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The X-ray crystal structure of laccase from PDB ID 1kya (Tra-
metes versicolor) at a resolution of 2.4 Å was used for the active
site model. Molegro Virtual Docker program was used to prepare
the binding cavity. A docking template was set up to determine
the constraints (15 Å around the ligand of reference, the key
hydrogen bonds, the steric factors and the preferential position
of the aromatic ring). The docking was set up using the default
parameter (Moldock SE algorithm, Moldock score, similarity
score, RMSD of 1 Å). Ten runs were programmed for each
ligand from which the best 5 results were kept. The total
MolDock Score energy (arbitrary units) is the sum of internal
ligand energies, protein interaction energies and soft penalties.39
Acknowledgements
This research was supported in part by the European Commis-
sion, Sixth Framework Program (NMP2-CT2004-505899,
SOPHIED), and in part by the UCL (Belgium) with the Con-
certed Research Program ARC 08/13-009 and the Inter-Univer-
sity Attraction Pôle (IAP) program P6/19 PROFUSA. J.M.-B.
and G.D. are senior research associates of FRS-FNRS
(Belgium). The authors wish to thank R. Rozenberg (Laboratoire
de Spectrométrie de Masse, UCL) for technical assistance in the
acquisition of the MS and HPLC-MS spectra. G. D. thanks the
FRS-FNRS for access to HPC equipments installed in Liège and
LLN.
Notes and references
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‡As the HPLC-MS chromatographic system was equipped with a
smaller XTerraMsC18 column (2.1 × 50 mm, 2.5 μm), the same column
was used here with the HPLC-PDA systems. The reference dyes 5d, 5f,
6f, and 5j were eluted to check the consistency of the retention times
due to the decrease of both the flow rate and the column dimensions (see
Table 3, footnotes).
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