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

In this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. From a PDB BLAST search, the selected haloalkane dehalogenase (PDB code: 1EDE) had a close structural homology with a lucifearse (PDB code: 2PSJ chain A) sharing an identity of 33%. Initially, the amino acids in luciferase interacting with chromophore colentrizine were analyzed by a 3 ns molecular dynamics simulation. Later, Colentrizine was docked to the haloalkane dehalogenase followed by 5 ns molecular dynamics simulation to find out the frequently interacting residues with the ligand and amino acid Asp170, Lys192, Arg193, Lys259, Lys261 were selected in haloalkane dehalogenase structure for substitution purpose. Four mutants were generated by substituting these positions with Phe, Tyr, Trp respectively as they have comparable molecular weight. Following several selection strategies based on energy minimization, structural accuracy, ligand binding score, % of hydrophobicity and aromaticity 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 dynamics simulation by Gromacs 4.5.0 software. The selected designed protein is further analysed for their substrate specificity towards 10 selected haloalkane ligands in comparison to the unmutated counterpart by Autodock 4.2 tool. The result shows, that the designed protein has also improved the substrate specificity towards four toxic pollutants.