The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes

• Published in: Journal of chemical information and modeling 2022-12, Vol.62 (24), p.6679-6690
• Main Authors: Yadav, Shalini, Kardam, Vandana, Tripathi, Ankita, T G, Shruti, Dubey, Kshatresh Dutta
• Format: Article
• Language: English
• Subjects: Catalytic Domain; Computational Biochemistry; Cytochrome; Cytochrome P-450 Enzyme System - metabolism; Cytochromes P450; Enzymes; Fluid dynamics; Hydrogen atoms; Modelling; Oxidation; Oxidation-Reduction; Oxidizing agents; Physical simulation; Simulation; Water - chemistry
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.2c00505

Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water modelsTIP3P, SPC/E, and OPCfor three different CYP450 enzymesCYP450BM3, CYP450OleT, and CYP450BSβduring MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450OleT and CYP450BSβ, while the TIP3P water model is superior for the hydrophobic site, such as CYP450BM3.