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Published on: April 22, 2016
Water as biocatalyst in cytochrome P450
Devesh Kumar1, Ahmet Altun, Sason Shaikh
1Max-Planck-Lnstitut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany.
A single water molecule significantly lowers the energy barrier for camphor hydroxylation in cytochrome P450 enzymes. This effect, observed across various substrates, stems from enhanced hydrogen bonding in the transition state.
Area of Science:
- Biochemistry
- Computational Chemistry
- Enzyme Catalysis
Background:
- Cytochrome P450 enzymes are crucial for metabolizing diverse substrates.
- Previous studies suggested a role for water in P450 catalysis, but its precise impact was unclear.
Purpose of the Study:
- To investigate the catalytic role of water molecules in cytochrome P450 reactions.
- To elucidate the mechanism by which water influences reaction barriers.
- To explore the generalizability of water's effect across different substrates.
Main Methods:
- Quantum mechanics/molecular mechanics (QM/MM) simulations.
- B3LYP/CHARMM level of theory for barrier calculations.
- Gas-phase B3LYP model studies for various substrates.
Main Results:
- A single water molecule lowers the computed barrier for camphor hydroxylation by approximately 4 kcal/mol.
- This water-mediated barrier lowering effect is general across different substrates.
- The mechanism involves electrostatic enhancement of hydrogen bonding in the transition state for hydrogen abstraction.
Conclusions:
- Water molecules play a significant catalytic role in cytochrome P450 reactions.
- Understanding water's influence is crucial for accurate QM/MM modeling of biocatalysis.
- Methodological considerations for incorporating water in QM/MM studies are discussed.
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