Molecular Dynamics Simulations of Lignin Peroxidase in Solution

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Presentation transcript:

Molecular Dynamics Simulations of Lignin Peroxidase in Solution M. Francesca Gerini, Danilo Roccatano, Enrico Baciocchi, Alfredo Di Nola Biophysical Journal Volume 84, Issue 6, Pages 3883-3893 (June 2003) DOI: 10.1016/S0006-3495(03)75116-9 Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 1 Structure of veratryl alcohol. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

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. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

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. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 4 Stereo view of the superimposition of 10 conformations sampled along the last 1ns 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. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 5 (a) Radius of gyration, (b) total accessible surface area, (c) and number of contacts (NC) within 0.6nm of the access channel residues along the HTR (black line) and W171A (gray line) simulations. (Dashed lines) The crystallographic values. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 6 LiP x-ray crystal structure (0ps) and snapshots extracted from the HTR simulation. The residues forming the access channel (see text) are represented as Connolly surfaces. (Blue sticks) The heme. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

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). Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 8 (Bottom to top) Behavior of different parameters along the SMD docking simulation are reported: (a) distance Fe-C14; (b) number of contacts (<0.4nm) between VA and the heme atoms; (c) number of contacts (<0.6nm) among the access channel residues (see text); and (d) constraint force along the Fe-C14 direction. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions

Figure 9 Stereo views of the starting conformation for the SMD docking simulation (bottom) and the conformation after 180ps 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. Biophysical Journal 2003 84, 3883-3893DOI: (10.1016/S0006-3495(03)75116-9) Copyright © 2003 The Biophysical Society Terms and Conditions