The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces

Abstract

The enzyme organophosphorous hydrolase (OPH) catalyzes the hydrolysis of a wide variety of organophosphorous compounds with high catalytic efficiency and broad substrate specificity. The immobilization of OPH in functionalized mesoporous silica (FMS) surfaces increases significantly its catalytic specific activity, as compared to the enzyme in solution, with important applications for the detection and decontamination of insecticides and chemical warfare agents. Experimental measurements of immobilization efficiency as a function of the charge and coverage percentage of different functional groups have been interpreted as electrostatic forces being the predominant interactions underlying the adsorption of OPH onto FMS surfaces. Explicit solvent molecular dynamics simulations have been performed for OPH in bulk solution and adsorbed onto two distinct interaction potential models of the FMS functional groups to investigate the relative contributions of nonbonded interactions to the conformational dynamics and adsorption of the protein. Our results support the conclusion that electrostatic interactions are responsible for the binding of OPH to the FMS surface. However, these results also show that van der Waals forces are detrimental for interfacial adhesion. In addition, it is found that OPH adsorption onto the FMS models favors a protein conformation whose active site is fully accessible to the substrate, in contrast to the unconfined protein.

Figure 1

Cartoon representation of the organophosphorous hydrolase structure adsorbed onto the functionalized mesoporous silica surface. (A) Top view of the OPH dimer. Regions of large atomic fluctuations in the MD simulations are indicated in violet (L1, residues 155-165), blue (L2, residues 172-182), yellow (L3, residues 201-215), orange (L4, residues 230-240), purple (L5, residues 255-275) and green (L6, residues 306-325) for only one monomer. (B) Close-up view of the active site pocket with residues represented in licorice and Zn²⁺ cations in the Corey–Pauling–Koltun (CPK) model (yellow). The residue Y³⁰⁹ in the gateway to the active site pocket is highlighted. (C) Side view of the OPH dimer. Positively charged residues in the protein that interact with the functionalized mesoporous silica are represented in licorice. The functionalized mesoporous silica is represented in CPK (red). The explicit model water molecules are omitted for clarity of visualization.

Figure 2

Root-mean-square deviation (RMSD) of backbone atoms of OPH from the X-ray structure (1HYZ) (A) and root-mean-square fluctuation (RMSF) of Cα atoms of OPH as function of residue sequence number (B). OPH_free (black), FMS_coul (red) and FMS_vdW (green). Rotational and translational fitting of pairs of structures was applied using all backbone atoms. RMSF is averaged for the two monomers over the final 40 ns and a time window of 10 ps.

Figure 3

Eigenvalues and atomic displacement along the most representative eigenvectors calculated from the MD simulations OPH_free (circle or bold line), FMS_coul (square or solid line) and FMS_vdW (triangle or dashed line). (A) Largest eigenvalues. (B) Atomic displacement along the first (i.), second (ii.) and third (iii.) eigenvectors. (C) Projection of atomic displacements along the first eigenvector onto the three-dimensional structure of (i.) OPH_free, (ii.) FMS_coul and (iii.) FMS_vdW. The width of the ribbons illustrates the amplitude of the atomic displacement. Only eigenvector components larger than 0.05 ps are shown for clarity. (D) Solvent accessibility surface of the trajectory frame at 50 ns for OPH in (i.) OPH_free, (ii.) FMS_coul and (iii.) FMS_vdW. The residue Y³⁰⁹ and Zn²⁺ cations are represented in CPK.

Figure 4

Mean-square displacement of OPH atoms from their initial positions over 50 ns of simulation (A) and minimum atom-atom distances between OPH atoms and the FMS surface (B) in simulations FMS_coul (black) and FMS_vdW (gray).

Figure 5

(A) Radial distribution function g(r) of intermolecular N-O pairs in the side-chains of residues at the FMS interface of OPH and in the water molecules and (B) the average solvent number density around OPH in the FMS_coul (a) and FMS_vdW (b) ensembles. Solvent density representation along the longitudinal y-axis. OPH_free (black), FMS_coul (red) and FMS_vdW (green).