Protein-ligand interactions in haloalkane
dehalogenases
Michal Kutý1,2, David Řeha1,2, and Ivana
Kuta Smatanova1,2
1Faculty of Science,
University of South Bohemia in Ceske Budejovice, Branisovska 31, 370 05 Ceske
Budejovice, Czech Republic
2Center for Nanobiology and Structural Biology, Institute of
Microbiology of the Academy of Sciences, Czech Republic, 142 20 Prague, Czech
Republic
Haloalkane dehalogenases (HLDs) are
enzymes that catalyze reactions of great environmental and
biotechnological significance. HLDs (EC 3.8.1.5) belong to the
a/b-hydrolase superfamily [1] of enzymes catalyzing hydrolytic
cleavage of carbon-halogen bonds in halogenated
hydrocarbons to yield the corresponding
alcohol, a proton and a halide [2]. This work is focused on the
protein-ligand interactions in a recently constructed stable
and solvent-resistant haloalkane dehalogenase DhaA
from Rhodococcus rhodochrous NCIMB 13064
and its variants with mutations in the residues that form the access tunnel
connecting the enzyme’s buried active site to the
surrounding solvent. The interactions and different binding sites between
a protein and a ligand were studied by using molecular dynamics method GROMACS
[3] and PELE [4,5] (an acronym Protein Energy Landscape Exploration)
that combines a Monte Carlo stochastic approach with protein structure
prediction and is capable of accurately reproducing long time scale processes.
This research is supported by the
GACR (P207/12/0775).
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