How Do Preorganized Electric Fields Function in Catalytic Cycles? The Case of the Enzyme Tyrosine Hydroxylase

Abstract

Nature has devised intrinsic electric fields (IEFs) that are engaged in electrostatic catalysis of enzymes. But, how does the IEF target its function in enzymes that involve several reaction steps in catalytic cycles? To decipher the impact of the IEF on the catalytic cycle of an enzyme system, we have performed molecular dynamics and quantum-mechanical/molecular-mechanical (QM/MM) simulations on tyrosine hydroxylase (TyrH). The catalytic cycle of TyrH involves two reaction stages: the activation of H2O2 to form the active species of compound I (Cpd I), in the first stage, and the Cpd I-mediated hydroxylation of l-tyrosine to l-DOPA, in the second stage. For the first stage, the QM/MM calculations show that a heme-propionate group functions as a base to catalyze the O–O heterolysis reaction. For the second stage, the study reveals that the reaction is initiated by the His88-mediated proton-coupled electron transfer followed by the oxygen atom transfer from compound II (Cpd II) to the l-Tyr substrate. Importantly, our calculations demonstrate that the IEF in TyrH is optimized to promote the O–O bond heterolysis that generates the active species of the enzyme, Cpd I. However, the same IEF slows down the subsequent aromatic hydroxylation. Thus, the IEF in the TyrH enzymes does not catalyze the product formation step, but will selectively boost one or more challenging steps in the catalytic cycle. These findings have general implications on O2/H2O2-dependent metalloenzymes, which can expand our understanding of how nature has used electric fields as “smart reagents” in modulating the catalytic reactivity.

How the Conformational Movement of the Substrate Drives the Regioselective C–N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations

“…The IEF was computed as described in previous studies. , Briefly, it is calculated with Coulomb’s law, whereby the atoms are treated as point charges and their positions are determined by the QM/MM-optimized structures. The magnitude of the point charge was obtained from the AMBER ff14SB force field and TIP3P model for the protein residues and water molecules, respectively.…”

Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase

“…To gain some clues on this, we have analyzed the intrinsic electric field (IEF) along the Fe–O bond from the MD trajectory of LiP-Cpd I at pH = 7 vs pH ∼ 3. Existing studies have shown that the IEF along the Fe–O bond has significant effects on the reactivity and redox potential of the Heme-Cpd I species . For pH = 7, the calculated average IEF value is −72 MV/cm (Figure S28).…”

“…Existing studies have shown that the IEF along the Fe–O bond has significant effects on the reactivity and redox potential of the Heme-Cpd I species. 89 For pH = 7, the calculated average IEF value is −72 MV/cm ( Figure S28 ). Such a negative value suggests that the redox potential of Cpd I is intrinsically inhibited by the protein environment of LiP.…”

Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach

“…The structures of the TyrH scaffold and the QM region in the reactant state (RS) and TS of the O–O heterolysis reaction were obtained from our previous QM/MM study . The QM region contains the heme with the Fe-OOH moiety, the ligand imidazole ring, and the substrate (see Scheme ).…”

“…Theoretical studies also provide significant insights into the catalytic effects of electric fields in enzymes. For instance, Warshel et al employed the empirical valence bond (EVB) method to quantify the catalytic effect of the preorganized electrostatic environment in various enzymes. ,,− Alexandrova’s group have shown that the effect of electrostatic preorganization can be reflected by the change of geometry of charge density in the theoretical framework of Quantum Theory of Atoms in Molecules (QTAIM). − Head-Gordon’s group evaluated the transition-state free energy stabilization based on the interaction energy of residue electric fields with bond dipoles in the reactant and TSs, which successfully guide the optimization of the electric field for improving the catalytic efficiency of a designed Kemp eliminase through mutation in the protein scaffold residues. ,, The application of oriented external electric fields (OEEFs) in computational models has also been used to infer how the electric fields affect the energetics of chemical reactions. ,,− …”