Reaction Mechanism of Low-Spin Iron(III)- and Cobalt(III)-Containing Nitrile Hydratases: A Quantum Mechanics Investigation

Abstract

To elucidate the catalytic mechanism of cobalt(III)-benzonitrile and iron(III)--pivalonitrile hydratases, we have performed at density functional level a study using the cluster model approach. Computations were made in a protein framework. Following the suggestions given in a recent work on the analogous enzyme Fe(III)-NHase, we have explored the feasibility of a new working mechanism of examined enzymes. According to our results, after the formation of enzyme substrate complex, the reaction evolves toward product in only three steps. The first one is the nucleophilic attack, led by the -OH group of the αCys113-S-OH on the nitrile carbon atom, followed by the amide formation and by the enzyme restoring phase that our computations indicate as the most expensive step from the energetic point of view in both catalytic processes.

How Lanthanide Ions Affect the Addition–Elimination Step of Methanol Dehydrogenases

“…This trend confirms that the LA of early Lns (Ce-Nd) can favor the catalytic activity in MDH enzymes with respect to other members of the series (Eu-Lu) [15] as well as other metal ions (Mg, Ca, Ba, Sr). [33] It is important to underline that variations in CN have not been observed in the ES complexes, contrary to what wase ncountered in some previoust heoretical works. [16,18] Ap ossible explanation for this discrepancy can reside in the use of different pseudopotentials andv alence orbital basis sets;w eu sed electron-core-potential( ECP) with smaller core electrons but with higherv alence ones (> 30 e À ).…”

“…The initial structures of Ln-MDHs adopted in the present investigation have been extracted from the X-ray structure of Eu-containing MDH (PDB:6FKW) [16] following the computational protocol successfully adopted for other metalloenzymes. [21,[29][30][31][32][33] The QM cluster used models that include the inner coordination shell of Eu 3 + and Yb 3 + ions (Glu172, Asn256, Asp299 and Asp301), the PQQ, and all amino acid residues (Glu55, Arg110, Ser169, Arg326 and Asp388) involved in H-bond interactions with the redox-cofactor as shown in Figure 1. The neutral charge of PQQ is retained, as occurred in previous similar systems.…”

“…[39][40][41][42][43][44] The nature of minima (no negative vibrational frequencies) and transition states (one negative vibrational frequency) along potential energy surfaces were established by frequencies calculation at the same level of theory.D ue to the nature of the computations performed with constrained atoms, small vibrational frequencies < 40i cm À1 were observed in all stationary points that do not alter the thermochemical analysis, and the zero-point energy corrections and do not obscure the main negative TS-frequency. [29][30][31][32][33][39][40][41][42][43][44][45][46] To model the protein environment effects, the C-PCM [47,48] polarizable continuum model was used, with ad ielectric constant e = 4, as suggested in other works. [29][30][31][32][33]45] To improve electronic energies, the more extended 6-311 + G(2d,2p) j SDD basis set was adopted in single-point energy calculations.…”

“…[29][30][31][32][33][39][40][41][42][43][44][45][46] To model the protein environment effects, the C-PCM [47,48] polarizable continuum model was used, with ad ielectric constant e = 4, as suggested in other works. [29][30][31][32][33]45] To improve electronic energies, the more extended 6-311 + G(2d,2p) j SDD basis set was adopted in single-point energy calculations. For the potential energy surfaces (PESs), the reported energies include the ZPE corrections, excluding the contributions of frozen atoms in vibrational analysis, [49] and standard approximation for free energy.…”

QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase

“…The surrounding protein environment not directly implicated in the chemical transformation, is modeled with implicit dielectric constant-based solvation models (Warshel, 1991 ). This method is highly versatile and widely applied to a large variety of enzyme families and to different classes of enzymes (Ramos and Fernandes, 2008 ; Liao et al, 2010 ; Amata et al, 2011a ; Himo, 2017 ; Piazzetta et al, 2017 ; Prejanò et al, 2017a ). A different approach developed in 1976 (Warshel and Levitt, 1976 ) is the hybrid quantum mechanics/molecular mechanics (QM/MM) (Senn and Thiel, 2009 ; Quesne et al, 2016 ; Ryde, 2016 ).…”