ArticleJournal of chemical theory and computation2009
QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism.
Article in Journal of chemical theory and computation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Role of Propionate Side Chain in Heme-Containing Metalloenzymes.ACS organic & inorganic Au · 2025Review
- Using phage display for rational engineering of a higher-affinity humanized 3' phosphohistidine-specific antibody.Communications chemistry · 2025Article
- Pi-pi stacking interactions with viral DNA contribute to the potency of naphthyridine-based HIV-1 integrase inhibitors.NAR molecular medicine · 2025Article
- Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems.Journal of computational chemistry · 2025Article
- Hydrogen-Bond-Assisted Catalysis: Hydroxylation of Paclitaxel by Human CYP2C8.Journal of the American Chemical Society · 2024Article
- Review
- Successful application of the DBLOC method to the hydroxylation of camphor by cytochrome p450.Protein science : a publication of the Protein Society · 2016Article
- Applications of density functional theory to iron-containing molecules of bioinorganic interest.Frontiers in chemistry · 2014Review
- In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB.PeerJ · 2013Article
- Insight into substituent effects in Cal-B catalyzed transesterification by combining experimental and theoretical approaches.Journal of molecular modeling · 2013Article
- Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase.The journal of physical chemistry. B · 2012Article
- Article
- IDSite: An accurate approach to predict P450-mediated drug metabolism.Journal of chemical theory and computation · 2011Article
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Authors and funding
2 authors.
Funding
Abstract
Using a structure generated by induced fit modeling of the protein-ligand complex, the reaction path for hydrogen atom abstraction in P450 BM3 is studied by means of mixed QM/MM methods to determine the structures and energetics along the reaction path. The IFD structure is suitable for hydrogen atom abstraction at the ω-1 position. The electronic structures obtained are similar to those observed in P450 cam. We show that the barrier for the hydrogen abstraction step from QM/MM modeling is 13.3 kcal/mol in quartet and 15.6 kcal/mol in doublet. Although there is some strain energy present in the ligand, the activation barrier is not dramatically affected. A crystal water molecule, HOH502, plays a role as catalyst and decreases the activation barrier by about 2 kcal/mol and reaction energy by about 3-4 kcal/mol. In order to achieve reactive chemistry at the remaining experimentally observed positions in the hydrocarbon tail of the ligand, other structures would have to be utilized as a starting point for the reaction. Finally, the present results still leave open the question of whether DFT methods provide an accurate computation of the barrier height in the P450 hydrogen atom abstraction reaction.
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Registered trials
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