Computer Aided Design of a Luciferase Like Haloalkane Dehalogenase Enzyme by Homology Based Rational Protein Design (HRPD) Method

Rational protein design is an important aspect to introduce novel characters to the enzymes. In this report, we describe a procedure for in-silico design of a novelhaloalkane dehalogenase protein that exhibits luciferase property, which can be potentially used in biosensor applications. The haloalkane dehalogenase have aclose structural homology with a lucifearse was used as the starting structure for design. Amino acids that are frequently interacts with the chromophre (colentrizine)was analyzed by docking and molecular dynamics simulation. The amino acids Asp170, Lys192, Arg193, Lys259, and Lys261 were selected in the enzyme structurefor substitution purpose to generate mutant enzyme. Following several selection strategies, it was observed that the protein substituted with Phe in all the positions is the best one which was further validated by a 10 ns molecular dynamicssimulation. The designed protein is then analyzed for its substrate specificity towards 10 selected toxic haloalkane compounds. The result shows, that thedesigned protein has also improved the substrate specificity towards four toxic pollutants.

Keywords:

Protein Design , Chromophore , Luciferase , Haloalkane Dehalogenase , Docking , Molecular Dynamics Simulation