Structural and mechanistic insights into the oxy form of tyrosinase from molecular dynamics simulations

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• 作者：Robert J. Deeth and Christian Diedrich
• 关键词：Computational chemistry ; Molecular dynamics ; Molecular modelling
• 刊名：Journal of Biological Inorganic Chemistry
• 出版年：2010
• 出版时间：February, 2010
• 年：2010
• 卷：15
• 期：2
• 页码：117-129
• 全文大小：701.1 KB

文摘

The first, long time scale (16-ns) ligand field molecular dynamics (LFMD) simulations of the oxy form of tyrosinase are reported. The calculations use our existing type 3 copper force field for the peroxido-bridged [Cu₂O₂]2+ unit which is here translated from MMFF into the AMBER format together with a new charge scheme. The protein secondary and tertiary structures are not significantly altered by removing the ‘caddie’ protein, ORF378, which must be bound to tyrosinase before crystals will grow. A comprehensive principal component analysis of the Cartesian coordinates from the final 8 ns shows that the protein backbone is relatively rigid. However, the significant butterfly fold of the [Cu₂O₂]2+ moiety observed in the X-ray structure, presumably due to the caddie protein tyrosine at the active site, is absent in the simulations. LFMD gives a clear and persistent distinction between equatorial and axial Cu–N distances, with the latter about 0.2 ? longer and remaining syn to each other. However, the two coordination spheres display important differences. LFMD simulations of the symmetric model complex [μ-η2:μ2-O₂{Cu(Meim)₃}₂]2+ (Meim is 5-methyl-1H-imidazole) provide a mechanism for syn–anti interchange of axial ligands which suggests, in combination with the old experimental X-ray data, the new LFMD simulations and traditional coordination chemistry arguments, that His₅₄ on Cu_A is ‘insipiently axial’ and that a combination of a butterfly distortion of the [Cu₂O₂]2+ group and a rotation of the Cu_A(His)₃ moiety converts the vacant, initially axial, binding site on Cu_A into a much more favourable equatorial site.