ONIOM (DFT:MM) Study of the Catalytic Mechanism of myo-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism

Abstract

myo-Inositol monophosphatase (IMPase), a putative target of lithium therapy for bipolar disorder, is an enzyme that catalyzes the hydrolysis of myo-inositol-1-phosphate (Ins(1)P) into myo-inositol (MI) and inorganic phosphate. It is known that either two or three Mg(2+) ions are used as cofactors in IMPase catalysis; however, the detailed catalytic mechanism and the specific number of Mg(2+) ions required have long remained obscure. To obtain a clearer view of the IMPase reaction, we undertook extensive ONIOM hybrid quantum mechanics and molecular mechanics (QM/MM) calculations, to evaluate the reaction with either three or two Mg(2+) ions. Our calculations show that the three-metal mechanism is energetically unfavorable; the initial inline attack of a hydroxide ion on the Ins(1)P substrate markedly destabilized the system without producing any stable transition state or intermediate. By contrast, for the two-metal mechanism, a favorable pathway was obtained from QM/MM calculations. In our proposed two-metal mechanism, the phosphoryl oxygen of the substrate acts as an acid-base catalyst, activating a water molecule in the first step, and the resultant hydroxide ion attacks the substrate in an inline fashion. A second water molecule, bound to a Mg(2+) ion, was found to play an essential role in the final proton-transfer step that leads to the formation of an MI product; this is achieved by lowering the energy barrier by 2.5 kcal/mol compared with the barrier for the mechanism that does not use this water molecule. Our results should advance our understanding of the IMPase mechanism, and this could have profound implications for the treatment of disease in the central nervous system.

Structural elucidation of the binding site and mode of inhibition of Li+ and Mg2+ in inositol monophosphatase

“…The proposed reaction scheme mediated by three Mg 2+ ions was verified by X–ray crystallographic studies on IMPase as well as in fructose‐1,6–bisphosphatases and 3′–phosphoadinosine‐5′–phosphate phosphatases . Computational methods have also been used to examine the two/three Mg 2+ ion‐mediated phosphate hydrolysis mechanism of IMPase .…”

QM/MM Study of the Reaction Catalyzed by Alkyladenine DNA Glycosylase: Examination of the Substrate Specificity of a DNA Repair Enzyme

“…A procedure consistent with that widely applied in the biochemical modeling literature was used to obtain reactant complexes (RC). ,,,− Specifically, each enzyme–DNA system was first optimized using ONIOM­(B3LYP/6-31G­(d):AMBER). Subsequently, the RESP charges were recalculated for the QM layer using the electrostatic grid obtained from a gas-phase HF/6-31G­(d) single-point calculation on the extracted QM layer with hydrogen atoms capping truncation points.…”

Implicit and explicit solvent effects on the selectivity of the cycloaddition reaction of cyclopentadiene and methyl acrylate; a theoretical study

“…All structures of the reactants, transition states (TSs) and products were optimised using the density functional theory (DFT) method at the B3LYP/6-311++G(d,p) level of theory [28]. Frequency calculations were used to confirm the nature of the Scheme 1 Cycloaddition reaction between cyclopentadiene (R1) and methyl acrylate (R2).…”