J. Kmuníček1, M. Boháč1, S. Luengo2, F. Gago2, R. C. Wade3 and J. Damborský1


1National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic

2Department of Pharmacology, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain

3European Media Laboratory, Villa Bosch, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany


The applicability of automated molecular docking techniques and quantum mechanical calculations for the construction of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis [1-6] was evaluated. The data set studied consists of the complexes of eighteen substrates with the haloalkane dehalogenase (DhlA) isolated from bacterium Xanthobacter autotrophicus strain GJ10. An automated molecular docking procedure provided the structures for a set of DhlA-substrate complexes that was used to derive a robust COMBINE model. Quantum-mechanical calculations were successfully used as an additional and complementary computational tool for selection of correct binding modes obtained from the docking. The resulting COMBINE model is compared with a previously reported COMBINE model [7] derived for the same data set using structures of complexes built according to experimentally determined structure of the DhlA-dichloroethane complex. Both models were similar in terms of overall fit and internal predictive power even though the conformations and orientations of the substrates in the complexes were significantly different. The new COMBINE model derived from the automatically docked structures performed notably better in external prediction. Small differences in the relative contributions of important residues to explaining binding affinities can be directly linked to structural differences in the modelled enzyme-substrate complexes.


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