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Reaction mechanism of cis-chloroacrylic acid dehalogenase: a theoretical study
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
(English)Manuscript (Other academic)
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-8245OAI: oai:DiVA.org:kth-8245DiVA: diva2:13515
Note
QC 20101123Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2010-11-23Bibliographically approved
In thesis
1. Quantum chemical modeling of enzymatic reactions: applications to the tautomerase superfamily
Open this publication in new window or tab >>Quantum chemical modeling of enzymatic reactions: applications to the tautomerase superfamily
2008 (English)Licentiate thesis, comprehensive summary (Other scientific)
Abstract [en]

In this thesis, quantum chemical methods are used to investigate enzymatic reaction mechanisms. The Density functional theory, in particular the hybrid B3LYP functional, is used to model two enzymes belonging to the tautomerase superfamily; 4-Oxalocrotonate Tautomerase (4-OT) and cis-Chloroacrylic Acid Dehalogenase (cis-CAAD). The methodology is presented and new mechanistic insights for the two enzymes are discussed.

For 4-OT, two different models are built and the potential energy curves are computed. This allows the methodology to be evaluated. The results give new insight into the energetics of the 4-OT reaction, indicating that the charge-separated intermediate is quite close in energy to the reactant species. The models also make it possible to perform in silico mutations to investigate the role of active site groups. Excellent agreement is found between the calculations and site-directed mutagenesis experiments, further substantiating the validity of the models.

For cis-CAAD, the uncatalyzed reaction is first considered and excellent agreement is found between the calculated barrier and the measured rate constant. The enzymatic reaction is then studied with a quite large active site model and a reaction mechanism is proposed.

Place, publisher, year, edition, pages
Stockholm: KTH, 2008. x, 38 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:7
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-4702 (URN)978-91-7178-933-4 (ISBN)
Presentation
2008-04-28, KTH, Stockholm, 10:00
Opponent
Supervisors
Note
QC 20101123Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2010-11-23Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf