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The modelling and kinetic investigation of the lipase-catalysed acetylation of stereoisomeric prostaglandins
KTH, Skolan för bioteknologi (BIO), Biokemi.
KTH, Skolan för bioteknologi (BIO), Biokemi.
Vise andre og tillknytning
2005 (engelsk)Inngår i: Journal of Molecular Catalysis B: Enzymatic, ISSN 1381-1177, E-ISSN 1873-3158, Vol. 35, nr 1-3, s. 62-69Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

The lipase-catalysed acetylation of the hydroxyl groups of five stereoisomeric prostaglandins of type F was investigated by means of molecular dynamics simulations and the results compared with experimental observations. An NMR spectroscopic monitoring was performed to estimate reaction velocities and the regioselectivity. A molecular modelling protocol that could qualitatively differentiate between the OH groups of prostaglandins being either accessible or unaccessible to the Candida antarctica lipase B (CALB) catalysed acetylation was developed. The protocol developed analysed the protein structure deformation, the content of essential hydrogen bonds and the function-based subset energy of tetrahedral intermediates along the molecular dynamics simulations trajectory. The tetrahedral intermediates displaying a deformation RMS value lower than 3.0 angstrom, an essential hydrogen bond content over 50% and a subset energy less than -95 kJ/mol were classified active. In total, the accessibility of 16 out of 17 different prostaglandin OH groups was correctly predicted.

sted, utgiver, år, opplag, sider
2005. Vol. 35, nr 1-3, s. 62-69
Emneord [en]
lipase-catalysed acetylation, Novozym 435, low-water media, monitoring by H-1 NMR, prostaglandin, molecular dynamics simulations, enantiomerically pure diastereomers, candida-antarctica, nucleic-acids, force-field, isoprostanes, physiology, proteins, ester
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-14929DOI: 10.1016/j.molcatb.2005.05.008ISI: 000230671100011Scopus ID: 2-s2.0-21644442447OAI: oai:DiVA.org:kth-14929DiVA, id: diva2:332970
Merknad
QC 20100525Tilgjengelig fra: 2010-08-05 Laget: 2010-08-05 Sist oppdatert: 2017-12-12bibliografisk kontrollert
Inngår i avhandling
1. Molecular modelling - understanding and prediction of enzyme selectivity.
Åpne denne publikasjonen i ny fane eller vindu >>Molecular modelling - understanding and prediction of enzyme selectivity.
2009 (engelsk)Licentiatavhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Molecular modelling strategies for evaluation of enzyme selectivity wereinvestigated with a focus on principles of how molecular interactionscould be evaluated to provide information about selectivity. Althoughmolecular modelling provides tools for evaluation of geometrical andenergy features of molecular systems, no general strategies for evaluationof enzyme selectivity exist. Geometrical analyses can be based uponinspection and reasoning about molecular interactions, which provide aneasily accessible way to gain information, but suffer from the risk of biasput in by the modeller. They can also be based on geometrical features ofmolecular interactions such as bond lengths and hydrogen-bond formation.Energy analyses are appealing for their modeller independenceand for the possibility to predict not only stereopreference, but also itsmagnitude.In this thesis, four examples of enantio- or regioselective serinehydrolase-catalysed reaction systems are presented together with developedmodelling protocols for explanation, prediction or enhancement ofselectivity. Geometrical as well as energy-based methodology were used,and provided an understanding of the structural basis of enzymeselectivity. In total, the protocols were successful in making qualitative explanationsand predictions of stereoselectivity, although quantitative determinationswere not achieved.

sted, utgiver, år, opplag, sider
Stockholm: KTH, 2009. s. 27
Serie
Trita-BIO-Report, ISSN 1654-2312 ; 2009:11
Emneord
molecular modelling; regioselectivity; enantioselectivity; molecular dynamics; serine hydrolase; stereospecificity
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-10532 (URN)978-91-7415-325-5 (ISBN)
Presentation
(engelsk)
Veileder
Tilgjengelig fra: 2009-05-26 Laget: 2009-05-25 Sist oppdatert: 2010-10-12bibliografisk kontrollert

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