{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T21:34:28Z","timestamp":1769549668035,"version":"3.49.0"},"reference-count":41,"publisher":"Wiley","issue":"13","license":[{"start":{"date-parts":[[2023,5,2]],"date-time":"2023-05-02T00:00:00Z","timestamp":1682985600000},"content-version":"am","delay-in-days":348,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#am"},{"start":{"date-parts":[[2022,5,19]],"date-time":"2022-05-19T00:00:00Z","timestamp":1652918400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100006132","name":"Office of Science","doi-asserted-by":"publisher","award":["DE-AC05-00OR22725"],"award-info":[{"award-number":["DE-AC05-00OR22725"]}],"id":[{"id":"10.13039\/100006132","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006132","name":"Office of Science","doi-asserted-by":"publisher","award":["CHM150"],"award-info":[{"award-number":["CHM150"]}],"id":[{"id":"10.13039\/100006132","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006132","name":"Office of Science","doi-asserted-by":"publisher","award":["PTDC\/QUI-QFI\/28714\/2017"],"award-info":[{"award-number":["PTDC\/QUI-QFI\/28714\/2017"]}],"id":[{"id":"10.13039\/100006132","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["chemistry-europe.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["ChemPhysChem"],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We employed QM\/MM molecular dynamics (MD) simulations to characterize the rate\u2010limiting step of the glycosylation reaction of pancreatic \u03b1\u2010amylase with combined DFT\/molecular dynamics methods (PBE\/def2\u2010SVP\u2009:\u2009AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1\u20132\u2005kcal\u2009\u22c5\u2009mol<jats:sup>\u22121<\/jats:sup>. Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8\u2005kcal\u2009\u22c5\u2009mol<jats:sup>\u22121<\/jats:sup> and \u22126.3 to +3.8\u2005kcal\u2009\u22c5\u2009mol<jats:sup>\u22121<\/jats:sup> depending on the starting conformations, showing that despite significant state\u2010of\u2010the\u2010art QM\/MM MD sampling (0.5\u2005ns\/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid\u2010base reaction by the Glu233, which are qualitatively similar to those from multi\u2010PES QM\/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.<\/jats:p>","DOI":"10.1002\/cphc.202200159","type":"journal-article","created":{"date-parts":[[2022,5,2]],"date-time":"2022-05-02T06:35:10Z","timestamp":1651473310000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms"],"prefix":"10.1002","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2032-9308","authenticated-orcid":false,"given":"Rui P. P.","family":"Neves","sequence":"first","affiliation":[{"name":"Departamento de Qu\u00edmica e Bioqu\u00edmica Faculdade de Ci\u00eancias Universidade do Porto LAQV@REQUIMTE  Rua do Campo Alegre s\/n 4169-007 Porto Portugal"}]},{"given":"Ana V.","family":"Cunha","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel Eenheid Algemene Chemie  Boulevard de la Plaine 2 1050 Ixelles Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2748-4722","authenticated-orcid":false,"given":"Pedro A.","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica e Bioqu\u00edmica Faculdade de Ci\u00eancias Universidade do Porto LAQV@REQUIMTE  Rua do Campo Alegre s\/n 4169-007 Porto Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7554-8324","authenticated-orcid":false,"given":"Maria J.","family":"Ramos","sequence":"additional","affiliation":[{"name":"Departamento de Qu\u00edmica e Bioqu\u00edmica Faculdade de Ci\u00eancias Universidade do Porto LAQV@REQUIMTE  Rua do Campo Alegre s\/n 4169-007 Porto Portugal"}]}],"member":"311","published-online":{"date-parts":[[2022,5,19]]},"reference":[{"key":"e_1_2_11_1_1","unstructured":"\u00a0"},{"key":"e_1_2_11_2_2","doi-asserted-by":"publisher","DOI":"10.1021\/ar500390e"},{"key":"e_1_2_11_3_2","doi-asserted-by":"publisher","DOI":"10.1021\/ar5002928"},{"key":"e_1_2_11_4_2","first-page":"144","author":"Warshel A.","year":"2016","journal-title":"J. Chem. Phys."