Deeth, Robert J. and Diedrich, Christian. (2010) Structural and mechanistic insights into the oxy form of tyrosinase from molecular dynamics simulations. Journal of Biological Inorganic Chemistry, Vol.15 (No.2). pp. 117-129. ISSN 0949-8257

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Abstract

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 angstrom longer and remaining syn to each other. However, the two coordination spheres display important differences. LFMD simulations of the symmetric model complex [mu-eta(2) :mu(2)-O-2{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 His(54) 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.

Item Type:	Journal Article
Subjects:	Q Science > QD Chemistry
Divisions:	Faculty of Science > Chemistry
Library of Congress Subject Headings (LCSH):	Chemistry -- Computer simulation, Chemistry -- Data processing, Molecular dynamics -- Mathematical models, Molecular dynamics -- Computer simulation, Phenol oxidase
Journal or Publication Title:	Journal of Biological Inorganic Chemistry
Publisher:	Springer
ISSN:	0949-8257
Date:	February 2010
Volume:	Vol.15
Number:	No.2
Number of Pages:	13
Page Range:	pp. 117-129
Identification Number:	10.1007/s00775-009-0577-6
Status:	Peer Reviewed
Publication Status:	Published
Funder:	Deutscher Akademischer Austauschdienst [German Academic Exchange Service] (DAAD), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)
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URI:	http://wrap.warwick.ac.uk/id/eprint/6374

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