Computer modelling of microbial hydrolytic dehalogenation

Abstract

The biodegradation of organic compounds by microorganisms is an intrinsically complex process. A large number of sub-processes, like penetration of the compounds to the cells, biochemical catalysis and the release of products are taking place during the biodegradation. The separation of these sub-processes from each other and their detailed study is needed for a better understanding of the basic mechanisms of microbial degradation and for the improvement of bioremediation technologies by means of the construction of a new efficient biocatalyst. This contribution attempts to view the biodegradation reaction - hydrolytic dehalogenation - at the level of catalysing biomolecules. Computer modelling is used to extend the knowledge obtained from X-ray analysis, kinetic measurements and site-directed mutagenesis experiments. Among the issues discussed in this article are the determination of the rate-limiting step of the biodegradation reaction, the identification of the active-site amino acids involved in the reaction mechanism, the prediction of proteins' modifications leading to higher activity and the molecular mechanisms of the adaptation of bacteria for the degradation of xenobiotic compounds.