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 .
A mild strategy for consecutive diazenylation and amination of indole moieties has been demonstrated. The functionalization occurs at C3 and C2 carbon atoms, respectively, at the indole scaffold in the presence of catalytic iodine and air at 40 °C in the 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) solvent. It is noteworthy that the aromatic amines are generated in situ by the reaction of aryl hydrazine with iodine. In general, bright red products are obtained in moderate to good yield. Control reactions are conducted to establish the reaction mechanism.
The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.
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.
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