229513","https://openalex.org/W2395116299"],"abstract_inverted_index":{"\u03b2-Lactamases":[0],"are":[1,24,87],"enzymes":[2],"produced":[3],"by":[4,141],"bacteria":[5],"to":[6,14,29,89,96],"hydrolyze":[7],"\u03b2-lactam-based":[8],"antibiotics,":[9],"and":[10,26,42,47,75,82,93,107,134,153,170,173,180],"pose":[11],"serious":[12],"threat":[13],"public":[15],"health":[16],"through":[17],"related":[18,28,71],"antibiotic":[19],"resistance.":[20],"Class":[21,150],"A":[22,79,151,178],"\u03b2-lactamases":[23,46,152,179],"structurally":[25],"functionally":[27],"penicillin-binding":[30],"proteins":[31,56,119,144,169],"(PBPs).":[32],"Despite":[33],"the":[34,38,49,128,161,171],"extensive":[35],"studies":[36],"of":[37,44,54,120,125,167],"structures,":[39,127],"catalytic":[40],"mechanisms":[41],"dynamics":[43,91],"both":[45,160],"PBPs,":[48,86],"potentially":[50],"different":[51,58,102],"dynamical":[52,99,165],"behaviors":[53,100,166],"these":[55,117,168],"in":[57,64,101],"functional":[59,103,172],"states":[60],"still":[61],"remain":[62],"elusive":[63],"general.":[65],"In":[66],"this":[67],"study,":[68],"four":[69,118,143],"evolutionarily":[70],"proteins,":[72],"including":[73],"TEM-1":[74],"TOHO-1":[76],"as":[77,84,113],"class":[78,177],"\u03b2-lactamases,":[80],"PBP-A":[81],"DD-transpeptidase":[83],"two":[85],"subjected":[88],"molecular":[90],"simulations":[92],"various":[94],"analyses":[95,124],"characterize":[97],"their":[98],"states.":[104],"Penicillin":[105],"G":[106],"its":[108],"ring":[109],"opening":[110],"product":[111],"serve":[112],"common":[114],"ligands":[115],"for":[116],"interest.":[121],"The":[122],"dynamic":[123],"overall":[126],"active":[129],"sites":[130],"with":[131],"penicillin":[132],"G,":[133],"three":[135],"catalytically":[136],"important":[137],"residues":[138],"commonly":[139],"shared":[140],"all":[142],"reveal":[145],"unexpected":[146],"cross":[147],"similarities":[148],"between":[149],"PBPs.":[154,181],"These":[155],"findings":[156],"shed":[157],"light":[158],"on":[159],"hidden":[162],"relations":[163,175],"among":[164,176],"evolutionary":[174]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}