},{"key":"e_1_2_11_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1281"},{"key":"e_1_2_11_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/cr0503106"},{"key":"e_1_2_11_7_1","unstructured":"\u00a0"},{"key":"e_1_2_11_8_2","doi-asserted-by":"publisher","DOI":"10.1021\/cr500628b"},{"key":"e_1_2_11_9_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.7b02671"},{"key":"e_1_2_11_10_2","doi-asserted-by":"publisher","DOI":"10.1039\/C8RE00213D"},{"key":"e_1_2_11_11_1","unstructured":"\u00a0"},{"key":"e_1_2_11_12_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.8b05177"},{"key":"e_1_2_11_13_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.8b01239"},{"key":"e_1_2_11_14_1","unstructured":"\u00a0"},{"key":"e_1_2_11_15_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja9733604"},{"key":"e_1_2_11_16_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.7809611"},{"key":"e_1_2_11_17_1","unstructured":"\u00a0"},{"key":"e_1_2_11_18_2","doi-asserted-by":"publisher","DOI":"10.2174\/1568026033452492"},{"key":"e_1_2_11_19_2","volume-title":"Iminosugars as Glycosidase Inhibitors: Nojirimycin and Beyond","author":"St\u00fctz A.","year":"1999"},{"key":"e_1_2_11_20_1","unstructured":"\u00a0"},{"key":"e_1_2_11_21_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-014-5790-8"},{"key":"e_1_2_11_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.07.014"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00222"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.7b04400"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2004.12.021"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1021\/bi011821z"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.5b00759"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja212117m"},{"key":"e_1_2_11_29_1","unstructured":"\u00a0"},{"key":"e_1_2_11_30_2","doi-asserted-by":"publisher","DOI":"10.1039\/C9SC01464K"},{"key":"e_1_2_11_31_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.0c03122"},{"key":"e_1_2_11_32_1","unstructured":"D.\u2005A. Case I.\u2005Y. Ben-Shalom S.\u2005R. Brozell D.\u2005S. Cerutti T.\u2005E. Cheatham III V.\u2005W.\u2005D. Cruzeiro T.\u2005A. Darden R.\u2005E. Duke D. Ghoreishi M.\u2005K. Gilson H. Gohlke A.\u2005W. Goetz D. Greene R. Harris N. Homeyer S. Izadi A. Kovalenko T. Kurtzman T.\u2005S. Lee S. LeGrand P. Li C. Lin J. Liu T. Luchko R. Luo D.\u2005J. Mermelstein K.\u2005M. Merz Y. Miao G. Monard C. Nguyen H. Nguyen I. Omelyan A. Onufriev F. Pan R. Qi D.\u2005R. Roe A. Roitberg C. Sagui S. Schott-Verdugo J. Shen C.\u2005L. Simmerling J. Smith R. Salomon-Ferrer J. Swails R.\u2005C. Walker J. Wang H. Wei R.\u2005M. Wolf X. Wu L. Xiao D.\u2005M. York P.\u2005A. Kollman inAmber 18 University of California 2018."},{"key":"e_1_2_11_33_1","first-page":"8","author":"Neese F.","year":"2018","journal-title":"WIREs Comput. Mol. Sci."},{"key":"e_1_2_11_34_1","unstructured":"\u00a0"},{"key":"e_1_2_11_35_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c01037"},{"key":"e_1_2_11_36_2","doi-asserted-by":"publisher","DOI":"10.1063\/5.0038120"},{"key":"e_1_2_11_37_2","doi-asserted-by":"publisher","DOI":"10.1063\/1.4926652"},{"key":"e_1_2_11_38_1","unstructured":"\u00a0"},{"key":"e_1_2_11_39_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.8b00369"},{"key":"e_1_2_11_40_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.0c05522"},{"key":"e_1_2_11_41_1","unstructured":"A. Grossfield inWHAM: the weighted histogram analysis method 2013."}],"container-title":["ChemPhysChem"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cphc.202200159","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cphc.202200159","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/am-pdf\/10.1002\/cphc.202200159","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cphc.202200159","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T13:33:43Z","timestamp":1760362423000},"score":1,"resource":{"primary":{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/10.1002\/cphc.202200159"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,19]]},"references-count":41,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2022,7,5]]}},"alternative-id":["10.1002\/cphc.202200159"],"URL":"https:\/\/doi.org\/10.1002\/cphc.202200159","archive":["Portico"],"relation":{},"ISSN":["1439-4235","1439-7641"],"issn-type":[{"value":"1439-4235","type":"print"},{"value":"1439-7641","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,19]]},"assertion":[{"value":"2022-03-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-05-19","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e202200159"}}