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Developing active site models of ODCase: from large quantum models to a QM/MM approach
Stockholm University. (Teoretisk kemi)ORCID iD: 0000-0002-1312-1202
2004 (English)In: Topics in current chemistry, ISSN 0340-1022, E-ISSN 1436-5049, Vol. 238, 79-112 p.Article in journal (Refereed) Published
Abstract [en]

The catalytic mechanism of orotidine monophosphate decarboxylase (ODCase) has been modeled using density functional theory with the B3LYP functional. Barriers for three different mechanisms have been calculated using large QM and QM/MM models. A concerted protonation mechanism where TS stabilization is provided only by the positive Lys93 has a high barrier around 35 kcal/mol. QM/MM calculations confirm the results obtained using QM models. For a base protonation mechanism, 02 protonation gives a barrier for decarboxylation of 26 kcal/mol. Extensions to this QM model indicate that the cost of protonation may be inderestimated and the support for the base protonation mechanism is uncertain. An initial QM/MM investigation of a stepwise mechanism, where water molecules seem to play an important role for TS stabilization, gives the most promising results with an estimated barrier of 22 kcal/mol.

Place, publisher, year, edition, pages
Berlin: Springer , 2004. Vol. 238, 79-112 p.
Keyword [en]
Enzymatic mechanism, Active site, ODCase, Density functional theory, QM/MM
National Category
Theoretical Chemistry
URN: urn:nbn:se:uu:diva-145463DOI: 10.1007/b94540ISBN: 3-540-20566-7OAI: oai:DiVA.org:uu-145463DiVA: diva2:396527
Available from: 2011-02-10 Created: 2011-02-09 Last updated: 2016-04-22

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Lundberg, Marcus
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