In-silico Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase Enzyme

Abstract

Thermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). In in silico design strategy rule-based approaches such as disulfide bond geometry, new hydrophobic pocket design, new salt bridge construction and multiple mutations (combination of the above approaches) were introduced to the original enzyme. After each design strategy the functional effect was confirmed in terms of enzyme substrate binding by molecular docking using Autodock vina tool. Best design strategy was evaluated by comparative molecular dynamics simulation applying simulated annealing method at 8 ns using GROMACS tool. The surface hydrophobicity which is the key factor for thermostability in haloalkane dehalogenase was obtained from the simulation result. Upon optimizing the parameters, thermostability of mutant enzyme under consideration was also confirmed by the 5 ns molecular dynamics simulation at 400, 500 and 600 K.