BIOPHYSICAL THEORY AND MODELING |
Enantioselective Substrate Binding in a Monooxygenase Protein Model by Molecular Dynamics and Docking
K. Anton Feenstra 1, Karin Hofstetter 2, Rolien Bosch 1, Andreas Schmid 3, Jan NM Commandeur 1 and Nico PE Vermeulen 1*
1 Div. of Molec. Toxicol., Dept. of Pharmacochem., Leiden/Amsterdam Center for Drug Research (LACDR)
2 Institute of Biotechnology, Swiss Federal Institute of Technology (ETH) Zurich
3 Chair of Chemical Biotechnology, Dept. of Biochemical and Chemical Engineering, Univ. of Dortmund
* To whom correspondence should be addressed. E-mail: npe.vermeulen{at}few.vu.nl.
Submitted on May 9, 2006
Revised on June 7, 2006
Accepted on 12 July 2006
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Abstract |
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The two-component flavoenzyme Styrene Monooxygenase (SMO) is an efficient alternative to several chemical epoxidation catalysts on a preparative scale. A first homology model of the catalytic domain (StyA) of SMO was constructed (PDB ID 2HD8) based on the structure of para-hydroxybenzoate hydroxylase (pHBH). The StyA protein structure was optimized by restrained molecular dynamics to reproduce specific pre-S binding orientations of styrene. Effects of all ten point mutations examined were explained by the distance of the site to the styrene and FAD binding sites. Thirteen out of twenty ligands could be accommodated in a catalytically active binding orientation and predicted affinities correlated well with experimental turnover and inhibition. The binding cavity is almost completely hydrophobic, except for a hydrogen-bonded network formed by three water molecules, the backbone of residues 300-302 and the flavin ribityl, similar to P293 and three crystal waters in pHBH, suggest that P302, T47 and the waters in StyA are a vital component of the catalytic mechanism. The current optimized and validated StyA model provides a good starting point for elucidation of the structural basis of StyA ligand binding and catalysis. Novel insights in the binding of ligands to SMO/StyA, provided by the current protein model, will aid the rational design of mutants with specific, altered enantioselective properties.
Key Words:
active site mutations, controlled-release optimization, homology model, ligand binding affinity prediction, model validation and optimization, styrene mono-oxygenase
