Molecular dynamics simulation of 1,2,3-trichloropropane in the active site of wild type and mutant haloalkane dehalogenase DhaA.

Banáš Pavel1, Otyepka Michal1 and Damborský Jiří2

1Department of Physical Chemistry, Faculty of Science, Palacký University, tř. Svobody 26, 771 46 Olomouc

2National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno


1,2,3-trichloropropane (TCP) is a toxic synthetic chlorinated hydrocarbon known to occur naturally. TCP is resistant to biological and chemical degradation and is often found as a water pollutant. Thermodynamics calculation shows that aerobic mineralization of TCP could provide sufficient energy to sustain microbial growth. The haloalkane dehalogenase (DhaA) from Rhodococcus sp. m15-3 hydrolyzes carbon-halogen bonds in a wide range of haloalkanes, including TCP, to the corresponding (halo)alcohol, releasing halide ions. Recently a way how to improve DhaA enzyme to utilize TCP as a substrate by double-point mutation (C176Y+Y273F) has been proposed by Bosma et al. [1].

The goal of the work was to explain by molecular modeling why is the mutated enzyme more effective than wild type DhaA. The molecular dynamics method was used to produce six 1 ns-long simulations; three of them with the DhaA wild-type in complex with TCP in tree different binding modes TCP(bm1), TCP(bm2), and TCP(bm3) and three of them with C176Y+Y273F double mutant of DhaA.. The binding mode TCP(bm1) corresponds to dehalogenation from Cb atom, while the binding modes TCP(bm2) and TCP(bm3) relates to the dehalogenation from either Ca atom.

Both simulations of wt/TCP(bm1) and C176Y+Y273F/TCP(bm1) show that the dehalogenation from Cb is not possible, due to a sterical hindrance of TCP in the active site. Moreover, TCP changes its binding mode from TCP(bm1) to TCP(bm2) in both these simulations. The other simulations (wt /TCP(bm2), wt /TCP(bm3), C176Y+Y273F/TCP(bm2) and C176Y+Y273F/TCP(bm3)) show that TCP frequently adopts a near attack conformation (NAC), i.e. conformation appropriate for SN2 attack during the whole simulation. Preliminary results indicate that NAC is more populated in simulation of double mutant (see Table 1).

Table 1: Population of NAC for studied systems.





20.7 %

6.5 %


28.9 %

11.7 %



 [1] Bosma T, Damborsky J, Stucki G, Janssen DB APPL. ENVIRON. MICROB. 68 (2002) 3582-3587 2002