Figure 1.
Schematic representation of the DMD/QM domains.
A) The dark shaded area defines the QM-only domain, the light shaded area is the QM-DMD domain, and the rest of the system constituted the DMD-only domain. Protein backbone is shown as thick green lines. Amino acids holding the metal (M) are depicted as thin green lines. The catechol substrate coordinated to M is shown in blue. SAM is shown in purple; notice that only part of it is included in the QM-DMD domain. B) Representation of the system as seen during the DMD phases of the simulation: red dots depict atoms that are frozen. C) Schematic model of the system during QM calculations: atoms that are bordering with the DMD-only domain are frozen and their valences are saturated with hydrogen atoms (orange dots).
Figure 2.
A) Topological representation of the system as treated during the QM calculations (QM-DMD domain). The color red marks the atoms whose positions are frozen during QM calculations, to retain the structure imposed by the rest of the protein. With the blue color, the atoms in the QM-only domain are marked. Green lines show additional constrains that are imposed during the DMD simulation, to retain the chemistry determined at the QM level of theory. B) QM-only domain embedded in the protein.
Figure 3.
Comparison between the QM/DMD ensembles of active site structures (thin sticks, small spheres), and the X-ray structure (bold sticks, large spheres) for A) 3,5-dinitrocatechol, and B) catechol bound to the Mg(II) form of COMT.
Hydrogen atoms, Met40, Lys46 and Asp205 are omitted for clarity.
Table 1.
Averaged structural parametersa characteristic of the active site of COMT as function of the bound metal cation and the substrate: 3,5-dinitrocatechol (DNC), or catechol (Cat). Experimental values for Mg-COMT/3,5-dinitrocatechol are shown for comparison.
Figure 4.
Comparison between Mg(II) and Ca(II) forms of COMT.
A) Simulated active site for the Ca based COMT (thin sticks, small spheres) and the active site derived from the X-ray structure of Mg-COMT (bold sticks, large spheres). Hydrogen atoms, Met40, Lys46 and Asp205 have been omitted for clarity. B) The overlay of the representative snapshots from the QM/DMD simulations on Mg(II)-COMT (green structure, gray metal) and Ca(II)-COMT (purple structure, orange metal), showing the overall structural adjustment in Ca(II)-COMT.
Table 2.
Averaged over the QM/DMD ensembles energies (ZPE-corrected), and structural parameters (in Å) of the stationary points along the methyl transfer path, for the Mg(II), Ca(II), Fe(II), and Fe(III) forms of COMT, with the catechol substrate, and the Mg(II) form with the inhibitor.