Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form

Abstract

There is some evidence linking the mammalian paraoxonase-1 (PON1) loops (L1 and L2) to an increased flexibility and reactivity of its active site with potential substrates. The aim of this work is to study the structural, dynamical, and functional effects of the most flexible regions close to the active site and to determine the impact of mutations on the protein. For both models, wild-type (PON1wild) and PON1 mutant (PON1mut) models, the L1 loop and Q/R and L/M mutations were constructed using MODELLER software. Molecular dynamics simulations of 20 ns at 300 K on fully modeled PON1wild and PON1mut apoenzyme have been done. Detailed analyses of the root-mean-square deviation and fluctuations, H-bonding pattern, and torsion angles have been performed. The PON1wild results were then compared with those obtained for the PON1mut. Our results show that the active site in the wild-type structure is characterized by two distinct movements of opened and closed conformations of the L1 and L2 loops. The alternating and repetitive movement of loops at specific times is consistent with the presence of 11 defined hydrogen bonds. In the PON1mut, these open-closed movements are therefore totally influenced and repressed by the Q/R and L/M mutations. In fact, these mutations seem to impact the PON1mut active site by directly reducing the catalytic core flexibility, while maintaining a significant mobility of the switch regions delineated by the loops surrounding the active site. The impact of the studied mutations on structure and dynamics proprieties of the protein may subsequently contribute to the loss of both flexibility and activity of the PON1 enzyme.

Pyrazinamide resistance of novel mutations inpncAand their dynamic behavior

“…37 The effects of these variants have also been found on the PZase stability (RMSD) and exibility (RMSF) which is consistent with the previous reports. 21,[23][24][25][26] For all structures, the RMSD and RMSF of R123P, T76P, G150A, and H71R seem more elevated in comparison with WT, indicating a level of instability for the PZase function (Fig. 2).…”

Challenges and advances in the computational modeling of biological phosphate hydrolysis

“…132,133 Indeed, experiments with this system are typically conducted in the presence of lipid or detergent micelles, [134][135][136] or reconstituted HDL (rHDL). 94,133 There have been a number of computational studies of both PON1 and DFPase that have primarily focused on either (1) trying to elucidate the catalytic mechanism for this enzyme, 94,95,120,128,137 or (2) to obtain insights into either membrane association 94,138 or the dynamics of a catalytically important active site loop 95,139 that is far more flexible in PON1 than in DFPase. 140 In our case, we have addressed a number of issues using a combination of EVB simulations and structural bioinformatics tools.…”

Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering

“…Unsurprisingly, therefore, PON1 has been the subject of substantial experimental and computational work. ,− ,− Here, computation has been demonstrated to be a powerful tool to aid in the design of biological agents capable of hydrolyzing organophosphates, through, for example, the case of the redesign of a mononuclear zinc enzyme for organophosphate hydrolysis . However, computational studies are made more challenging by the fact that this enzyme is a membrane-associated enzyme, which associates with high-density lipoprotein (HDL) in vivo, ,,, and no structure exists of PON1 (or in fact any enzyme) in complex with HDL to be used as a starting point for simulations. , While simplified approximations of at least the structural role of the membrane can be made, for example, by restraining membrane-associating regions of the enzyme as we have done in our previous computational work, , this is clearly not ideal, making PON1 a more challenging system for computational design.…”