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.
System |
TCP(bm2) |
TCP(bm3) |
wt-DhaA |
20.7 % |
6.5 % |
C176Y+Y273F-DhaA |
28.9 % |
11.7 % |
[1] Bosma T, Damborsky J, Stucki G, Janssen
DB APPL.
ENVIRON. MICROB. 68 (2002) 3582-3587 2002