Molecular dynamics simulations of lignin peroxidase in solution

Abstract

The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.

FIGURE 1

Structure of veratryl alcohol.

FIGURE 2

Backbone-backbone RMSD, with respect to the crystallographic structure of LiP (a) and radius of gyration (b) along the simulations. HTR (black) and W171A (gray) simulations are reported. (Dashed line) The crystallographic value of the gyration radius.

FIGURE 3

Backbone RMSD (a) and RMSF (b) with respect to the crystallographic structure of LiP residues. HTR (black) and W171A (dashed) simulations are reported. (a, gray bands) The α-helix regions of the protein. (b, vertical lines) The residues forming the access channel to the heme.

FIGURE 4

Stereo view of the superimposition of 10 conformations sampled along the last 1 ns of HTR simulation. (Bold solid line) The crystallographic structure. The active site, the distal (upper) and proximal (lower) calcium binding sites and the HTR171 region are reported.

FIGURE 5

(a) Radius of gyration, (b) total accessible surface area, (c) and number of contacts (NC) within 0.6 nm of the access channel residues along the HTR (black line) and W171A (gray line) simulations. (Dashed lines) The crystallographic values.

FIGURE 6

LiP x-ray crystal structure (0 ps) and snapshots extracted from the HTR simulation. The residues forming the access channel (see text) are represented as Connolly surfaces. (Blue sticks) The heme.

FIGURE 7

Components of the first eight eigenvectors for the HTR (black line) and W171A (gray line) simulations. (Dashed vertical lines) The position of the access channel residues (see text).

FIGURE 8

(Bottom to top) Behavior of different parameters along the SMD docking simulation are reported: (a) distance Fe-C14; (b) number of contacts (<0.4 nm) between VA and the heme atoms; (c) number of contacts (<0.6 nm) among the access channel residues (see text); and (d) constraint force along the Fe-C14 direction.

FIGURE 9

Stereo views of the starting conformation for the SMD docking simulation (bottom) and the conformation after 180 ps of the SMD docking simulation (top). In this figure, only the access channel residues (see in the text), the heme, and the VA molecule are reported.