Quantum chemical modeling of enzymatic reactions: applications to the tautomerase superfamily
2008 (English)Licentiate thesis, comprehensive summary (Other scientific)
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.
Trita-BIO-Report, ISSN 1654-2312 ; 2008:7
IdentifiersURN: urn:nbn:se:kth:diva-4702ISBN: 978-91-7178-933-4OAI: oai:DiVA.org:kth-4702DiVA: diva2:13516
2008-04-28, KTH, Stockholm, 10:00
Blomberg, Margaretha, Professor
QC 201011232008-04-222008-04-222010-11-23Bibliographically approved
List of papers