QM/MM Molecular Dynamics Simulation on the Mechanisms for the Hydrolytic Deamination of Nicotinamidase†

doi:10.7503/cjcu20150365

Abstract

Abstract:

The deamination process of nicotinamide to nicotinic acid by nicotinamidase simulated with combined QM(PM3)/MM molecular dynamics(MD) method. Our calculated results show that the whole mechanism includes four steps, transition of H_S, nucleophilic attack by sulfur group, nucleophilic attack by hydroxyl group and proton transfer from Asp16 to Cys159. The rate-determined step is the nucleophilic attack by sulfur group. Through conformational analyses, we are able to indicate that high energy consumption mainly because the nucleophilic attack needs to break the hydrogen bond between substrate and Ala155. We suggest that mutation of the loop, which make Ala155 far from nicotinamide, could weaken the hydrogen bond and increase the reactivity of nicotinamidase. Based on this ground, release of ammonia and proton transfer processes are discussed in details. The results could give some useful suggestions to enzyme design and site-directed mutagenesis studies.

Key words: Nicotinamidase, Deamination, Mechanism, Quantum mechanics/molecular mechanics(QM/MM) method, Molecular dynamics simulation(Ed.: Y,Z)

CLC Number:

O641

TrendMD:

DUAN Xinli, ZHANG Xin, LEI Ming. QM/MM Molecular Dynamics Simulation on the Mechanisms for the Hydrolytic Deamination of Nicotinamidase^†[J]. Chem. J. Chinese Universities, 2015, 36(12): 2491.

Figures/Tables 8

Scheme 1 Catalytic reaction of nicotinamidase

Fig.1 Crystal structure of nicotinamidase(A)(PDB entry: 2WTA) and details in QM part(B) (A) The active site with nicotinamide is highlighted in yellow; (B) QM/MM boundary is shown by the red break lines.

Fig.2 Reaction pathways for the deamination process in QM/MM MD simulations

Fig.3 Free energy profile from the binding state B to the intermediate state(I1)(A) and fluctuations of the distances of the breaking and forming bonds in HS transfer process(B) RC1 refers to the distance difference between the HS—S@Cys159 and HS—OD3@Asp16.

Fig.4 Free energy profile from the intermediate state(I1) to the intermediate state(I2) via a transition state(TS2)(A) and fluctuations of the distances of the breaking and forming bonds in nucleophilic attack of sulfur(B) RC2 refers to the distance difference between the C7—S@Cys159 and C7—N8.

Fig.5 Snapshots of the micro-environments for QM part at the I1(A), TS2(B) and I2 states(C) Hydrogen bond lengths(nm) in step 2 are shown by the dash lines. The values in parentheses are standard deviations.

Fig.6 Free energy profile from the intermediate state(I2') to the intermediate state(I3) via a transition state(TS3)(A) and fluctuations of the distances of the breaking and forming bonds in nucleophilic attack of hydroxyl group(B) RC3 refers to the minus distance between the OW3—C7 and HW6—OD3.

Fig.7 Free energy profile from the intermediate state(I3) to the product state(P) via a transition state(TS4)(A) and fluctuations of the distances of the breaking and forming bonds in nicotinic acid formation process(B) RC4 refers to the minus distance between the O9—HW6 and HW5—S.

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