{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Jafari S"],"funding":["University of Kurdistan","Vetenskapsr?det"],"pagination":["1822-1841"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8023669"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["17(3)"],"pubmed_abstract":["Myrosinase from <i>Sinapis alba</i> hydrolyzes glycosidic bonds of β-d-<i>S</i>-glucosides. The enzyme shows an enhanced activity in the presence of l-ascorbic acid. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations to study the catalytic reaction of wild-type myrosinase and its E464A, Q187A, and Q187E mutants. Test calculations show that a proper QM region to study the myrosinase reaction must contain the whole substrate, models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464, Arg-259, and a water molecule. Furthermore, to make the deglycosylation step possible, Arg-259 must be charged, Glu-464 must be protonated on OE2, and His-141 must be protonated on the NE2 atom. The results indicate "],"journal":["Journal of chemical theory and computation"],"pubmed_title":["QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues."],"pmcid":["PMC8023669"],"funding_grant_id":["GRC98-00036-1","2018-05003"],"pubmed_authors":["Jafari S","Ryde U","Irani M"],"additional_accession":[]},"is_claimable":false,"name":"QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues.","description":"Myrosinase from <i>Sinapis alba</i> hydrolyzes glycosidic bonds of β-d-<i>S</i>-glucosides. The enzyme shows an enhanced activity in the presence of l-ascorbic acid. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations to study the catalytic reaction of wild-type myrosinase and its E464A, Q187A, and Q187E mutants. Test calculations show that a proper QM region to study the myrosinase reaction must contain the whole substrate, models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464, Arg-259, and a water molecule. Furthermore, to make the deglycosylation step possible, Arg-259 must be charged, Glu-464 must be protonated on OE2, and His-141 must be protonated on the NE2 atom. The results indicate ","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Mar","modification":"2026-05-07T20:03:23.458Z","creation":"2022-02-09T14:28:32.139Z"},"accession":"S-EPMC8023669","cross_references":{"pubmed":["33543623"],"doi":["10.1021/acs.jctc.0c01121"]}}