Modelling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods, one among which is the choice of water model. Water molecules play a crucial role in all sorts of chemistry. Cytochrome P450 (CYP450), in particular, water molecules are crucial for the formation of active oxidants which perform the oxidation and metabolism of several substrates. Computational chemistry tools such as MD simulations and QM/MM calculations, nowadays, have become complementary tools to study the structure and functions of CYP450 enzymes, and therefore, accurate modeling of water molecules is crucial. 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 in the first solvation shell, and Hydrogen Atom Transfer (HAT) using QM/MM calculations and compared them for all the three water models.Our study shows that, the stability of the enzymes structure is well maintained in all the three water models. However, OPC water model performs well for the polar active sites, i.e., in CYP450OleT, CYP450BSβ while the TIP3P water model is superior for the hydrophobic site such as CYP450BM3 .

Alkylating agents pose the biggest threat to the genomic integrity of cells by damaging DNA bases through regular alkylation. Such damages are repaired by several automated types of machinery inside the cell. O6-alkylguanine-DNA alkyltransferase (AGT) is an enzyme that performs the direct repair of an alkylated guanine base by transferring the alkyl group to a cysteine residue. In the present study, using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of the damaged base as a three-step process in a thermodynamically feasible and irreversible manner. Our calculations show that the final product forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.

Alkylating agents possess the biggest threat to the genomic integrity of cell by damaging DNA bases through regular alkylation. Such damages are repaired by several automated machinery inside cell. O6-alkylguanine-DNA alkyltransferase (AGT) is such an enzyme which performs the direct repair of an alkylated guanine base by transferring the alkyl group to a Cysteine residue. In the present study using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of damaged base as a three step in thermodynamically feasible and irreversible manner. Our calculations show that the final products forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.

Modelling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods, one among which is the choice of the water model. Water molecules play a crucial role in all sorts of chemistry. Cytochrome P450 (CYP450), in particular, water molecules are crucial for the formation of active oxidants which perform the oxidation and metabolism of several substrates. Computational chemistry tools such as MD simulations and QM/MM calculations, nowadays, have become complementary tools to study the structure and functions of CYP450 enzymes, and therefore, accurate modeling of water molecules is crucial. 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 in the first solvation shell, and Hydrogen Atom Transfer (HAT) using QM/MM calculations and compared them for all the three water models. Our study shows that the stability of the enzyme structure is well maintained in all three water models. However, OPC water model performs well for the polar active sites, i.e., in CYP450OleT, CYP450BSβ while the TIP3P water model is superior for the hydrophobic site such as CYP450BM3.