biostudies-literatureJafari SUniversity of KurdistanVetenskapsr?det1822-1841https://www.ebi.ac.uk/biostudies/studies/S-EPMC8023669biostudies-literatureUnknown17(3)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 of chemical theory and computationQM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues.PMC8023669GRC98-00036-12018-05003Jafari SRyde UIrani MfalseQM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues.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 2021-01-01T00:00:00Z2021 Mar2026-05-07T20:03:23.458Z2022-02-09T14:28:32.139ZS-EPMC80236693354362310.1021/acs.jctc.0c01121