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Evaluation of Electronic and Geometrical Properties of the Blue Copper Site in Fully Solvated Azurin by QM/MM Hybrid Calculations Using a New Interface Program Connecting QM and MM Engines

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The electronic and geometrical properties of the blue copper site in azurin were investigated using our newly developed interface program for joint quantum mechanics (QM) and molecular mechanics (MM) calculations. Our QM/MM energy evaluation method is based on an additive scheme, which calculates the electrostatic interaction between QM and MM regions using a QM Hamiltonian. To assess the accuracy of the additive energy scheme, we employed two computational models. In Model I, a long distance electrostatic interaction between the QM region atoms and the partial point charges of protein and solvent water was calculated by the QM Hamiltonian, in which the spin-unrestricted Hartree-Fock (UHF)/density functional theory (DFT) hybrid all-electron calculation with the B3LYP functional was adopted in the present study. In Model II, the QM Hamiltonian was not allowed to be polarized by the partial point charges. Models I and II provided different descriptions of the copper coordination geometry, particularly for the coordinative bonds including a large dipole. In fact, the Cu–O(Gly45) and Cu–S(Cys112) bonds were sensitive to the treatment of the long-distance electrostatic interaction by the QM Hamiltonian. In addition, an H-bond between the HHis117 atom and a water molecule was polarizable under the modified QM Hamiltonian, which in turn affected the Cu–His117 coordination. Furthermore, the additive energy scheme was crucial for accurate calculation of spin polarization in the Cu–S(Cys112) bond. Thus, it is suggested that modification of the QM Hamiltonian to interact with the long-distance partial point charges of the environment is crucial for an accurate QM/MM description of the geometrical and electronic properties of metal active sites. This could be of particular importance to the functional properties of metalloenzymes, such as the redox potential and ET rates, particularly in the case where the size of the QM region is not taken as sufficiently large and where the inner region includes a large dipole.
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Keywords: AB INITIO CALCULATION; CU COORDINATION; LONG-RANGE ELECTROSTATIC INTERACTION; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE

Document Type: Research Article

Publication date: 01 December 2009

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  • Journal of Computational and Theoretical Nanoscience is an international peer-reviewed journal with a wide-ranging coverage, consolidates research activities in all aspects of computational and theoretical nanoscience into a single reference source. This journal offers scientists and engineers peer-reviewed research papers in all aspects of computational and theoretical nanoscience and nanotechnology in chemistry, physics, materials science, engineering and biology to publish original full papers and timely state-of-the-art reviews and short communications encompassing the fundamental and applied research.
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