Release of halide ions from the buried active site of the haloalkane dehalogenase LinB revealed by stopped-flow fluorescence analysis and free energy calculations

Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications

The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.

Accurate Prediction of the Hydration Free Energies of 20 Salts through Adaptive Force Matching and the Proper Comparison with Experimental References

Simple pairwise potentials for five alkali ions and four halide ions were developed by only fitting to ab initio MP2 forces with the adaptive force matching (AFM) method. Without fitting to any experimental information, the AFM models predict the hydration free energies of all 10 fluoride and chloride salts formed by these ions within 1.5% of experimental references. The predicted hydration free energies for the 10 bromide and iodide salts are within 5-6% of experimental references with the larger error likely due to the neglect of explicit treatment of polarization and charge transfer. An inconsistency in the treatment of the gas phase entropy term between experimental and theoretical approaches is discussed. A new simplified hydration free energy for the ions is reported for use as a more appropriate experimental reference for further theoretical studies. The simulations show different dipole alignments for the hydration waters of cations and anions. While hydration waters of small cations tend to align their molecular dipole toward the ion, the dipole of one of the water OH bonds is aligned with the field of an anion.

Dithieno[3,2-a:2′,3′-c]phenazine-based chemical probe for anions: a spectroscopic study of binding

The synthesis and binding studies of N,N′-(2,5-bis(4-(tert-butyl)phenyl)dithieno[3,2-a:2′,3′-c]phenazine-9,10-diyl)bis(4-methylbenzenesulfonamide) (1) are reported.