Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation

dc.contributor.author Petersen, Luis
dc.contributor.author Ardèvol, Albert
dc.contributor.author Rovira, Carme
dc.contributor.author Reilly, Peter
dc.contributor.department Chemical and Biological Engineering
dc.date 2018-02-13T03:07:02.000
dc.date.accessioned 2020-06-30T01:08:00Z
dc.date.available 2020-06-30T01:08:00Z
dc.date.copyright Fri Jan 01 00:00:00 UTC 2010
dc.date.embargo 2012-11-10
dc.date.issued 2010-05-26
dc.description.abstract <p>Golgi α-mannosidase II (GMII), a member of glycoside hydrolase family 38, cleaves two mannosyl residues from GlcNAcMan<sub>5</sub>GlcNAc<sub>2</sub> as part of the N-linked glycosylation pathway. To elucidate the molecular and electronic details of the reaction mechanism, in particular the conformation of the substrate at the transition state, we performed quantum mechanics/molecular mechanics metadynamics simulations of the glycosylation reaction catalyzed by GMII. The calculated free energy of activation for mannosyl glycosylation (23 kcal/mol) agrees very well with experiments, as does the conformation of the glycon mannosyl ring in the product of the glycosylation reaction (the covalent intermediate). In addition, we provide insight into the electronic aspects of the molecular mechanism that were not previously available. We show that the substrate adopts an <sup>O</sup><em>S</em><sub>2</sub>/<em>B</em><sub>2,5</sub> conformation in the GMII Michaelis complex and that the nucleophilic attack occurs before complete departure of the leaving group, consistent with a D<sub>N</sub>A<sub>N</sub> reaction mechanism. The transition state has a clear oxacarbenium ion (OCI) character, with the glycosylation reaction following an <sup>O</sup><em>S</em><sub>2</sub>/<em>B</em><sub>2,5</sub> → <em>B</em><sub>2,5</sub> [TS] → <sup>1</sup><em>S</em><sub>5</sub> itinerary, agreeing with an earlier proposal based on comparing α- and β-mannanases. The simulations also demonstrate that an active-site Zn ion helps to lengthen the O2′−H<sub>O2′</sub> bond when the substrate acquires OCI character, relieving the electron deficiency of the OCI-like species. Our results can be used to explain the potency of recently formulated GMII anticancer inhibitors, and they are potentially relevant in deriving new inhibitors.</p>
dc.description.comments <p>Posted with permission from <em>Journal of the American Chemical Society, </em>132, no. 24 (2010): 8291–8300, doi:<a href="http://dx.doi.org/10.1021/ja909249u" target="_self">10.1021/ja909249u</a>. Copyright 2010 American Chemical Society.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/cbe_pubs/15/
dc.identifier.articleid 1009
dc.identifier.contextkey 3459848
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath cbe_pubs/15
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/13239
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/cbe_pubs/15/ja909249u.pdf|||Fri Jan 14 20:30:00 UTC 2022
dc.source.uri 10.1021/ja909249u
dc.subject.disciplines Biochemical and Biomolecular Engineering
dc.subject.disciplines Biological Engineering
dc.subject.disciplines Chemical Engineering
dc.title Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 0727532a-2892-42e2-84ab-5af5088f76c6
relation.isOrgUnitOfPublication 86545861-382c-4c15-8c52-eb8e9afe6b75
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