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Quantum chemical modeling of enzymatic reactions: applications to the tautomerase superfamily
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
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: urn:nbn:se:kth:diva-4702ISBN: 978-91-7178-933-4 (print)OAI: oai:DiVA.org:kth-4702DiVA: diva2:13516
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
List of papers
1. Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase
Open this publication in new window or tab >>Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase
2007 (English)In: Bioorganic chemistry (Print), ISSN 0045-2068, E-ISSN 1090-2120, Vol. 35, no 6, 444-457 p.Article in journal (Refereed) Published
Abstract [en]

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pK(a) values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

Keyword
4-oxalocrotonate tautomerase, density functional theory, reaction mechanism
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-8244 (URN)10.1016/j.bioorg.2007.08.003 (DOI)000251363100003 ()2-s2.0-35448993293 (Scopus ID)
Note
QC 20100928. Uppdaterad från Accepted till Published (20100928).Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2010-11-23Bibliographically approved
2. Reaction mechanism of cis-chloroacrylic acid dehalogenase: a theoretical study
Open this publication in new window or tab >>Reaction mechanism of cis-chloroacrylic acid dehalogenase: a theoretical study
(English)Manuscript (Other academic)
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-8245 (URN)
Note
QC 20101123Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2010-11-23Bibliographically approved

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Citation style
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  • Other locale
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Output format
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