Zinc–Homocysteine binding in cobalamin‐dependent methionine synthase and its role in the substrate activation: DFT, ONIOM, and QM/MM molecular dynamics studies

Abstract

Cobalamin-dependent methionine synthase (MetH) is an important metalloenzyme responsible for the biosynthesis of methionine. It catalyzes methyl transfer from N(5)-methyl-tetrahydrofolate to homocysteine (Hcy) by using a zinc ion to activate the Hcy substrate. Density functional theory (B3LYP) calculations on the active-site model in gas phase and in a polarized continuum model were performed to study the Zn coordination changes from the substrate-unbound state to the substrate-bound state. The protein effect on the Zn(2+) coordination exchange was further investigated by ONIOM (B3LYP:AMBER)-ME and EE calculations. The Zn(2+)-coordination exchange is found to be highly unfavorable in the gas phase with a high barrier and endothermicity. In the water solution, the reaction becomes exothermic and the reaction barrier is drastically decreased to about 10.0 kcal/mol. A considerable protein effect on the coordination exchange was also found; the reaction is even more exothermic and occurs without barrier. The enzyme was suggested to constrain the zinc coordination sphere in the reactant state (Hcy-unbound state) more than that in the product state (Hcy-bound state), which promotes ligation of the Hcy substrate. Molecular dynamics simulations using molecular mechanics (MM) and PM3/MM potentials suggest a correlation between the flexibility of the Zn(2+)-binding site and regulation of the enzyme function. Directed in silico mutations of selected residues in the active site were also performed. Our studies support a dissociative mechanism starting with the Zn-O(Asn234) bond breaking followed by the Zn-S((Hcy)) bond formation; the proposed associative mechanism for the Zn(2+)-coordination exchange is not supported.

A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation

“…At present, QM/MM method and MD simulations have been combined to successfully study the inhibitorprotein interactions, functions of metalloproteins, and enzyme catalysis (Abdel-Azeim, Li, Chung, & Morokuma, 2011;Chen, Liang, Wang, Yi, Zhang, & Zhang, 2014;Duan, Mei, Zhang, Zhang, & Zhang, 2010;Duan, Mei, Zhang, & Zhang, 2009;Fan, Cembran, Ma, & Gao, 2013;Gao, Lu, Duan, Zhang, & Mei, 2011;Hou & Cui, 2013;Hou, McLaughlin, & Wang, 2007;Hu, Zhu, Zhang, Wang, & Zhang, 2010;Hu & Wang,2014;Ke, Wang, Xie, & Zhang, 2009;Keerthana & Kolandaivel, 2014;Meher, Kumar, & Bandyopadhyay, 2014;Smith, Ke, Guo, & Hengge, 2011;Wang et al, 2010Wang et al, , 2013Wang, Wu, Xu, Xie, & Guo, 2011;Wong, Richard, & Gao, 2009;Zhu, He, & Zhang, 2012;Zhu, Xiao et al, 2013). This method can take the polarizable electrostatic effect into account explicitly and accurately treat hydrogen bonding interactions.…”

Update on Zinc Biology

“…Biochemists continue to isolate zinc metalloenzymes relevant to mammalian biology which conform with the Parisi-Vallee postulates [6]. Table 1 illustrates several of the enzymes most recently identified as zinc metalloenzymes in the continuing elucidation of their extent and functions in nature [7,8,9]. Meanwhile, studies on the active site of carbonic anhydrase, the first of the zinc metalloenzymes identified, and its mode of operation continue to advance six decades later [10].…”

Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes

“…The geometries of interested species were fully optimized in conjunction with the SMD 36 continuum solvation model at the B3LYP/def2-SVP level of theory. B3LYP was proven to be a successful functional for studying zinc-based metalloenzymes 37 – 39 . The energies were further refined with the larger basis set def2-TZVP for all atoms.…”

“…Besides, the electronic embedding scheme 43 was employed to account for the polarizing effect of the enzyme environment on the QM region, while the hydrogen link atoms with the charge-shift model was used to deal with the QM/MM boundary. Here, the QM region was studied with the hybrid B3LYP 44 , 45 density functional, which has been proven to be reliable for the simulation of zinc-containing metalloenzymes 37 , 39 , 46 , 47 . In this study, the double-ζ basis set def2-SVP were used for geometry optimization, while the energies were corrected with the larger basis set def2-TZVP for all the QM region atoms.…”